Science.gov

Sample records for dna model compounds

  1. XAFS Model Compound Library

    DOE Data Explorer

    Newville, Matthew

    The XAFS Model Compound Library contains XAFS data on model compounds. The term "model" compounds refers to compounds of homogeneous and well-known crystallographic or molecular structure. Each data file in this library has an associated atoms.inp file that can be converted to a feff.inp file using the program ATOMS. (See the related Searchable Atoms.inp Archive at http://cars9.uchicago.edu/~newville/adb/) This Library exists because XAFS data on model compounds is useful for several reasons, including comparing to unknown data for "fingerprinting" and testing calculations and analysis methods. The collection here is currently limited, but is growing. The focus to date has been on inorganic compounds and minerals of interest to the geochemical community. [Copied, with editing, from http://cars9.uchicago.edu/~newville/ModelLib/

  2. Modeling DNA Replication.

    ERIC Educational Resources Information Center

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  3. Modeling DNA Replication Intermediates

    SciTech Connect

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

    1997-06-01

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

  4. Polyimidazopyrrolone model compounds.

    NASA Technical Reports Server (NTRS)

    Young, P. R.

    1972-01-01

    The model reactions between phthalic anhydride and o-phenylenediamine were studied under conditions analogous to the polymerization and post-cyclization of dianhydrides with bis(o-diamines) to form polyimidazopyrrolones (Pyrrones). The route from the initial amide-acid-amine to the tetracyclic Pyrrone model when the reactions are conducted in aprotic solvents is highly competitive between isolatable benzimidazole-acid and imide-amine intermediates. Solid-state thermal conversion of the amide-acid-amine affords a unique dimeric species containing amide, imide, and benzimidazole functions. It was confirmed that melt techniques lead to disproportionation products. The application of these findings to related polymer synthesis is discussed.

  5. Polyimidazopyrrolone model compounds.

    NASA Technical Reports Server (NTRS)

    Young, P. R.

    1972-01-01

    Study of model reactions between phthalic anhydride and o-phenylenediamine under conditions analogous to the polymerization and post cyclization of dianhydrides with bis(o-diamines) to form polyimidazopyrrolones (Pyrrones). Solid-state thermal conversion of the amide-acid-amine affords a unique dimeric species containing amide, imide, and benzimidazole functions. It was confirmed that melt techniques lead to disproportionation products. The application of these findings to related polymer syntheses is discussed.

  6. Making Models of Chemical Compounds.

    ERIC Educational Resources Information Center

    Hoehn, Robert G.

    1992-01-01

    Describes the benefits and techniques of having students create models of chemical compounds. This hands-on approach uses colored paper and other inexpensive materials to construct the models. A step-by-step approach provides objectives, materials, an explanation on how to calculate chemical ratios, procedures, follow-up activities, and a resource…

  7. Multiscale modelling of DNA mechanics

    NASA Astrophysics Data System (ADS)

    Dršata, Tomáš; Lankaš, Filip

    2015-08-01

    Mechanical properties of DNA are important not only in a wide range of biological processes but also in the emerging field of DNA nanotechnology. We review some of the recent developments in modeling these properties, emphasizing the multiscale nature of the problem. Modern atomic resolution, explicit solvent molecular dynamics simulations have contributed to our understanding of DNA fine structure and conformational polymorphism. These simulations may serve as data sources to parameterize rigid base models which themselves have undergone major development. A consistent buildup of larger entities involving multiple rigid bases enables us to describe DNA at more global scales. Free energy methods to impose large strains on DNA, as well as bead models and other approaches, are also briefly discussed.

  8. A new compound, withangulatin A, promotes type II DNA topoisomerase-mediated DNA damage.

    PubMed

    Juang, J K; Huang, H W; Chen, C M; Liu, H J

    1989-03-31

    Withangulatin A, a new compound with a known chemical structure and from the antitumor Chinese herb Physalis angulata L, was found to act on topoisomerase II to induce topoisomerase II-mediated DNA damage in vitro. It has two effective dosage ranges of approximate 0.5 and 20 microM, with about one-third the activity of 20 microM VM-26.

  9. Investigation of DNA binding, DNA photocleavage, topoisomerase I inhibition and antioxidant activities of water soluble titanium(IV) phthalocyanine compounds.

    PubMed

    Özel, Arzu; Barut, Burak; Demirbaş, Ümit; Biyiklioglu, Zekeriya

    2016-04-01

    The binding mode of water soluble peripherally tetra-substituted titanium(IV) phthalocyanine (Pc) compounds Pc1, Pc2 and Pc3 with calf thymus (CT) DNA was investigated by using UV-Vis spectroscopy and thermal denaturation studies in this work. The results of DNA binding constants (Kb) and the changes in the thermal denaturation profile of DNA with the addition of Pc compounds indicated that Pc1, Pc2 and Pc3 are able to bind to CT-DNA with different binding affinities. DNA photocleavage studies of Pc compounds were performed in the absence and presence of oxidizing agents such as hydrogen peroxide (H2O2), ascorbic acid (AA) and 2-mercaptoethanol (ME) using the agarose gel electrophoresis method at irradiation 650 nm. According to the results of electrophoresis studies, Pc1, Pc2 and Pc3 cleaved of supercoiled pBR322 DNA via photocleavage pathway. The Pc1, Pc2 and Pc3 compounds were examined for topoisomerase I inhibition by measuring the relaxation of supercoiled pBR322 DNA. The all of Pc compounds inhibited topoisomerase I at 20 μM concentration. A series of antioxidant assays, including 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay, superoxide radical scavenging (SOD) assay and metal chelating effect assay were performed for Pc1, Pc2 and Pc3 compounds. The results of antioxidant assays indicated that Pc1, Pc2 and Pc3 compounds have remarkable superoxide radical scavenging activities, moderate 2,2-diphenyl-1-picrylhydrazyl activities and metal chelating effect activities. All the experimental studies showed that Pc1, Pc2 and Pc3 compounds bind to CT-DNA via minor groove binding, cleave of supercoiled pBR322 DNA via photocleavage pathway, inhibit topoisomerase I and have remarkable superoxide radical scavenging activities. Thanks to these properties the Pc1, Pc2 and Pc3 compounds are suitable agents for photo dynamic therapy.

  10. Use of model compounds in coal chemistry

    SciTech Connect

    Collins, C J

    1980-01-01

    The use of model compounds in coal chemistry has been summarized. Several examples from the literature, and also from work at Oak Ridge National Laboratory have been used to illustrate the main principles involved. The current controversy on the subject of model compounds is believed to stem from a semantic misunderstanding owing to different definitions of what a model compound is. The definition of a model compound from the organic chemist's point of view is that it is a substance which may possess at least one property or structural feature suspected of being present in the sample investigated. The sample may be coal itself, a maceral, a coal-derived material or a hydrogen-donor solvent. It is stressed that a recognition of the structure-reactivity relationship in organic compounds is necessary to avoid false conclusions.

  11. Computed structures of polyimides model compounds

    NASA Technical Reports Server (NTRS)

    Tai, H.; Phillips, D. H.

    1990-01-01

    Using a semi-empirical approach, a computer study was made of 8 model compounds of polyimides. The compounds represent subunits from which NASA Langley Research Center has successfully synthesized polymers for aerospace high performance material application, including one of the most promising, LARC-TPI polymer. Three-dimensional graphic display as well as important molecular structure data pertaining to these 8 compounds are obtained.

  12. Model Compound Interactions Characterizing Aquatic Humic Substances

    DTIC Science & Technology

    1990-01-01

    Isolation...............48 3.3.2 Titration Apparatus..............49 3.3.3 Potentiometric Titrations ..........52 3.3.4 Complexometric Titrations ...Potentiometric Titrations ..........57 4.2.2 Complexometric Titrations ..........61 4.3 Natural Sources and Model Compound Mixtures . .. 69 4.3.1...groundwater ........ .................... 50 3.4 Milli-Q complexometric titrations ... ......... .54 4.1a Potentiometric titration of model compounds

  13. Enhanced anti-fibrotic activity of plasmid DNA expressing small interference RNA for TGF-beta type II receptor for a mouse model of obstructive nephropathy by cationized gelatin prepared from different amine compounds.

    PubMed

    Kushibiki, Toshihiro; Nagata-Nakajima, Natsuki; Sugai, Manabu; Shimizu, Akira; Tabata, Yasuhiko

    2006-02-21

    The objective of this study is to increase the transfection efficiency of a plasmid DNA expressing small interference RNA (siRNA) for transforming growth factor-beta receptor (TGF-betaR) by various cationized gelatins of non-viral carrier and evaluate the anti-fibrotic effect with a mouse model of unilateral ureteral obstruction (UUO). Ethylenediamine, putrescine, spermidine or spermine was chemically introduced to the carboxyl groups of gelatin for the cationization. The plasmid DNA of TGF-betaR siRNA expression vector with or without complexation of each cationized gelatin was injected to the left kidney of mice via the ureter to prevent the progression of renal fibrosis of UUO mice. Irrespective of the type of cationized gelatin, the injection of plasmid DNA-cationized gelatin complex significantly decreased the renal level of TGF-betaR over-expression and the collagen content of mice kidney, in marked contrast to free plasmid DNA injection. It is concluded that retrograde injection of TGF-betaR siRNA expression vector plasmid DNA complexed with the cationized gelatin is available to suppress the progression of renal interstitial fibrosis.

  14. Model compound vulcanization studied by XANES

    NASA Astrophysics Data System (ADS)

    Taweepreda, W.; Nu-Mard, R.; Pattanasiriwisawa, W.; Songsiriritthigul, P.

    2009-11-01

    Squalene has been used as a model compound for the investigation of sulphur crosslink in the vulcanization process. The effects of the accelerator on the crosslink were deduced from the sulfur K-edge absorption spectra. The majority of the crosslinks for the squalene vulcanized with ZDEC or TMTD is likely disulfidic, while that vulcanized with CBS or MBTS is monosulfidic.

  15. A nonlinear model for DNA dynamics

    SciTech Connect

    Muto, V.; Scott, A.C.; Christiansen, P.L.

    1989-07-01

    In this paper the thermal equilibrium number of solitons in DNA as a function of absolute temperature and the number of base pairs is calculated. These calculations are effected by modeling DNA as a Toda lattice with parameters chosen to match experimentally measured properties of DNA. It is found that a significant number of solitons is generated at physiological temperature. 23 refs., 2 figs.

  16. Quantitative risk modelling for new pharmaceutical compounds.

    PubMed

    Tang, Zhengru; Taylor, Mark J; Lisboa, Paulo; Dyas, Mark

    2005-11-15

    The process of discovering and developing new drugs is long, costly and risk-laden. Faced with a wealth of newly discovered compounds, industrial scientists need to target resources carefully to discern the key attributes of a drug candidate and to make informed decisions. Here, we describe a quantitative approach to modelling the risk associated with drug development as a tool for scenario analysis concerning the probability of success of a compound as a potential pharmaceutical agent. We bring together the three strands of manufacture, clinical effectiveness and financial returns. This approach involves the application of a Bayesian Network. A simulation model is demonstrated with an implementation in MS Excel using the modelling engine Crystal Ball.

  17. Structure elucidation and DNA binding specificity of natural compounds from Cassia siamea leaves: A biophysical approach.

    PubMed

    Parveen, Mehtab; Ahmad, Faheem; Malla, Ali Mohammed; Khan, Mohd Sohrab; Rehman, Sayeed Ur; Tabish, Mohammad; Silva, Manuela Ramos; Silva, P S Pereira

    2016-06-01

    A novel isoflavone, 5,6,7-trimethoxy-3-(3',4',5'-trimethoxyphenyl)-4H-chromen-4-one (1) along with a known pyranocoumarin, Seselin (2) have been isolated from the ethanolic extract of the leaves of Cassia siamea (Family: Fabaceae). Compound 1 has been reported for the first time from any natural source and has not been synthesized so far. Their structures were elucidated on the basis of chemical and physical evidences viz. elemental analysis, UV, FT-IR, (1)H-NMR, (13)C-NMR and mass spectral analysis. Structure of compound (1) was further authenticated by single-crystal X-ray analysis and density functional theory (DFT) calculations. A multi-technique approach employing UV-Visible spectroscopy, fluorescence, KI quenching studies, competitive displacement assay, circular dichroism and viscosity studies have been utilized to probe the extent of interaction and possible binding modes of isolated compounds (1-2) with calf thymus DNA (CT-DNA). Both the compounds were found to interact with DNA via non-intercalative binding mode with moderate proficiencies. Groove binding was the major interaction mode in the case of compound 2 while compound 1 probably interacts with DNA through electrostatic interactions. These studies provide deeper insight in understanding of DNA-drug (natural products) interaction which could be helpful to improve their bioavailability for therapeutic purposes.

  18. A coarse grain model for DNA.

    PubMed

    Knotts, Thomas A; Rathore, Nitin; Schwartz, David C; de Pablo, Juan J

    2007-02-28

    Understanding the behavior of DNA at the molecular level is of considerable fundamental and engineering importance. While adequate representations of DNA exist at the atomic and continuum level, there is a relative lack of models capable of describing the behavior of DNA at mesoscopic length scales. We present a mesoscale model of DNA that reduces the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base, thereby rendering the investigation of DNA up to a few microns in length computationally tractable. The charges on these sites are considered explicitly. The model is parametrized using thermal denaturation experimental data at a fixed salt concentration. The validity of the model is established by its ability to predict several aspects of DNA behavior, including salt-dependent melting, bubble formation and rehybridization, and the mechanical properties of the molecule as a function of salt concentration.

  19. A coarse grain model for DNA

    NASA Astrophysics Data System (ADS)

    Knotts, Thomas A.; Rathore, Nitin; Schwartz, David C.; de Pablo, Juan J.

    2007-02-01

    Understanding the behavior of DNA at the molecular level is of considerable fundamental and engineering importance. While adequate representations of DNA exist at the atomic and continuum level, there is a relative lack of models capable of describing the behavior of DNA at mesoscopic length scales. We present a mesoscale model of DNA that reduces the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base, thereby rendering the investigation of DNA up to a few microns in length computationally tractable. The charges on these sites are considered explicitly. The model is parametrized using thermal denaturation experimental data at a fixed salt concentration. The validity of the model is established by its ability to predict several aspects of DNA behavior, including salt-dependent melting, bubble formation and rehybridization, and the mechanical properties of the molecule as a function of salt concentration.

  20. Modelling the emplacement of compound lava flows

    NASA Astrophysics Data System (ADS)

    Blake, S.; Bruno, B. C.

    2000-12-01

    The physical variables controlling crust-dominated lava flow have been investigated using laboratory experiments in which molten polyglycol wax was extruded from a point source on to a horizontal plane under cold water. The wax initially spread axisymmetrically and a crust of solid wax grew. Eventually wax broke out from the flow's periphery, sending out a flow lobe which in turn cooled and produced another breakout. The process repeated itself many times, building a 'compound lava'. The time for the first breakout to form correlates well with the theoretically predicted time ( tc) required for cooling to form a crust thick enough for its strength to limit the flow's spreading rate. This time is proportional to the product of effusion rate ( Q) and initial magma viscosity ( μ) and inversely proportional to the square of the crust strength at the flow front. The number of flow units and the apparent fractal dimension of the flow perimeter increase with time normalised by tc. Our model illuminates the physical basis for the observation by Walker [G.P.L. Walker, Bull. Volcanol. 35 (1972) 579-590] that compound lava flows form by slow effusion of low viscosity magma, whereas faster effusion and higher viscosity favour lavas with fewer flow units. Because compound flows require t≫ tc, and given that tc∝ Qμ and the relationship between volume and effusion rate is V= Qt, simple and compound lava flows are predicted to fall in separate fields on a graph of μ against V/ Q2, all else being equal. Compound flows plot at small values of μ and large values of V/ Q2, with the position of the simple/compound boundary defined by field data implying a crust strength of order 10 4 Pa for basaltic to intermediate lavas. Whether a flow remains as a simple flow or matures into a compound flow field depends on the combined effect of viscosity, eruption rate and eruption duration (and hence volume) and these parameters need to be taken in to account when using morphology to infer

  1. First paraben substituted cyclotetraphosphazene compounds and DNA interaction analysis with a new automated biosensor.

    PubMed

    Çiftçi, Gönül Yenilmez; Şenkuytu, Elif; İncir, Saadet Elif; Yuksel, Fatma; Ölçer, Zehra; Yıldırım, Tuba; Kılıç, Adem; Uludağ, Yıldız

    2016-06-15

    Cancer, as one of the leading causes of death in the world, is caused by malignant cell division and growth that depends on rapid DNA replication. To develop anti-cancer drugs this feature of cancer could be exploited by utilizing DNA-damaging molecules. To achieve this, the paraben substituted cyclotetraphosphazene compounds have been synthesized for the first time and their effect on DNA (genotoxicity) has been investigated. The conventional genotoxicity testing methods are laborious, take time and are expensive. Biosensor based assays provide an alternative to investigate this drug/compound DNA interactions. Here for the first time, a new, easy and rapid screening method has been used to investigate the DNA damage, which is based on an automated biosensor device that relies on the real-time electrochemical profiling (REP™) technology. Using both the biosensor based screening method and the in vitro biological assay, the compounds 9 and 11 (propyl and benzyl substituted cyclotetraphosphazene compounds, respectively), have resulted in higher DNA damage than the others with 65% and 80% activity reduction, respectively.

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

    PubMed

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

    2006-01-01

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

  3. Controlled release of plasmid DNA from hydrogels prepared from gelatin cationized by different amine compounds.

    PubMed

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

    2006-05-15

    This paper is an investigation to compare the in vivo controlled release of a plasmid DNA from biodegradable hydrogels prepared from gelatin cationized by different amine compounds, ethylenediamine, putrescine, spermidine, and spermine and the consequent profile of gene expression. Cationized gelatin prepared through the chemical introduction of each amine compound was crosslinked by various concentrations of glutaraldehyde to obtain cationized gelatin hydrogels for the carrier of plasmid DNA release. When the cationized gelatin hydrogels incorporating 125I-labeled plasmid DNA were implanted into the femoral muscle of mice, the radioactivity remaining decreased with time and the retention period of radioactivity prolonged with a decrease in the water content of hydrogels. When 125I-labeled cationized gelatin hydrogels with the higher water content was implanted, the radioactivity remaining was decreased faster with time. The remaining time profile of plasmid DNA radioactivity was in good accordance with that of hydrogel radioactivity, irrespective of the type of cationized gelatin. Following intramuscular implantation, any cationized gelatin hydrogel incorporating plasmid DNA enhanced the expression level of plasmid DNA to a significantly higher extent than the free plasmid DNA injection. In addition, prolonged time period of gene expression was observed although there was no significant difference in the expressed period between the cationized gelatin hydrogels. It was concluded that plasmid DNA of biological activity was released from every cationized gelatin hydrogel accompanied with the in vivo degradation, resulting in enhanced and prolonged gene expression.

  4. G-quadruplex-interacting compounds alter latent DNA replication and episomal persistence of KSHV

    PubMed Central

    Madireddy, Advaitha; Purushothaman, Pravinkumar; Loosbroock, Christopher P.; Robertson, Erle S.; Schildkraut, Carl L.; Verma, Subhash C.

    2016-01-01

    Kaposi's sarcoma associated herpesvirus (KSHV) establishes life-long latent infection by persisting as an extra-chromosomal episome in the infected cells and by maintaining its genome in dividing cells. KSHV achieves this by tethering its epigenome to the host chromosome by latency associated nuclear antigen (LANA), which binds in the terminal repeat (TR) region of the viral genome. Sequence analysis of the TR, a GC-rich DNA element, identified several potential Quadruplex G-Rich Sequences (QGRS). Since quadruplexes have the tendency to obstruct DNA replication, we used G-quadruplex stabilizing compounds to examine their effect on latent DNA replication and the persistence of viral episomes. Our results showed that these G-quadruplex stabilizing compounds led to the activation of dormant origins of DNA replication, with preferential bi-directional pausing of replications forks moving out of the TR region, implicating the role of the G-rich TR in the perturbation of episomal DNA replication. Over time, treatment with PhenDC3 showed a loss of viral episomes in the infected cells. Overall, these data show that G-quadruplex stabilizing compounds retard the progression of replication forks leading to a reduction in DNA replication and episomal maintenance. These results suggest a potential role for G-quadruplex stabilizers in the treatment of KSHV-associated diseases. PMID:26837574

  5. Superstatistical model of bacterial DNA architecture

    PubMed Central

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

    2017-01-01

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

  6. Superstatistical model of bacterial DNA architecture

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  7. Synthesis of a naphthalene-hydroxynaphthalene polymer model compound

    SciTech Connect

    Not Available

    1991-10-02

    The objective of this project was the synthesis of one pound of a new naphthalene-hydroxynaphthalene polymer model compound for use in coal combustion studies. Since this compound was an unreported compound, this effort also required the development of a synthetic route to this compound (including routes to the unique and unreported intermediates leading to its synthesis).

  8. Radio- and photosensitization of DNA with compounds containing platinum and bromine atoms

    NASA Astrophysics Data System (ADS)

    Śmiałek, Małgorzata A.; Ptasińska, Sylwia; Gow, Jason; Vrønning Hoffmann, Søren; Mason, Nigel J.

    2015-05-01

    Irradiations of plasmid DNA by both X-rays and UV light in the presence and absence of compounds containing platinum and bromine atoms were performed in order to asses the sensitization potential of these compounds. Plasmid DNA pBR322 was incubated with platinum (II) bromide, hydrogen hexabromoplatinate (IV), hydrogen hexahydroxyplatinate (IV) and sodium hexahydroxyplatinate (IV). Incubation was followed by X-ray or UV irradiations. It was found that amongst the sensitizers tested, during irradiations carried out in the presence of platinum (II) bromide, the highest levels of double strand breaks formation upon X-ray treatment were recorded. In contrast much less damage was induced by UV light. Data presented here suggests that this compound may be a promising radiosensitizer for cancer treatment. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

  9. Modelling of DNA-protein recognition

    NASA Technical Reports Server (NTRS)

    Rein, R.; Garduno, R.; Colombano, S.; Nir, S.; Haydock, K.; Macelroy, R. D.

    1980-01-01

    Computer model-building procedures using stereochemical principles together with theoretical energy calculations appear to be, at this stage, the most promising route toward the elucidation of DNA-protein binding schemes and recognition principles. A review of models and bonding principles is conducted and approaches to modeling are considered, taking into account possible di-hydrogen-bonding schemes between a peptide and a base (or a base pair) of a double-stranded nucleic acid in the major groove, aspects of computer graphic modeling, and a search for isogeometric helices. The energetics of recognition complexes is discussed and several models for peptide DNA recognition are presented.

  10. Model for melting of confined DNA

    NASA Astrophysics Data System (ADS)

    Werner, E.; Reiter-Schad, M.; Ambjörnsson, T.; Mehlig, B.

    2015-06-01

    When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively investigated. Recently there has been a surge of interest in this question, in part caused by experiments determining the properties of partially bound DNA confined to nanochannels. But how does such confinement affect the melting transition? To answer this question we introduce and solve a model predicting how confinement affects the melting transition for a simple model system by first disregarding the effect of self-avoidance. We find that the transition is smoother for narrower channels. By means of Monte Carlo simulations we then show that a model incorporating self-avoidance shows qualitatively the same behavior and that the effect of confinement is stronger than in the ideal case.

  11. Palladium(II) and platinum(II) organometallic complexes with the model nucleobase anions of thymine, uracil, and cytosine: antitumor activity and interactions with DNA of the platinum compounds.

    PubMed

    Ruiz, José; Lorenzo, Julia; Sanglas, Laura; Cutillas, Natalia; Vicente, Consuelo; Villa, María Dolores; Avilés, Francesc X; López, Gregorio; Moreno, Virtudes; Pérez, José; Bautista, Delia

    2006-08-07

    Pd(II) and Pt(II) complexes with the anions of the model nucleobases 1-methylthymine (1-MethyH), 1-methyluracil (1-MeuraH), and 1-methylcytosine (1-MecytH) of the types [Pd(dmba)(mu-L)]2 [dmba = N,C-chelating 2-((dimethylamino)methyl)phenyl; L = 1-Methy, 1-Meura or 1-Mecyt] and [M(dmba)(L)(L')] [L = 1-Methy or 1-Meura; L' = PPh(3) (M = Pd or Pt), DMSO (M = Pt)] have been obtained. Palladium complexes of the types [Pd(C6F5)(N-N)(L)] [L = 1-Methy or 1-Meura; N-N = N,N,N',N'-tetramethylethylenediamine (tmeda), 2,2'-bipyridine (bpy), or 4,4'-dimethyl-2,2'-bipyridine (Me2bpy)] and [NBu4][Pd(C6F5)(1-Methy)2(H2O)] have also been prepared. The crystal structures of [Pd(dmba)(mu-1-Methy)]2, [Pd(dmba)(mu-1-Mecyt)]2.2CHCl3, [Pd(dmba)(1-Methy)(PPh3)].3CHCl3, [Pt(dmba)(1-Methy)(PPh3)], [Pd(tmeda)(C6F5)(1-Methy)], and [NBu4][Pd(C6F5)(1-Methy)2(H2O)].H2O have been established by X-ray diffraction. The DNA adduct formation of the new platinum complexes synthesized was followed by circular dichroism and electrophoretic mobility. Atomic force microscopy images of the modifications caused by the platinum complexes on plasmid DNA pBR322 were also obtained. Values of IC50 were also calculated for the new platinum complexes against the tumor cell line HL-60. All the new platinum complexes were more active than cisplatin (up to 20-fold in some cases).

  12. Modeling and Global Optimization of DNA separation

    PubMed Central

    Fahrenkopf, Max A.; Ydstie, B. Erik; Mukherjee, Tamal; Schneider, James W.

    2014-01-01

    We develop a non-convex non-linear programming problem that determines the minimum run time to resolve different lengths of DNA using a gel-free micelle end-labeled free solution electrophoresis separation method. Our optimization framework allows for efficient determination of the utility of different DNA separation platforms and enables the identification of the optimal operating conditions for these DNA separation devices. The non-linear programming problem requires a model for signal spacing and signal width, which is known for many DNA separation methods. As a case study, we show how our approach is used to determine the optimal run conditions for micelle end-labeled free-solution electrophoresis and examine the trade-offs between a single capillary system and a parallel capillary system. Parallel capillaries are shown to only be beneficial for DNA lengths above 230 bases using a polydisperse micelle end-label otherwise single capillaries produce faster separations. PMID:24764606

  13. Study on the Keggin zinctungstates based hybrid compound with like DNA spiral chain

    NASA Astrophysics Data System (ADS)

    Li, Liang; Sha, Jing-Quan; Zong, Xi-Ming; Liu, Cui-Juan; Zhang, Qian-Nan; Wang, Dong-Wen; Yang, Xiao-Ning; Wang, Yu

    2014-05-01

    A new compound based on polyoxometalates (POMs) and the quinolone antibacterial pipemidic acid (HPPA), {[Zn(HPPA)2H2O]2[H2ZnW12O40]}ṡ9H2O (1), was hydrothermally synthesized and characterized by elemental analyses, IR and XPRD. Single-crystal X-ray diffraction analysis reveals that the [ZnW12O40 ] 6 - clusters and Zn-HPPA complexes constructed both right- and left-double-stranded like DNA helical chains in the title compound, and these helical chains are further connected together forming the fascinating quadruple-stranded helices via sharing the ZnW12 clusters. Note that the compound 1 represents the first example of zinctungstate POMs modified by antibacterial drugs. In addition, the antibacterial properties of the compound 1 were investigated.

  14. New compound with DNA Topo I inhibitory activity purified from Penicillium oxalicum HSY05.

    PubMed

    Liu, Bing; Wang, Hai-Feng; Zhang, Li-Hua; Liu, Fang; He, Feng-Jun; Bai, Jiao; Hua, Hui-Ming; Chen, Gang; Pei, Yue-Hu

    2015-01-01

    Strain HSY05 was isolated from sea sediment collected from the South China Sea and was later identified as Penicillium oxalicum by 16S rDNA sequence analysis. Various chromatographic processes led to the isolation and purification of two metabolites from the fermentation culture of HSY05, including one new compound, 2,2',4,4'-tetrahyoxy-8'-methyl-6-methoxy-acyl-ethyl-diphenylmethanone (1), and a known compound secalonic acid D (SAD, 2), as characterised by UV, IR, 1D, 2D-NMR and MS data. The inhibitory activities against topoisomerase I of these two compounds were evaluated. The result showed that in addition to the known topo I inhibitor SAD (2), compound 1 also exhibited a moderate inhibitory effect.

  15. Modeling biominerals formed by apatites and DNA.

    PubMed

    Revilla-López, Guillermo; Casanovas, Jordi; Bertran, Oscar; Turon, Pau; Puiggalí, Jordi; Alemán, Carlos

    2013-12-01

    Different aspects of biominerals formed by apatite and DNA have been investigated using computer modeling tools. Firstly, the structure and stability of biominerals in which DNA molecules are embedded into hydroxyapatite and fluoroapatite nanopores have been examined by combining different molecular mechanics methods. After this, the early processes in the nucleation of hydroxyapatite at a DNA template have been investigated using molecular dynamics simulations. Results indicate that duplexes of DNA adopting a B double helix can be encapsulated inside nanopores of hydroxyapatite without undergoing significant distortions in the inter-strand hydrogen bonds and the intra-strand stacking. This ability of hydroxyapatite is practically independent of the DNA sequence, which has been attributed to the stabilizing role of the interactions between the calcium atoms of the mineral and the phosphate groups of the biomolecule. In contrast, the fluorine atoms of fluoroapatite induce pronounced structural distortions in the double helix when embedded in a pore of the same dimensions, resulting in the loss of its most relevant characteristics. On the other hand, molecular dynamics simulations have allowed us to observe the formation of calcium phosphate clusters at the surface of the B-DNA template. Electrostatic interactions between the phosphate groups of DNA and Ca(2+) have been found to essential for the formation of stable ion complexes, which were the starting point of calcium phosphate clusters by incorporating PO3(4) from the solution.

  16. Radiosensitization of DNA in presence of Pt(II)-based compounds

    NASA Astrophysics Data System (ADS)

    Śmiałek, Małgorzata A.; Ptasińska, Sylwia; Gow, Jason; Pieve, Chiara Da; Mason, Nigel J.

    2014-04-01

    X-ray irradiation of plasmid DNA in presence of platinum (II)-based compounds was carried out in order to assess the radiosensitization capabilities of these drugs. In present investigations pBR322 plasmid DNA was used to monitor the effectiveness of chosen compounds in inducing strand breaks. Samples were incubated in the presence of potential radiosensitisers: platinum (II) bromide and cis-diamminedibromoplatinum (II). The results were examined against a common cancer chemotherapy drug cis-diamminedichloroplatinum (II). It was found that platinum (II) bromide can greatly increase the levels of single- and double-strand break formation observed in the irradiated samples with respect to the samples containing platinum as a radiosensitizer only, possessing very little chemotherapeutic activity. The suggested drugs exhibit much higher level of radiosensitivity than widely used cisplatin and thus may be good candidates for cancer treatment.

  17. Flash vacuum pyrolysis of lignin model compounds

    SciTech Connect

    Cooney, M.J.; Britt, P.F.; Buchanan, A.C. III

    1997-03-01

    Despite the extensive research into the pyrolysis of lignin, the underlying chemical reactions that lead to product formation are poorly understood. Detailed mechanistic studies on the pyrolysis of biomass and lignin under conditions relevant to current process conditions could provide insight into utilizing this renewable resource for the production of chemicals and fuel. Currently, flash or fast pyrolysis is the most promising process to maximize the yields of liquid products (up to 80 wt %) from biomass by rapidly heating the substrate to moderate temperatures, typically 500{degrees}C, for short residence times, typically less than two seconds. To provide mechanistic insight into the primary reaction pathways under process relevant conditions, we are investigating the flash vacuum pyrolysis (FVP) of lignin model compounds that contain a {beta}-ether. linkage and {alpha}- or {gamma}-alcohol, which are key structural elements in lignin. The dominant products from the FVP of PhCH{sub 2}CH{sub 2}OPh (PPE), PhC(OH)HCH{sub 2}OPh, and PhCH{sub 2}CH(CH{sub 2}OH)OPh at 500{degrees}C can be attributed to homolysis of the weakest bond in the molecule (C-O bond) or 1,2-elimination. Surprisingly, the hydroxy-substituent dramatically increases the decomposition of PPE. It is proposed that internal hydrogen bonding is accelerating the reaction.

  18. Application of the DNA adductome approach to assess the DNA-damaging capability of in vitro micronucleus test-positive compounds.

    PubMed

    Kato, Kyoko; Yamamura, Eiji; Kawanishi, Masanobu; Yagi, Takashi; Matsuda, Tomonari; Sugiyama, Akio; Uno, Yoshifumi

    2011-03-18

    The in vitro micronucleus (MN) test is widely used for screening genotoxic compounds, but it often produces false-positive results. To consider the significance of positive results, it is important to know whether DNA adducts are formed in the cells treated with the test compound. Recently, Matsuda et al. developed the DNA adductome approach to detect DNA adducts comprehensively ([4] Kanaly, et al., Antioxid. Redox Signal., 2006, 8, 993-1001). We applied this method to assess the DNA-damaging capability of in vitro MN test-positive compounds. CHL/IU cells were treated with compounds from three categories: (1) carcinogens causing DNA alkylation, ethyl methanesulfonate and N-methyl-N'-nitro-N-nitrosoguanidine; (2) carcinogens producing DNA bulky adducts, 2-amino-6-phenyl-1-methylimidazo[4,5-b]pyrene, benzo[a]pyrene, 7,12-dimethylbenz[a]anthracene, and 4-nitroquinoline-1-oxide, and (3) non-carcinogens, caffeine, maltol, and sodium chloride, with or without metabolic activation. With the conditions in which all test compounds gave positive results in the MN tests, DNA was extracted from the cells and hydrolyzed to deoxyribonucleosides, which were subsequently subjected to LC/ESI-MS/MS analysis. All carcinogens (categories 1 and 2) produced various DNA adduct peaks, and some of the m/z peak values corresponded to known adducts. No non-carcinogens produced DNA adducts, indicating that these compounds produced MN through different mechanisms from the adduct formation. These results indicate that the adductome approach is useful to demonstrate DNA damage formation of MN test-positive compounds and to understand their mechanisms of action.

  19. Molecular Models for DNA Damaged by Photoreaction

    NASA Astrophysics Data System (ADS)

    Pearlman, David A.; Holbrook, Stephen R.; Pirkle, David H.; Kim, Sung-Hou

    1985-03-01

    Structural models of a DNA molecule containing a radiation-induced psoralen cross-link and of a DNA containing a thymine photodimer were constructed by applying energy-minimization techniques and model-building procedures to data from x-ray crystallographic studies. The helical axes of the models show substantial kinking and unwinding at the sites of the damage, which may have long-range as well as local effects arising from the concomitant changes in the supercoiling and overall structure of the DNA. The damaged areas may also serve as recognition sites for repair enzymes. These results should help in understanding the biologic effects of radiation-induced damage on cells.

  20. Molecular models for DNA damaged by photoreaction

    SciTech Connect

    Pearlman, D.A.; Holbrook, S.R.; Pirkle, D.H.; Kim, S.H.

    1985-03-15

    Structural models of a DNA molecule containing a radiation-induced psoralen cross-link and of a DNA containing a thymine photodimer were constructed by applying energy-minimization techniques and model-building procedures to data from x-ray crystallographic studies. The helical axes of the models show substantial kinking and unwinding at the sites of the damage, which may have long-range as well as local effects arising from the concomitant changes in the supercoiling and overall structure of the DNA. The damaged areas may also serve as recognition sites for repair enzymes. These results should help in understanding the biologic effects of radiation-induced damage on cells.

  1. Structure-based design, synthesis and biological testing of etoposide analog epipodophyllotoxin-N-mustard hybrid compounds designed to covalently bind to topoisomerase II and DNA

    PubMed Central

    Yadav, Arun A.; Wu, Xing; Patel, Daywin; Yalowich, Jack C.; Hasinoff, Brian B.

    2014-01-01

    Drugs that target DNA topoisomerase II isoforms and alkylate DNA represent two mechanistically distinct and clinically important classes of anticancer drugs. Guided by molecular modeling and docking a series of etoposide analog epipodophyllotoxin-N-mustard hybrid compounds were designed, synthesized and biologically characterized. These hybrids were designed to alkylate nucleophilic protein residues on topoisomerase II and thus produce inactive covalent adducts and to also alkylate DNA. The most potent hybrid had a mean GI50 in the NCI-60 cell screen 17-fold lower than etoposide. Using a variety of in vitro and cell-based assays all of the hybrids tested were shown to target topoisomerase II. A COMPARE analysis indicated that the hybrids had NCI 60-cell growth inhibition profiles matching both etoposide and the N-mustard compounds from which they were derived. These results supported the conclusion that the hybrids displayed characteristics that were consistent with having targeted both topoisomerase II and DNA. PMID:25282653

  2. Ligand substitutions between ruthenium–cymene compounds can control protein versus DNA targeting and anticancer activity

    PubMed Central

    Adhireksan, Zenita; Davey, Gabriela E.; Campomanes, Pablo; Groessl, Michael; Clavel, Catherine M.; Yu, Haojie; Nazarov, Alexey A.; Yeo, Charmian Hui Fang; Ang, Wee Han; Dröge, Peter; Rothlisberger, Ursula; Dyson, Paul J.; Davey, Curt A.

    2014-01-01

    Ruthenium compounds have become promising alternatives to platinum drugs by displaying specific activities against different cancers and favourable toxicity and clearance properties. Nonetheless, their molecular targeting and mechanism of action are poorly understood. Here we study two prototypical ruthenium-arene agents—the cytotoxic antiprimary tumour compound [(η6-p-cymene)Ru(ethylene-diamine)Cl]PF6 and the relatively non-cytotoxic antimetastasis compound [(η6-p-cymene)Ru(1,3,5-triaza-7-phosphaadamantane)Cl2]—and discover that the former targets the DNA of chromatin, while the latter preferentially forms adducts on the histone proteins. Using a novel ‘atom-to-cell’ approach, we establish the basis for the surprisingly site-selective adduct formation behaviour and distinct cellular impact of these two chemically similar anticancer agents, which suggests that the cytotoxic effects arise largely from DNA lesions, whereas the protein adducts may be linked to the other therapeutic activities. Our study shows promise for developing new ruthenium drugs, via ligand-based modulation of DNA versus protein binding and thus cytotoxic potential, to target distinguishing epigenetic features of cancer cells. PMID:24637564

  3. Discrete model for DNA-promoter dynamics

    NASA Astrophysics Data System (ADS)

    Salerno, Mario

    1991-10-01

    We introduce a discrete model for DNA that takes into account the information about specific base sequences along the double helix. We use this model to study nonlinear wave dynamics of the T7A1 DNA promoter. As results we show the existence in the promoter of a dynamically active region in which static solitons acquire finite velocities, which contrasts with regions where solitons simply remain static. Furthermore, when they pass through this region moving solitons are accelerated, decelerated, or reflected, depending on their initial velocities. The possibility that these dynamical effects play a role in the mechanism of genetic activation is suggested.

  4. All-atom polarizable force field for DNA based on the classical Drude oscillator model.

    PubMed

    Savelyev, Alexey; MacKerell, Alexander D

    2014-06-15

    Presented is a first generation atomistic force field (FF) for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages, and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting quantum mechanical (QM) data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude FF yields stable DNA duplexes on the 100-ns time scale and satisfactorily reproduce (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII substates of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive FF, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA.

  5. Identification of genotoxic compounds using isogenic DNA repair deficient DT40 cell lines on a quantitative high throughput screening platform

    PubMed Central

    Nishihara, Kana; Huang, Ruili; Zhao, Jinghua; Shahane, Sampada A.; Witt, Kristine L.; Smith-Roe, Stephanie L.; Tice, Raymond R.; Takeda, Shunichi; Xia, Menghang

    2016-01-01

    DNA repair pathways play a critical role in maintaining cellular homeostasis by repairing DNA damage induced by endogenous processes and xenobiotics, including environmental chemicals. Induction of DNA damage may lead to genomic instability, disruption of cellular homeostasis and potentially tumours. Isogenic chicken DT40 B-lymphocyte cell lines deficient in DNA repair pathways can be used to identify genotoxic compounds and aid in characterising the nature of the induced DNA damage. As part of the US Tox21 program, we previously optimised several different DT40 isogenic clones on a high-throughput screening platform and confirmed the utility of this approach for detecting genotoxicants by measuring differential cytotoxicity in wild-type and DNA repair-deficient clones following chemical exposure. In the study reported here, we screened the Tox21 10K compound library against two isogenic DNA repair-deficient DT40 cell lines (KU70 −/−/RAD54 −/− and REV3 −/−) and the wild-type cell line using a cell viability assay that measures intracellular adenosine triphosphate levels. KU70 and RAD54 are genes associated with DNA double-strand break repair processes, and REV3 is associated with translesion DNA synthesis pathways. Active compounds identified in the primary screening included many well-known genotoxicants (e.g. adriamycin, melphalan) and several compounds previously untested for genotoxicity. A subset of compounds was further evaluated by assessing their ability to induce micronuclei and phosphorylated H2AX. Using this comprehensive approach, three compounds with previously undefined genotoxicity—2-oxiranemethanamine, AD-67 and tetraphenylolethane glycidyl ether—were identified as genotoxic. These results demonstrate the utility of this approach for identifying and prioritising compounds that may damage DNA. PMID:26243743

  6. Assessing Uncertainty of Interspecies Correlation Estimation Models for Aromatic Compounds

    EPA Science Inventory

    We developed Interspecies Correlation Estimation (ICE) models for aromatic compounds containing 1 to 4 benzene rings to assess uncertainty in toxicity extrapolation in two data compilation approaches. ICE models are mathematical relationships between surrogate and predicted test ...

  7. Braiding DNA: experiments, simulations, and models.

    PubMed

    Charvin, G; Vologodskii, A; Bensimon, D; Croquette, V

    2005-06-01

    DNA encounters topological problems in vivo because of its extended double-helical structure. As a consequence, the semiconservative mechanism of DNA replication leads to the formation of DNA braids or catenanes, which have to be removed for the completion of cell division. To get a better understanding of these structures, we have studied the elastic behavior of two braided nicked DNA molecules using a magnetic trap apparatus. The experimental data let us identify and characterize three regimes of braiding: a slightly twisted regime before the formation of the first crossing, followed by genuine braids which, at large braiding number, buckle to form plectonemes. Two different approaches support and quantify this characterization of the data. First, Monte Carlo (MC) simulations of braided DNAs yield a full description of the molecules' behavior and their buckling transition. Second, modeling the braids as a twisted swing provides a good approximation of the elastic response of the molecules as they are intertwined. Comparisons of the experiments and the MC simulations with this analytical model allow for a measurement of the diameter of the braids and its dependence upon entropic and electrostatic repulsive interactions. The MC simulations allow for an estimate of the effective torsional constant of the braids (at a stretching force F = 2 pN): C(b) approximately 48 nm (as compared with C approximately 100 nm for a single unnicked DNA). Finally, at low salt concentrations and for sufficiently large number of braids, the diameter of the braided molecules is observed to collapse to that of double-stranded DNA. We suggest that this collapse is due to the partial melting and fraying of the two nicked molecules and the subsequent right- or left-handed intertwining of the stretched single strands.

  8. The structure-based design, synthesis and biological evaluation of DNA-binding bisintercalating bisanthrapyrazole anticancer compounds

    PubMed Central

    Hasinoff, Brian B.; Liang, Hong; Wu, Xing; Guziec, Lynn J.; Guziec, Frank S.; Marshall, Kyle; Yalowich, Jack C.

    2008-01-01

    Anticancer drugs that bind to DNA and inhibit DNA-processing enzymes represent an important class of anticancer drugs. In order to find stronger DNA binding and more potent cytotoxic compounds, a series of ester-coupled bisanthrapyrazole derivatives of 7-chloro-2-[2-[(2-hydroxyethyl)methylamino]ethyl]anthra[1,9-cd]pyrazol-6(2H)-one (AP9) were designed and evaluated by molecular docking techniques. Because the anthrapyrazoles are unable to be reductively activated like doxorubicin and other anthracyclines, they should not be cardiotoxic like the anthracyclines. Based on the docking scores of a series of bisanthrapyrazoles with different numbers of methylene linkers (n) that were docked into an X-ray structure of double-stranded DNA, five bisanthrapyrazoles (n = 1 to 5) were selected for synthesis and physical and biological evaluation. The synthesized compounds were evaluated for DNA binding and bisintercalation by measuring the DNA melting temperature increase, for growth inhibitory effects on the human erythroleukemic K562 cell line, and for DNA topoisomerase IIα-mediated cleavage of DNA and inhibition of DNA topoisomerase IIα decatenation activities. The results suggest that the bisanthrapyrazoles with n = 2 to 5 formed bisintercalation complexes with DNA. In conclusion, a novel group of bisintercalating anthrapyrazole compounds have been designed, synthesized and biologically evaluated as possible anticancer agents. PMID:18258442

  9. Is DNA a Good Model Polymer?

    PubMed Central

    Tree, Douglas R.; Muralidhar, Abhiram; Doyle, Patrick S.; Dorfman, Kevin D.

    2013-01-01

    The details surrounding the cross-over from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the Pruned-Enriched Rosenbluth Method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike chains over an extremely large range of contour lengths. From our calculations, we find that very large DNA chains (≈ 1,000,000 base pairs depending on the choice of size metric) are required to reach flexible, swollen non-draining coils. Furthermore, our results indicate that the commonly used model polymer λ-DNA (48,500 base pairs) does not exhibit “ideal” scaling, but exists in the middle of the transition to long-chain behavior. We subsequently conclude that typical DNA used in experiments are too short to serve as an accurate model of long-chain, universal polymer behavior. PMID:24347685

  10. Computational studies on DNA recognition of novel organic and copper anti-tumor compounds

    NASA Astrophysics Data System (ADS)

    Nascimento, Rafael R.; Gonçalves, Marcos B.; Petrilli, Helena M.; Ferreira, Ana M. D. C.; Ippoliti, Emiliano; Dreyer, Jens; Carloni, Paolo

    2013-03-01

    The ability of many organic and coordination compounds to bind to DNA and/or damage cellular structures has been largely exploited in anticancer research. Identifying DNA recognition mechanisms have thus important impact on the chemical biology of gene expression and the development of new drugs and therapies. Previous studies on copper(II) complexes with oxindole-Schiff base ligands have shown their potential anti-tumor activity towards different cells, inducing apoptosis through a preferential attack to DNA and/or mitochondria [SIL11]. The binding mechanism of the organic and copper(II) complexes [Cu(isaepy)2]2 + (1) and [Cu(isaenim)]2 + (2) and their modulation at DNA is investigated through theoretical studies. Here we adopted a multi-scale procedure to simulate this large system using molecular docking and classical molecular dynamics. Hybrid Car-Parrinello/Molecular Mechanics calculations were applied to parameterize the copper(II) complexes by using the force matching approach. Free energies of binding are investigated by metadynamics enhanced sampling methods[VAR08]. [SIL11] V. C. da Silveira et. al. JIB 105 (2011) 1692.[VAR08] A. V. Vargiu et. al. Nucl. Acids Res. 36 (2008) 5910.

  11. Curcumin, resveratrol and flavonoids as anti-inflammatory, cyto- and DNA-protective dietary compounds.

    PubMed

    Bisht, Kavita; Wagner, Karl-Heinz; Bulmer, Andrew C

    2010-11-28

    Numerous dietary compounds, ubiquitous in fruits, vegetables and spices have been isolated and evaluated during recent years for their therapeutic potential. These compounds include flavonoid and non-flavonoid polyphenols, which describe beneficial effects against a variety of ailments. The notion that these plant products have health promoting effects emerged because their intake was related to a reduced incidence of cancer, cardiovascular, neurological, respiratory, and age-related diseases. Exposure of the body to a stressful environment challenges cell survival and increases the risk of chronic disease developing. The polyphenols afford protection against various stress-induced toxicities through modulating intercellular cascades which inhibit inflammatory molecule synthesis, the formation of free radicals, nuclear damage and induce antioxidant enzyme expression. These responses have the potential to increase life expectancy. The present review article focuses on curcumin, resveratrol, and flavonoids and seeks to summarize their anti-inflammatory, cytoprotective and DNA-protective properties.

  12. A low-density DNA microchip for the detection of (anti-)estrogenic compounds and their relative potencies.

    PubMed

    Wang, Si; Rijk, Jeroen C W; Pen, Marieke J; Aarts, Jac M M J G; Peijnenburg, Ad A C M; Rietjens, Ivonne M C M; Bovee, Toine F H

    2013-04-01

    In the current study, a set of 12 reference compounds was tested in a low-density DNA microchip that contains probes for 11 different estrogen-responsive marker genes. Our results show that the seven most informative marker genes on the chip resulted in fingerprints that correctly predicted the (anti-)estrogenic activity of the model compounds except that of the negative control testosterone. Two marker genes, myeloid leukemia factor-1 interacting protein and ubiquitin-conjugating enzyme E2C, were even capable of correctly predicting the estrogenic potency of all five estrogen receptor (ER) agonists tested and correlated well with the potencies as determined in the MCF-7/BOS proliferation assay and the in vivo uterotrophic assay. In addition, it was demonstrated that the estrogenic responses of testosterone, both in the array tube assay and in the proliferation assay, were partially due to the conversion of testosterone into 17β-estradiol by aromatase but also due to formation of other estrogenic metabolites, the presence and estrogenic potency of which were confirmed by gas chromatography-tandem mass spectrometry analysis and a yeast-based reporter gene assay, respectively. It is concluded that low-density DNA microchip-based fingerprinting in MCF-7/BOS cells for estrogenicity marker genes provides a faster in vitro alternative to the current MCF-7/BOS cell proliferation assay (E-screen).

  13. A mathematical model for intracellular effects of toxins on DNA adduction and repair

    SciTech Connect

    Gaver, D.P.; Jacobs, P.A.; Carpenter, R.L.; Burkhart, J.G.

    1997-01-01

    The processes by which certain classes of toxic compounds or their metabolites may react with DNA to alter the genetic information contained in subsequent generations of cells or organisms are a major component of hazard associated with exposure to chemicals in the environment. Many classes of chemicals may form DNA adducts and there may or may not be a defined mechanism to remove a particular adduct from DNA independent of replication. Many compounds and metabolites that bind DNA also readily bind existing proteins; some classes of toxins and DNA adducts have the capacity to inactive a repair enzyme and divert the repair process competitively. This paper formulates an intracellular dynamic model for one aspect of the action of toxins that form DNA adducts, recognizing a capacity for removal of those adducts by a repair enzyme combined with reaction of the toxin and/or the DNA adduct to inactive the repair enzyme. This particular model illustrates the possible saturation of repair enzyme capacity by the toxin dosage and shows that bistable behavior can occur, with the potential to induce abrupt shifts away from steady-state equilibria. The model suggests that bistable behavior, dose and variation between individuals or tissues may combine under certain conditions to amplify the biological effect of dose observed as DNA adduction and its consequences as mutation. A model recognizing stochastic phenomena also indicates that variation in within-cell toxin concentration may promote jumps between stable equilibria.

  14. Compound

    NASA Astrophysics Data System (ADS)

    Suzumura, Akitoshi; Watanabe, Masaki; Nagasako, Naoyuki; Asahi, Ryoji

    2014-06-01

    Recently, Cu-based chalcogenides such as Cu3SbSe4, Cu2Se, and Cu2SnSe3 have attracted much attention because of their high thermoelectric performance and their common feature of very low thermal conductivity. However, for practical use, materials without toxic elements such as selenium are preferable. In this paper, we report Se-free Cu3SbS4 thermoelectric material and improvement of its figure of merit ( ZT) by chemical substitutions. Substitutions of 3 at.% Ag for Cu and 2 at.% Ge for Sb lead to significant reductions in the thermal conductivity by 37% and 22%, respectively. These substitutions do not sacrifice the power factor, thus resulting in enhancement of the ZT value. The sensitivity of the thermal conductivity to chemical substitutions in these compounds is discussed in terms of the calculated phonon dispersion and previously proposed models for Cu-based chalcogenides. To improve the power factor, we optimize the hole carrier concentration by substitution of Ge for Sb, achieving a power factor of 16 μW/cm K2 at 573 K, which is better than the best reported for Se-based Cu3SbSe4 compounds.

  15. Solid-State, Dye-Labeled DNA Detects Volatile Compounds in the Vapor Phase

    PubMed Central

    White, Joel; Truesdell, Kathleen; Williams, Lloyd B; AtKisson, Mary S; Kauer, John S

    2008-01-01

    This paper demonstrates a previously unreported property of deoxyribonucleic acid—the ability of dye-labeled, solid-state DNA dried onto a surface to detect odors delivered in the vapor phase by changes in fluorescence. This property is useful for engineering systems to detect volatiles and provides a way for artificial sensors to emulate the way cross-reactive olfactory receptors respond to and encode single odorous compounds and mixtures. Recent studies show that the vertebrate olfactory receptor repertoire arises from an unusually large gene family and that the receptor types that have been tested so far show variable breadths of response. In designing biomimetic artificial noses, the challenge has been to generate a similarly large sensor repertoire that can be manufactured with exact chemical precision and reproducibility and that has the requisite combinatorial complexity to detect odors in the real world. Here we describe an approach for generating and screening large, diverse libraries of defined sensors using single-stranded, fluorescent dye–labeled DNA that has been dried onto a substrate and pulsed with brief exposures to different odors. These new solid-state DNA-based sensors are sensitive and show differential, sequence-dependent responses. Furthermore, we show that large DNA-based sensor libraries can be rapidly screened for odor response diversity using standard high-throughput microarray methods. These observations describe new properties of DNA and provide a generalized approach for producing explicitly tailored sensor arrays that can be rationally chosen for the detection of target volatiles with different chemical structures that include biologically derived odors, toxic chemicals, and explosives. PMID:18215112

  16. New spiro tria(thia)zolidine-acridines as topoisomerase inhibitors, DNA binders and cytostatic compounds.

    PubMed

    Salem, Othman M; Vilková, Mária; Janočková, Jana; Jendželovský, Rastislav; Fedoročko, Peter; Žilecká, Eva; Kašpárková, Jana; Brabec, Viktor; Imrich, Ján; Kožurková, Mária

    2016-05-01

    Three new diphenylsubstituted spirotriazolidine- and thiazolidinone-acridines were prepared and their interaction with calf thymus DNA investigated with UV-vis, fluorescence, circular dichroism spectroscopy and viscometry. The binding constants K were estimated to range from 0.34 to 0.93 × 10(4) M(-1). UV-vis, fluorescence and circular dichroism measurements indicated that the compounds act as effective DNA-interacting agents. Electrophoretic separation proved that ligands inhibited topoisomerase I and II. The biological activity of compounds 3, 5 &6 at several different concentrations (10, 20 and 50 μM) was evaluated both 48 h and 72 h following their addition to HL-60 cancer cells. The results were analysed using various different techniques (MMP detection, changes in metabolic activity/viability and analysis of cell cycle distribution). Acridine was also used as the positive control in these assays. The results from MMP analysis demonstrate the strong effect of 3-diphenylamino-2-(acridin-9-yl)imino-1,3-thiazolidin-4-one (5) on mitochondrial physiology. Cell viability analysis showed that acridine derivatives 3 and 6 were less effective than derivative 5 and the acridine control.

  17. How aromatic compounds block DNA binding of HcaR catabolite regulator

    DOE PAGES

    Kim, Youngchang; Joachimiak, Grazyna; Bigelow, Lance; ...

    2016-04-25

    Bacterial catabolism of aromatic compounds from various sources including phenylpropanoids and flavonoids that are abundant in soil plays an important role in the recycling of carbon in the ecosystem. We have determined the crystal structures of apo-HcaR from Acinetobacter sp. ADP1, a MarR/SlyA transcription factor, in complexes with hydroxycinnamates and a specific DNA operator. The protein regulates the expression of the hca catabolic operon in Acinetobacter and related bacterial strains, allowing utilization of hydroxycinnamates as sole sources of carbon. HcaR binds multiple ligands, and as a result the transcription of genes encoding several catabolic enzymes is increased. The 1.9-2.4 Åmore » resolution structures presented here explain how HcaR recognizes four ligands (ferulate, 3,4-dihydroxybenzoate, p-coumarate, and vanillin) using the same binding site. The ligand promiscuity appears to be an adaptation to match a broad specificity of hydroxycinnamate catabolic enzymes while responding to toxic thioester intermediates. Structures of apo-HcaR and in complex with a specific DNA hca operator when combined with binding studies of hydroxycinnamates show how aromatic ligands render HcaR unproductive in recognizing a specific DNA target. Furthermore, the current study contributes to a better understanding of the hca catabolic operon regulation mechanism by the transcription factor HcaR.« less

  18. How aromatic compounds block DNA binding of HcaR catabolite regulator

    SciTech Connect

    Kim, Youngchang; Joachimiak, Grazyna; Bigelow, Lance; Babnigg, Gyorgy; Joachimiak, Andrzej

    2016-04-25

    Bacterial catabolism of aromatic compounds from various sources including phenylpropanoids and flavonoids that are abundant in soil plays an important role in the recycling of carbon in the ecosystem. We have determined the crystal structures of apo-HcaR from Acinetobacter sp. ADP1, a MarR/SlyA transcription factor, in complexes with hydroxycinnamates and a specific DNA operator. The protein regulates the expression of the hca catabolic operon in Acinetobacter and related bacterial strains, allowing utilization of hydroxycinnamates as sole sources of carbon. HcaR binds multiple ligands, and as a result the transcription of genes encoding several catabolic enzymes is increased. The 1.9-2.4 Å resolution structures presented here explain how HcaR recognizes four ligands (ferulate, 3,4-dihydroxybenzoate, p-coumarate, and vanillin) using the same binding site. The ligand promiscuity appears to be an adaptation to match a broad specificity of hydroxycinnamate catabolic enzymes while responding to toxic thioester intermediates. Structures of apo-HcaR and in complex with a specific DNA hca operator when combined with binding studies of hydroxycinnamates show how aromatic ligands render HcaR unproductive in recognizing a specific DNA target. Furthermore, the current study contributes to a better understanding of the hca catabolic operon regulation mechanism by the transcription factor HcaR.

  19. Polymers modified with double-tailed fluorous compounds for efficient DNA and siRNA delivery.

    PubMed

    He, Bingwei; Wang, Yitong; Shao, Naimin; Chang, Hong; Cheng, Yiyun

    2015-08-01

    Cationic polymers are widely used as gene carriers, however, these polymers are usually associated with low transfection efficacy and non-negligible toxicity. Fluorination on polymers significantly improves their performances in gene delivery, but a high density of fluorous chains must be conjugated on a single polymer. Here we present a new strategy to construct fluorinated polymers with minimal fluorous chains for efficient DNA and siRNA delivery. A double-tailed fluorous compound 2-chloro-4,6-bis[(perfluorohexyl)propyloxy]-1,3,5-triazine (CBT) was conjugated on dendrimers of different generations and low molecular weight polyethylenimine via a facile synthesis. The yielding products with average numbers of 1-2 conjugated CBT moieties showed much improved EGFP and luciferase transfection efficacy compared to unmodified polymers. In addition, these polymers show high siRNA delivery efficacy on different cell lines. Among the synthesized polymers, generation 1 (G1) dendrimer modified with an average number of 1.9 CBT moieties (G1-CBT1.9) shows the highest efficacy when delivering both DNA and siRNA and its efficacy approaches that of Lipofectamine 2000. G1-CBT1.9 also shows efficient gene silencing in vivo. All of the CBT-modified polymers exhibit minimal toxicity on the cells at their optimal transfection conditions. This study provides a new strategy to design efficient fluorous polymers for DNA and siRNA delivery.

  20. Exploring the DNA binding mode of transition metal based biologically active compounds

    NASA Astrophysics Data System (ADS)

    Raman, N.; Sobha, S.

    2012-01-01

    Few novel 4-aminoantipyrine derived Schiff bases and their metal complexes were synthesized and characterized. Their structural features and other properties were deduced from the elemental analysis, magnetic susceptibility and molar conductivity as well as from mass, IR, UV-vis, 1H NMR and EPR spectral studies. The binding of the complexes with CT-DNA was analyzed by electronic absorption spectroscopy, viscosity measurement, and cyclic voltammetry. The interaction of the metal complexes with DNA was also studied by molecular modeling with special reference to docking. The experimental and docking results revealed that the complexes have the ability of interaction with DNA of minor groove binding mode. The intrinsic binding constants ( Kb) of the complexes with CT-DNA were found out which show that they are minor groove binders. Gel electrophoresis assay demonstrated the ability of the complexes to cleave the pUC19 DNA in the presence of AH 2 (ascorbic acid). Moreover, the oxidative cleavage studies using distamycin revealed the minor groove binding for the newly synthesized 4-aminoantipyrine derived Schiff bases and their metal complexes. Evaluation of antibacterial activity of the complexes against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epidermidis, and Klebsiella pneumoniae exhibited that the complexes have potent biocidal activity than the free ligands.

  1. Exploring the DNA binding mode of transition metal based biologically active compounds.

    PubMed

    Raman, N; Sobha, S

    2012-01-01

    Few novel 4-aminoantipyrine derived Schiff bases and their metal complexes were synthesized and characterized. Their structural features and other properties were deduced from the elemental analysis, magnetic susceptibility and molar conductivity as well as from mass, IR, UV-vis, (1)H NMR and EPR spectral studies. The binding of the complexes with CT-DNA was analyzed by electronic absorption spectroscopy, viscosity measurement, and cyclic voltammetry. The interaction of the metal complexes with DNA was also studied by molecular modeling with special reference to docking. The experimental and docking results revealed that the complexes have the ability of interaction with DNA of minor groove binding mode. The intrinsic binding constants (K(b)) of the complexes with CT-DNA were found out which show that they are minor groove binders. Gel electrophoresis assay demonstrated the ability of the complexes to cleave the pUC19 DNA in the presence of AH(2) (ascorbic acid). Moreover, the oxidative cleavage studies using distamycin revealed the minor groove binding for the newly synthesized 4-aminoantipyrine derived Schiff bases and their metal complexes. Evaluation of antibacterial activity of the complexes against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epidermidis, and Klebsiella pneumoniae exhibited that the complexes have potent biocidal activity than the free ligands.

  2. Quantum dynamics of a hole migration through DNA: A single strand DNA model.

    PubMed

    Shirmovsky, S Eh

    2016-10-01

    A model predicting the behavior of a hole acting on the DNA strand was investigated. The hole-DNA interaction on the basis of a quantum-classical, non-linear DNA single strand model was described. The fact that a DNA molecule is formed by a furanose ring as its sugar, phosphate group and bases was taken into consideration. Based on the model, results were obtained for the probability of a hole location on the DNA base sequences, such as GTTGGG, GATGTGGG, GTTGTTGGG as well as on the sugar-phosphate groups mated with them.

  3. Potential bioactive Schiff base compounds: Synthesis, characterization, X-ray structures, biological screenings and interaction with Salmon sperm DNA

    NASA Astrophysics Data System (ADS)

    Sirajuddin, Muhammad; Uddin, Noor; Ali, Saqib; Tahir, Muhammad Nawaz

    2013-12-01

    Three Schiff base compounds ofN‧-substituted benzohydrazide and sulfonohydrazide derivatives: N‧-(2-hydroxy-3-methoxybenzylidene)-4-tert-butyl- benzohydrazide (1), N‧-(5-bromo-2-hydroxybenzylidene)-4-tert-butylbenzohydrazide (2) and N‧-(2-hydroxy-3-methoxybenzylidene)-4-methylbenzenesulfonohydrazide (3) were synthesized and characterized by elemental analysis, FT-IR, 1H, 13C NMR spectroscopy and single crystal analysis. The title compounds have been screened for their biological activities including, antibacterial, antifungal, antioxidant, cytotoxic, enzymatic activities as well as interaction with SS-DNA which showed remarkable activities in each area of research. The DNA binding of the compounds 1-3 with SS-DNA has been carried out with absorption spectroscopy, which reveals the binding propensity towards SS-DNA via intercalation mode of interaction. The intercalative mode of interaction is also supported by viscometric results. The synthesized compounds were also found to be effective against alkaline phosphatase enzyme. They also show significant to good antimicrobial activity against six bacterial and five fungal strains. The MIC (minimum inhibitory concentration) for antibacterial activity ranges from 1.95-500 μg/mL. Compounds 1-3 show cytotoxic activity comparable to the control. At higher conc. (100 μg/L) compound 3 shows 100% activity means that it has killed all brine shrimps. They were also found to be effective antioxidant of 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) and show almost comparable antioxidant activity to that of the standard and known antioxidant, ascorbic acid.

  4. The discovery of macrocyclic XIAP antagonists from a DNA-programmed chemistry library, and their optimization to give lead compounds with in vivo antitumor activity.

    PubMed

    Seigal, Benjamin A; Connors, William H; Fraley, Andrew; Borzilleri, Robert M; Carter, Percy H; Emanuel, Stuart L; Fargnoli, Joseph; Kim, Kyoung; Lei, Ming; Naglich, Joseph G; Pokross, Matthew E; Posy, Shana L; Shen, Henry; Surti, Neha; Talbott, Randy; Zhang, Yong; Terrett, Nicholas K

    2015-03-26

    Affinity selection screening of macrocycle libraries derived from DNA-programmed chemistry identified XIAP BIR2 and BIR3 domain inhibitors that displace bound pro-apoptotic caspases. X-ray cocrystal structures of key compounds with XIAP BIR2 suggested potency-enhancing structural modifications. Optimization of dimeric macrocycles with similar affinity for both domains were potent pro-apoptotic agents in cancer cell lines and efficacious in shrinking tumors in a mouse xenograft model.

  5. Synthesis of a naphthalene-hydroxynaphthalene polymer model compound

    SciTech Connect

    Kwong, C.D.

    1991-04-15

    The objective of this contract is the synthesis of a new naphthalene-hydroxynaphthalene polymer model compound for coal combustion studies. This effort also requires the development of a synthetic procedure for this compound since it has not been reported before. We can only report that we are still unable to provide the target polymer or even any of the key intermediates leading to this target Dr. Rao has been informed of our progress (or lack of progress), and he has suggested that we begin to design other alternative compounds which contain the functionalities required by the target compound. In response to this suggestion, we have quickly designed the potential targets shown in Scheme VIL We are currently evaluating the schemes further and we will continue designing routes to the other analogous compounds.

  6. Combining a Ru(II) "Building Block" and Rapid Screening Approach to Identify DNA Structure-Selective "Light Switch" Compounds.

    PubMed

    Wachter, Erin; Moyá, Diego; Glazer, Edith C

    2017-02-13

    A chemically reactive Ru(II) "building block", able to undergo condensation reactions with substituted diamines, was utilized to create a small library of luminescent "light switch" dipyrido-[3,2-a:2',3'-c] phenazine (dppz) complexes. The impact of substituent identity, position, and the number of substituents on the light switch effect was investigated. An unbiased, parallel screening approach was used to evaluate the selectivity of the compounds for a variety of different biomolecules, including protein, nucleosides, single stranded DNA, duplex DNA, triplex DNA, and G-quadruplex DNA. Combining these two approaches allowed for the identification of hit molecules that showed different selectivities for biologically relevant DNA structures, particularly triplex and quadruplex DNA.

  7. Theoretical modelling of epigenetically modified DNA sequences

    PubMed Central

    Carvalho, Alexandra Teresa Pires; Gouveia, Maria Leonor; Raju Kanna, Charan; Wärmländer, Sebastian K. T. S.; Platts, Jamie; Kamerlin, Shina Caroline Lynn

    2015-01-01

    We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts. PMID:26448859

  8. Chemotherapeutic compounds targeting the DNA double-strand break repair pathways: the good, the bad, and the promising.

    PubMed

    Jekimovs, Christian; Bolderson, Emma; Suraweera, Amila; Adams, Mark; O'Byrne, Kenneth J; Richard, Derek J

    2014-01-01

    The repair of DNA double-strand breaks (DSBs) is a critical cellular mechanism that exists to ensure genomic stability. DNA DSBs are the most deleterious type of insult to a cell's genetic material and can lead to genomic instability, apoptosis, or senescence. Incorrectly repaired DNA DSBs have the potential to produce chromosomal translocations and genomic instability, potentially leading to cancer. The prevalence of DNA DSBs in cancer due to unregulated growth and errors in repair opens up a potential therapeutic window in the treatment of cancers. The cellular response to DNA DSBs is comprised of two pathways to ensure DNA breaks are repaired: homologous recombination and non-homologous end joining. Identifying chemotherapeutic compounds targeting proteins involved in these DNA repair pathways has shown promise as a cancer therapy for patients, either as a monotherapy or in combination with genotoxic drugs. From the beginning, there have been a number of chemotherapeutic compounds that have yielded successful responses in the clinic, a number that have failed (CGK-733 and iniparib), and a number of promising targets for future studies identified. This review looks in detail at how the cell responds to these DNA DSBs and investigates the chemotherapeutic avenues that have been and are currently being explored to target this repair process.

  9. Impact of estrogenic compounds on DNA integrity in human spermatozoa: evidence for cross-linking and redox cycling activities.

    PubMed

    Bennetts, L E; De Iuliis, G N; Nixon, B; Kime, M; Zelski, K; McVicar, C M; Lewis, S E; Aitken, R J

    2008-05-10

    A great deal of circumstantial evidence has linked DNA damage in human spermatozoa with adverse reproductive outcomes including reduced fertility and high rates of miscarriage. Although oxidative stress is thought to make a significant contribution to DNA damage in the male germ line, the factors responsible for creating this stress have not been elucidated. One group of compounds that are thought to be active in this context are the estrogens, either generated as a result of the endogenous metabolism of androgens within the male reproductive tract or gaining access to the latter as a consequence of environmental exposure. In this study, a wide variety of estrogenic compounds were assessed for their direct effects on human spermatozoa in vitro. DNA integrity was assessed using the Comet and TUNEL assays, lesion frequencies were quantified by QPCR using targets within the mitochondrial and nuclear (beta-globin) genomes, DNA adducts were characterized by mass spectrometry and redox activity was monitored using dihydroethidium (DHE) as the probe. Of the estrogenic and estrogen analogue compounds evaluated, catechol estrogens, quercetin, diethylstilbestrol and pyrocatechol stimulated intense redox activity while genistein was only active at the highest doses tested. Other estrogens and estrogen analogues, such as 17beta-estradiol, nonylphenol, bisphenol A and 2,3-dihydroxynaphthalene were inactive. Estrogen-induced redox activity was associated with a dramatic loss of motility and, in the case of 2-hydroxyestradiol, the induction of significant DNA fragmentation. Mass spectrometry also indicated that catechol estrogens were capable of forming dimers that can cross-link the densely packed DNA strands in sperm chromatin, impairing nuclear decondensation. These results highlight the potential importance of estrogenic compounds in creating oxidative stress and DNA damage in the male germ line and suggest that further exploration of these compounds in the aetiology of male

  10. Comparison of DNA strand-break simulated with different DNA models

    NASA Astrophysics Data System (ADS)

    Xie, Wenzhang; Li, Junli; Li, Chunyan; Qiu, Rui; Yan, Congchong; Zeng, Zhi

    2014-06-01

    In Monte Carlo simulation of DNA damage, the geometric model of DNA is of great importance. To study the influence of DNA model on the simulation of DNA damage, three DNA models were created in this paper. They were a volume model and two atomic models with different parameters. Direct DNA strand-break induced by low-energy electrons were simulated respectively with the three models. The results show that most of the energy depositions in the DNA segments do not lead to strand-breaks. The simple single strand-break (SSB) tends to be the predominant damage type, and the contribution of complex double strand-break (DSB) to the total DSB cannot be neglected. Among the yields of all the three DNA target models applied here, the yields of the volume model are the highest, the yields of the atomic model with double van der Waals radii (r) take the second place, whereas the yields of the atomic model with single r come last. On average, the ratios of SSB yields are approximately equivalent to the corresponding ratios of the models' volume. However, there seems to be no clear relationship between the DSB yields and the models' volume.

  11. Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles.

    PubMed

    Hedman, Johannes; Nordgaard, Anders; Rasmusson, Birgitta; Ansell, Ricky; Rådström, Peter

    2009-11-01

    DNA evidence, linking perpetrators to crime scenes, is central to many legal proceedings. However, DNA samples from crime scenes often contain PCR-inhibitory substances, which may generate blank or incomplete DNA profiles. Extensive DNA purification can be required to rid the sample of these inhibitors, although these procedures increase the risk of DNA loss. Most forensic laboratories use commercial DNA amplification kits (e.g., AmpFlSTR SGM Plus) with the DNA polymerase AmpliTaq Gold as the gold standard. Here, we show that alternative DNA polymerase-buffer systems can improve the quality of forensic DNA analysis and efficiently circumvent PCR inhibition in crime scene samples, without additional sample preparation. DNA profiles from 20 of 32 totally or partially inhibited crime scene saliva samples were significantly improved using Bio-X-Act Short, ExTaq Hot Start, or PicoMaxx High Fidelity instead of AmpliTaq Gold. A statistical model for unbiased quality control of forensic DNA profiles was developed to quantify the results. Our study demonstrates the importance of adjusting the chemistry of the PCR to enhance forensic DNA analysis and diagnostic PCR, providing an alternative to laborious sample preparation protocols.

  12. Behavior of asphaltene model compounds at w/o interfaces.

    PubMed

    Nordgård, Erland L; Sørland, Geir; Sjöblom, Johan

    2010-02-16

    Asphaltenes, present in significant amounts in heavy crude oil, contains subfractions capable of stabilizing water-in-oil emulsions. Still, the composition of these subfractions is not known in detail, and the actual mechanism behind emulsion stability is dependent on perceived interfacial concentrations and compositions. This study aims at utilizing polyaromatic surfactants which contains an acidic moiety as model compounds for the surface-active subfraction of asphaltenes. A modified pulse-field gradient (PFG) NMR method has been used to study droplet sizes and stability of emulsions prepared with asphaltene model compounds. The method has been compared to the standard microscopy droplet counting method. Arithmetic and volumetric mean droplet sizes as a function of surfactant concentration and water content clearly showed that the interfacial area was dependent on the available surfactant at the emulsion interface. Adsorption of the model compounds onto hydrophilic silica has been investigated by UV depletion, and minor differences in the chemical structure of the model compounds caused significant differences in the affinity toward this highly polar surface. The cross-sectional areas obtained have been compared to areas from the surface-to-volume ratio found by NMR and gave similar results for one of the two model compounds. The mean molecular area for this compound suggested a tilted geometry of the aromatic core with respect to the interface, which has also been proposed for real asphaltenic samples. The film behavior was further investigated using a liquid-liquid Langmuir trough supporting the ability to form stable interfacial films. This study supports that acidic, or strong hydrogen-bonding fractions, can promote stable water-in-oil emulsion. The use of model compounds opens up for studying emulsion behavior and demulsifier efficiency based on true interfacial concentrations rather than perceived interfaces.

  13. Aroma compound sorption by oak wood in a model wine.

    PubMed

    Ramirez Ramirez, G; Lubbers, S; Charpentier, C; Feuillat, M; Voilley, A; Chassagne, D

    2001-08-01

    Oak wood used for wine barrels was immersed into a model wine containing eight aroma compounds (e.g., aromatic and terpene alcohols, ethyl esters, and aldehyde), for which activity coefficients in water and model wine were determined using the mutual solubility measurement. A mass balance of these volatiles considering their reactivity in model wine was established. For most of the studied aroma compounds, and mainly for linalool and ethyl octanoate, a sorption behavior into wood was reported for the first time. This phenomenon was selective and could not be related to the solubilities in model wine and hydrophobicities of the studied aroma compounds, suggesting that acid-base and polar characteristics of wood were more involved in this sorption mechanism. This study has also shown that the level of sorption is a function of the ratio of wood surface area/solution volume.

  14. Two Half-Sandwiched Ruthenium (II) Compounds Containing 5-Fluorouracil Derivatives: Synthesis and Study of DNA Intercalation

    PubMed Central

    Li, Zhao-Jun; Hou, Yong; Qin, Da-An; Jin, Zhi-Min; Hu, Mao-Lin

    2015-01-01

    Two novel coordination compounds of half-sandwiched ruthenium(II) containing 2-(5-fluorouracil)-yl-N-(pyridyl)-acetamide were synthesized, and their intercalation binding modes with calf thymus DNA were revealed by hyperchromism of ultraviolet-visible spectroscopy; the binding constants were determined according to a Langmuir adsorption equation that was deduced on the base of careful cyclic voltammetry measurements. The two compounds exhibited DNA intercalation binding activities with the binding constants of 1.13×106 M-1 and 5.35 ×105 M-1, respectively. PMID:25789618

  15. DNA gel electrophoresis: the reptation model(s).

    PubMed

    Slater, Gary W

    2009-06-01

    DNA gel electrophoresis has been the most important experimental tool to separate DNA fragments for several decades. The introduction of PFGE in the 1980s and capillary gel electrophoresis in the 1990s made it possible to study, map and sequence entire genomes. Explaining how very large DNA molecules move in a gel and why PFGE is needed to separate them has been an active field of research ever since the launch of the journal Electrophoresis. This article presents a personal and historical overview of the development of the theory of gel electrophoresis, focusing on the reptation model, the band broadening mechanisms, and finally the factors that limit the read length and the resolution of electrophoresis-based sequencing systems. I conclude with a short discussion of some of the questions that remain unanswered.

  16. Langmuir films of asphaltene model compounds and their fluorescent properties.

    PubMed

    Nordgård, Erland L; Landsem, Eva; Sjöblom, Johan

    2008-08-19

    The relationship between the physicochemical properties of asphaltenes and asphaltene structure is an issue of increasing focus. Surface pressure-area isotherms of asphaltene model compounds have been investigated to gain more knowledge of their arrangement at an aqueous surface. Variations in interfacial activity have been correlated to proposed arrangements. The presence of a carboxylic acid has shown to be crucial for their interfacial activity and film properties. The acid group directs the molecules normal to the surface, forming a stable monolayer film. The high stability was absent when no acidic groups were present. Fluorescence spectra of deposited Langmuir-Blodgett films showed only the presence of the excimer emission for thin films of acidic model compounds, indicating a close face-to-face arrangement of the molecules. Time-correlated single photon counting (TCSPC) of the model compounds in toluene indicated the presence of aggregates for two of four compounds at low concentrations. However, a sudden drop of interfacial tension observed could not be correlated to the aggregation. Instead, aggregation induced by addition of a "poor" solvent showed decreased interfacial activity when aggregated due to decrease of monomers in bulk. The findings regarding these asphaltene model compounds and their structural differences show the great effect an acidic group has on their physicochemical properties.

  17. Insights on protein-DNA recognition by coarse grain modelling.

    PubMed

    Poulain, P; Saladin, A; Hartmann, B; Prévost, C

    2008-11-30

    Coarse grain modelling of macromolecules is a new approach, potentially well adapted to answer numerous issues, ranging from physics to biology. We propose here an original DNA coarse grain model specifically dedicated to protein-DNA docking, a crucial, but still largely unresolved, question in molecular biology. Using a representative set of protein-DNA complexes, we first show that our model is able to predict the interaction surface between the macromolecular partners taken in their bound form. In a second part, the impact of the DNA sequence and electrostatics, together with the DNA and protein conformations on docking is investigated. Our results strongly suggest that the overall DNA structure mainly contributes in discriminating the interaction site on cognate proteins. Direct electrostatic interactions between phosphate groups and amino acid side chains strengthen the binding. Overall, this work demonstrates that coarse grain modeling can reveal itself a precious auxiliary for a general and complete description and understanding of protein-DNA association mechanisms.

  18. Synthesis of a naphthalene-hydroxynaphthalene polymer model compound

    SciTech Connect

    Kwong, C.D.

    1990-10-09

    This goal is to synthesize a new naphthalene hydroxynaphthalene polymer model compound for use in coal combustion studies. na effort will also require the development of a synthetic procedure to synthesize this compound since it is unreported. As a result of our synthesis efforts, a number of potential precursors and Area's Analytical Section for characterization and identification. The synthesis of the pre-Bakefite intermediate has been identified as being key to the evaluation of our synthetic approach to the target compound. During this quarter, we have been reevaluating our synthetic approach while we have begun trying to synthesize this compound. As a result of our reevaluation, we also have been considering slightly modified target compounds which might be obtained by more direct routes or from commercially available materials. We also targeted simplified intermediates which would expedite our evaluation of the feasibility of the Bakelite process for the final polymerization, the key step of our suggested scheme. The results of our simplified model compound will also provide data to help us determine any modifications that will be required.

  19. Synthesis of a naphthalene-hydroxynaphthalene polymer model compound

    SciTech Connect

    Kwong, C.D.

    1991-01-15

    The goal is to synthesize a new naphthalene-hydroxynaphthalene polymer model compound for use in coal combustion studies. This effort will also require the development of a synthetic procedure to synthesize this compound since it is unreported. Our synthesis efforts have resulted in the preparation of a number of potential precursors and intermediates. These compounds were submitted to the Organic Chemistry Research Area's Analytical Section for characterization and identification. The synthesis of the pre-Bakelite intermediate has continued to be the focus of our efforts. We first modified the target intermediate slightly to allow this compound to be obtained by a more direct route, using commercially available materials. Since then, we have further simplified intermediate to expedite our evaluation of the feasibility of the Bakelite process for the final polymerization, the key step of our suggested scheme.

  20. Sensitivity Analysis of QSAR Models for Assessing Novel Military Compounds

    DTIC Science & Technology

    2009-01-01

    erties, such as log P, would aid in estimating a chemical’s environmental fate and toxicology when applied to QSAR modeling. Granted, QSAR mod- els, such...ER D C TR -0 9 -3 Strategic Environmental Research and Development Program Sensitivity Analysis of QSAR Models for Assessing Novel...Environmental Research and Development Program ERDC TR-09-3 January 2009 Sensitivity Analysis of QSAR Models for Assessing Novel Military Compound

  1. An autonomous DNA model for finite state automata.

    PubMed

    Martinez-Perez, Israel M; Zimmermann, Karl-Heinz; Ignatova, Zoya

    2009-01-01

    In this paper we introduce an autonomous DNA model for finite state automata. This model called sticker automaton model is based on the hybridisation of single stranded DNA molecules (stickers) encoding transition rules and input data. The computation is carried out in an autonomous manner by one enzyme which allows us to determine whether a resulting double-stranded DNA molecule belongs to the automaton's language or not.

  2. Molecular mechanisms of DNA damage initiated by. alpha. ,. beta. -unsaturated carbonyl compounds as criteria for genotoxicity and mutagenicity

    SciTech Connect

    Eder, E.; Hoffman, C.; Bastian, H.; Deininger, C.; Scheckenbach, S. )

    1990-08-01

    {alpha},{beta}-Unsaturated carbonyl compounds are important not only from a theoretical but also a practical standpoint. These ubiquitous compounds can interact with DNA through various mechanisms. The predominant interaction is the formation of cyclic 1,N{sup 2}-deoxyguanosine adducts; 7,8-cyclic guanine adducts are also found. The authors have synthesized and characterized the stereoisomers of adducts formed by about 20 {alpha},{beta}-unsaturated carbonyl compounds. The different types of adducts and the mutagenic and genotoxic response can be explained by the molecular structures of the agents. Metabolic epoxidation of the double bond and other metabolic activation, e.g., activation of the nitrogroups via nitroreductases, were also found to contribute to genotoxic and mutagenic activities. The results have further elucidated the genotoxic mechanisms of these compounds; however, additional investigations are required for a complete understanding of the genotoxic activity of this class of compounds.

  3. The role of model compound studies in coal research

    SciTech Connect

    Buchanan, A.C. III; Britt, P.F.

    1994-03-01

    The extraordinarily complex chemical and physical structure of coals continues to present coal scientists with major challenges in advancing the base of scientific knowledge required for the development of substantially improved coal utilization technologies. As a consequence, model compound studies play a foundational role in advancing coal science. Model compounds are employed in studies for: (a) determination of kinetic and mechanistic information relevant to coal pyrolysis and liquefaction chemistry, and to computational modeling of these processes; (b) development of new catalysts for coal conversion or upgrading of coal-derived liquids; (c) development and benchmarking of various spectroscopic methods for analysis of coal structure and constitution by NMR, FTIR, mass spectrometry, X-ray techniques (XPS, XANES), etc.; and, (d) exploration and development of new chemical reactions for coal such as deploymerization under mild conditions, selective heteroatom removal etc. The choice of a model compound should not be prescribed, and the rational for the selection can vary with the goal of the research. The breadth of use of model compounds in coal research precludes a thorough examination in this report.

  4. Base-modified thymidines capable of terminating DNA synthesis are novel bioactive compounds with activity in cancer cells

    PubMed Central

    Borland, Kayla M.; AbdulSalam, Safnas F.; Solivio, Morwena J.; Burke, Matthew P.; Wolfkiel, Patrick R.; Lawson, Sean M.; Stockman, Courtney A.; Andersen, Joel M.; Smith, Skyler; Tolstolutskaya, Julia N.; Gurjar, Purujit N.; Bercz, Aron P.; Merino, Edward J.; Litosh, Vladislav A.

    2015-01-01

    Current FDA-approved chemotherapeutic antimetabolites elicit severe side effects that warrant their improvement; therefore, we designed compounds with mechanisms of action focusing on inhibiting DNA replication rather than targeting multiple pathways. We previously discovered that 5-(α-substituted-2-nitrobenzyloxy)methyluridine-5′-triphosphates were exquisite DNA synthesis terminators; therefore, we synthesized a library of 35 thymidine analogs and evaluated their activity using an MTT cell viability assay of MCF7 breast cancer cells chosen for their vulnerability to these nucleoside derivatives. Compound 3a, having an α-tert-butyl-2-nitro-4-(phenyl)alkynylbenzyloxy group, showed an IC50 of 9 ± 1 μM. The compound is more selective for cancer cells than for fibroblast cells compared with 5-fluorouracil. Treatment of MCF7 cells with 3a elicits the DNA damage response as indicated by phosphorylation of γ-H2A. A primer extension assay of the 5′-triphosphate of 3a revealed that 3aTP is more likely to inhibit DNA polymerase than to lead to termination events upon incorporation into the DNA replication fork. PMID:25778768

  5. A model capturing novel strand symmetries in bacterial DNA

    SciTech Connect

    Sobottka, Marcelo; Hart, Andrew G.

    2011-07-15

    Highlights: {yields} We propose a simple stochastic model to construct primitive DNA sequences. {yields} The model provide an explanation for Chargaff's second parity rule in primitive DNA sequences. {yields} The model is also used to predict a novel type of strand symmetry in primitive DNA sequences. {yields} We extend the results for bacterial DNA sequences and compare distributional properties intrinsic to the model to statistical estimates from 1049 bacterial genomes. {yields} We find out statistical evidences that the novel type of strand symmetry holds for bacterial DNA sequences. -- Abstract: Chargaff's second parity rule for short oligonucleotides states that the frequency of any short nucleotide sequence on a strand is approximately equal to the frequency of its reverse complement on the same strand. Recent studies have shown that, with the exception of organellar DNA, this parity rule generally holds for double-stranded DNA genomes and fails to hold for single-stranded genomes. While Chargaff's first parity rule is fully explained by the Watson-Crick pairing in the DNA double helix, a definitive explanation for the second parity rule has not yet been determined. In this work, we propose a model based on a hidden Markov process for approximating the distributional structure of primitive DNA sequences. Then, we use the model to provide another possible theoretical explanation for Chargaff's second parity rule, and to predict novel distributional aspects of bacterial DNA sequences.

  6. Synthesis, spectroscopic characterization and structural investigations of new adduct compound of carbazole with picric acid: DNA binding and antimicrobial studies

    NASA Astrophysics Data System (ADS)

    Saravanabhavan, Munusamy; Sathya, Krishnan; Puranik, Vedavati G.; Sekar, Marimuthu

    2014-01-01

    Carbazole picrate (CP), a new organic compound has been synthesized, characterized by various analytical and spectroscopic technique such as FT-IR, UV-Vis, 1H and 13C NMR spectroscopy. An orthorhombic geometry was proposed based on single crystal XRD study. The thermal stability of the crystal was studied by using thermo-gravimetric and differential thermal analyses and found that it was stable up to 170 °C. Further, the newly synthesized title compound was tested for its in vitro antibacterial and antifungal activity against various bacterial and fungal species. Also, the compound was tested for its binding activity with Calf thymus (CT) DNA and the results show a considerable interaction between CP and CT-DNA.

  7. Rapid Diminution in the Level and Activity of DNA-Dependent Protein Kinase in Cancer Cells by a Reactive Nitro-Benzoxadiazole Compound

    PubMed Central

    Silva, Viviane A. O.; Lafont, Florian; Benhelli-Mokrani, Houda; Breton, Magali Le; Hulin, Philippe; Chabot, Thomas; Paris, François; Sakanyan, Vehary; Fleury, Fabrice

    2016-01-01

    The expression and activity of DNA-dependent protein kinase (DNA-PK) is related to DNA repair status in the response of cells to exogenous and endogenous factors. Recent studies indicate that Epidermal Growth Factor Receptor (EGFR) is involved in modulating DNA-PK. It has been shown that a compound 4-nitro-7-[(1-oxidopyridin-2-yl)sulfanyl]-2,1,3-benzoxadiazole (NSC), bearing a nitro-benzoxadiazole (NBD) scaffold, enhances tyrosine phosphorylation of EGFR and triggers downstream signaling pathways. Here, we studied the behavior of DNA-PK and other DNA repair proteins in prostate cancer cells exposed to compound NSC. We showed that both the expression and activity of DNA-PKcs (catalytic subunit of DNA-PK) rapidly decreased upon exposure of cells to the compound. The decline in DNA-PKcs was associated with enhanced protein ubiquitination, indicating the activation of cellular proteasome. However, pretreatment of cells with thioglycerol abolished the action of compound NSC and restored the level of DNA-PKcs. Moreover, the decreased level of DNA-PKcs was associated with the production of intracellular hydrogen peroxide by stable dimeric forms of Cu/Zn SOD1 induced by NSC. Our findings indicate that reactive oxygen species and electrophilic intermediates, generated and accumulated during the redox transformation of NBD compounds, are primarily responsible for the rapid modulation of DNA-PKcs functions in cancer cells. PMID:27187356

  8. Rapid Diminution in the Level and Activity of DNA-Dependent Protein Kinase in Cancer Cells by a Reactive Nitro-Benzoxadiazole Compound.

    PubMed

    Silva, Viviane A O; Lafont, Florian; Benhelli-Mokrani, Houda; Breton, Magali Le; Hulin, Philippe; Chabot, Thomas; Paris, François; Sakanyan, Vehary; Fleury, Fabrice

    2016-05-11

    The expression and activity of DNA-dependent protein kinase (DNA-PK) is related to DNA repair status in the response of cells to exogenous and endogenous factors. Recent studies indicate that Epidermal Growth Factor Receptor (EGFR) is involved in modulating DNA-PK. It has been shown that a compound 4-nitro-7-[(1-oxidopyridin-2-yl)sulfanyl]-2,1,3-benzoxadiazole (NSC), bearing a nitro-benzoxadiazole (NBD) scaffold, enhances tyrosine phosphorylation of EGFR and triggers downstream signaling pathways. Here, we studied the behavior of DNA-PK and other DNA repair proteins in prostate cancer cells exposed to compound NSC. We showed that both the expression and activity of DNA-PKcs (catalytic subunit of DNA-PK) rapidly decreased upon exposure of cells to the compound. The decline in DNA-PKcs was associated with enhanced protein ubiquitination, indicating the activation of cellular proteasome. However, pretreatment of cells with thioglycerol abolished the action of compound NSC and restored the level of DNA-PKcs. Moreover, the decreased level of DNA-PKcs was associated with the production of intracellular hydrogen peroxide by stable dimeric forms of Cu/Zn SOD1 induced by NSC. Our findings indicate that reactive oxygen species and electrophilic intermediates, generated and accumulated during the redox transformation of NBD compounds, are primarily responsible for the rapid modulation of DNA-PKcs functions in cancer cells.

  9. Understanding DNA under oxidative stress and sensitization: the role of molecular modeling.

    PubMed

    Dumont, Elise; Monari, Antonio

    2015-01-01

    DNA is constantly exposed to damaging threats coming from oxidative stress, i.e., from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanisms and also to the rational design of new chemo-therapeutic agents.

  10. Understanding DNA Under Oxidative Stress and Sensitization: The Role of Molecular Modeling

    NASA Astrophysics Data System (ADS)

    Monari, Antonio; Dumont, Elise

    2015-07-01

    DNA is constantly exposed to damaging threats coming from oxidative stress, i.e. from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, that dynamical effects are to be taken into account, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanism and also to the rational design of new chemo-therapeutic agents.

  11. Understanding DNA under oxidative stress and sensitization: the role of molecular modeling

    PubMed Central

    Dumont, Elise; Monari, Antonio

    2015-01-01

    DNA is constantly exposed to damaging threats coming from oxidative stress, i.e., from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanisms and also to the rational design of new chemo-therapeutic agents. PMID:26236706

  12. Modeling emissions of volatile organic compounds from silage

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Volatile organic compounds (VOCs), necessary reactants for photochemical smog formation, are emitted from numerous sources. Limited available data suggest that dairy farms emit VOCs with cattle feed, primarily silage, being the primary source. Process-based models of VOC transfer within and from si...

  13. Laccase-mediator catalyzed conversion of model lignin compounds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Laccases play an important role in the biological breakdown of lignin and have great potential in the deconstruction of lignocellulosic feedstocks. We examined a variety of laccases, both commercially prepared and crude extracts, for their ability to oxidize three model lignol compounds (p-coumaryl...

  14. QSAR modeling and chemical space analysis of antimalarial compounds.

    PubMed

    Sidorov, Pavel; Viira, Birgit; Davioud-Charvet, Elisabeth; Maran, Uko; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

    2017-04-03

    Generative topographic mapping (GTM) has been used to visualize and analyze the chemical space of antimalarial compounds as well as to build predictive models linking structure of molecules with their antimalarial activity. For this, a database, including ~3000 molecules tested in one or several of 17 anti-Plasmodium activity assessment protocols, has been compiled by assembling experimental data from in-house and ChEMBL databases. GTM classification models built on subsets corresponding to individual bioassays perform similarly to the earlier reported SVM models. Zones preferentially populated by active and inactive molecules, respectively, clearly emerge in the class landscapes supported by the GTM model. Their analysis resulted in identification of privileged structural motifs of potential antimalarial compounds. Projection of marketed antimalarial drugs on this map allowed us to delineate several areas in the chemical space corresponding to different mechanisms of antimalarial activity. This helped us to make a suggestion about the mode of action of the molecules populating these zones.

  15. The Peyrard-Bishop-Dauxois Model of DNA Dynamics

    NASA Astrophysics Data System (ADS)

    Alexandrov, Boian; Bishop, Alan; Usheva, Anny; Rasmussen, Kim

    2008-03-01

    This presentation details aspects of the rapid development of the connection between the dynamics of double strand DNA, and experimental findings that has occurred in the recent years. We will approach this topic by demonstrating the Peyrard-Bishop-Dauxois model's ability to provide useful insight on several experimental observations. Specifically, we will discuss the melting behavior of various DNA sequences, and mechanical unzipping through dynamic force spectroscopy. Focusing on viral transcription initiation we will further show how the connection between DNA dynamics and DNA's biological functionality is becoming increasingly strong. Finally, we will describe a probable connection between DNA dynamics and the ability of repair proteins to recognize UV-radiation damages.

  16. Monitoring the Activation of the DNA Damage Response Pathway in a 3D Spheroid Model.

    PubMed

    Mondesert, Odile; Frongia, Céline; Clayton, Olivia; Boizeau, Marie-Laure; Lobjois, Valérie; Ducommun, Bernard

    2015-01-01

    Monitoring the DNA-Damage Response (DDR) activated pathway in multicellular tumor spheroid models is an important challenge as these 3D models have demonstrated their major relevance in pharmacological evaluation. Herein we present DDR-Act-FP, a fluorescent biosensor that allows detection of DDR activation through monitoring of the p21 promoter p53-dependent activation. We show that cells expressing the DDR-Act-FP biosensor efficiently report activation of the DDR pathway after DNA damage and its pharmacological manipulation using ATM kinase inhibitors. We also report the successful use of this assay to screen a small compound library in order to identify activators of the DDR response. Finally, using multicellular spheroids expressing the DDR-Act-FP we demonstrate that DDR activation and its pharmacological manipulation with inhibitory and activatory compounds can be efficiently monitored in live 3D spheroid model. This study paves the way for the development of innovative screening and preclinical evaluation assays.

  17. Modeling toxic compounds from nitric oxide emission measurements

    NASA Astrophysics Data System (ADS)

    Vallero, Daniel A.; Peirce, Jeffrey; Cho, Ki Don

    Determining the amount and rate of degradation of toxic pollutants in soil and groundwater is difficult and often requires invasive techniques, such as deploying extensive monitoring well networks. Even with these networks, degradation rates across entire systems cannot readily be extrapolated from the samples. When organic compounds are degraded by microbes, especially nitrifying bacteria, oxides or nitrogen (NO x) are released to the atmosphere. Thus, the flux of nitric oxide (NO) from the soil to the lower troposphere can be used to predict the rate at which organic compounds are degraded. By characterizing and applying biogenic and anthropogenic processes in soils the rates of degradation of organic compounds. Toluene was selected as a representative of toxic aromatic compounds, since it is inherently toxic, it is a substituted benzene compound and is listed as a hazardous air pollutant under Section 12 of the Clean Air Act Amendments of 1990. Measured toluene concentrations in soil, microbial population growth and NO fluxes in chamber studies were used to develop and parameterize a numerical model based on carbon and nitrogen cycling. These measurements, in turn, were used as indicators of bioremediation of air toxic (i.e. toluene) concentrations. The model found that chemical concentration, soil microbial abundance, and NO production can be directly related to the experimental results (significant at P < 0.01) for all toluene concentrations tested. This indicates that the model may prove useful in monitoring and predicting the fate of toxic aromatic contaminants in a complex soil system. It may also be useful in predicting the release of ozone precursors, such as changes in reservoirs of hydrocarbons and oxides of nitrogen. As such, the model may be a tool for decision makers in ozone non-attainment areas.

  18. A Paper Model of DNA Structure and Replication.

    ERIC Educational Resources Information Center

    Sigismondi, Linda A.

    1989-01-01

    A paper model which is designed to give students a hands-on experience during lecture and blackboard instruction on DNA structure is provided. A list of materials, paper patterns, and procedures for using the models to teach DNA structure and replication are given. (CW)

  19. Inhibition of DNA topoisomerases I and II and growth inhibition of HL-60 cells by novel acridine-based compounds.

    PubMed

    Janočková, Jana; Plšíková, Jana; Kašpárková, Jana; Brabec, Viktor; Jendželovský, Rastislav; Mikeš, Jaromír; Kovaľ, Ján; Hamuľaková, Slávka; Fedoročko, Peter; Kuča, Kamil; Kožurková, Mária

    2015-08-30

    HL-60 cancer cells were treated with a series of novel acridine derivatives (derivatives 1-4) in order to test the compounds' ability to inhibit both cancer cell growth and topoisomerase I and II activity. Binding studies of derivatives 1-4 with calf thymus DNA were also performed using a number of techniques (UV-Vis and fluorescence spectroscopy, thermal denaturation, linear dichroism and viscometry) to determine the nature of the interaction between the compounds and ctDNA. The binding constants for the complexes of the studied acridine derivatives with DNA were calculated from UV-Vis spectroscopic titrations (K=3.1×10(4)-2.0×10(3)M(-1)). Some of the compounds showed a strong inhibitory effect against Topo II at the relatively low concentration of 5μM. Topo I/II inhibition mode assays were also performed and verified that the novel compounds are topoisomerase suppressors rather than poisons. The biological activities of derivatives were studied using MTT assay and flow cytometric methods (detection of mitochondrial membrane potential, measurement of cell viability) after 24 and 48h incubation. The ability of derivatives to impair cell proliferation was tested by an analysis of cell cycle distribution.

  20. Mycofumigation by the Volatile Organic Compound-Producing Fungus Muscodor albus Induces Bacterial Cell Death through DNA Damage

    PubMed Central

    Alpha, Cambria J.; Campos, Manuel; Jacobs-Wagner, Christine

    2014-01-01

    Muscodor albus belongs to a genus of endophytic fungi that inhibit and kill other fungi, bacteria, and insects through production of a complex mixture of volatile organic compounds (VOCs). This process of mycofumigation has found commercial application for control of human and plant pathogens, but the mechanism of the VOC toxicity is unknown. Here, the mode of action of these volatiles was investigated through a series of genetic screens and biochemical assays. A single-gene knockout screen revealed high sensitivity for Escherichia coli lacking enzymes in the pathways of DNA repair, DNA metabolic process, and response to stress when exposed to the VOCs of M. albus. Furthermore, the sensitivity of knockouts involved in the repair of specific DNA alkyl adducts suggests that the VOCs may induce alkylation. Evidence of DNA damage suggests that these adducts lead to breaks during DNA replication or transcription if not properly repaired. Additional cytotoxicity profiling indicated that during VOC exposure, E. coli became filamentous and demonstrated an increase in cellular membrane fluidity. The volatile nature of the toxic compounds produced by M. albus and their broad range of inhibition make this fungus an attractive biological agent. Understanding the antimicrobial effects and the VOC mode of action will inform the utility and safety of potential mycofumigation applications for M. albus. PMID:25452287

  1. Nanoparticles inhibit DNA replication by binding to DNA: modeling and experimental validation.

    PubMed

    Li, Kungang; Zhao, Xiaonan; K Hammer, Brian; Du, Songyan; Chen, Yongsheng

    2013-11-26

    Predictive models are beneficial tools for researchers to use in prioritizing nanoparticles (NPs) for toxicological tests, but experimental evaluation can be time-consuming and expensive, and thus, priority should be given to tests that identify the NPs most likely to be harmful. For characterization of NPs, the physical binding of NPs to DNA molecules is important to measure, as interference with DNA function may be one cause of toxicity. Here, we determined the interaction energy between 12 types of NPs and DNA based on the Derjaguin-Landau-Verwey-Overbeek (DLVO) model and then predicted the affinity of the NPs for DNA. Using the single-molecule imaging technique known as atomic force microscopy (AFM), we experimentally determined the binding affinity of those NPs for DNA. Theoretical predictions and experimental observations of the binding affinity agreed well. Furthermore, the effect of NPs on DNA replication in vitro was investigated with the polymerase chain reaction (PCR) technique. The results showed that NPs with a high affinity for DNA strongly inhibited DNA replication, whereas NPs with low affinity had no or minimal effects on DNA replication. The methodology here is expected to benefit the genotoxicological testing of NPs as well as the design of safe NPs.

  2. Modeling Emissions of Volatile Organic Compounds from New Carpets

    SciTech Connect

    Little, J.C.; Hodgson, A.T.; Gadgil, A.J.

    1993-02-01

    A simple model is proposed to account for observed emissions of volatile organic compounds (VOCs) from new carpets. The model assumes that the VOCs originate predominantly in a uniform slab of polymer backing material. Parameters for the model (the initial concentration of a VOC in the polymer, a diffusion coefficient and an equilibrium polymer/air partition coefficient) are obtained from experimental data produced by a previous chamber study. The diffusion coefficients generally decrease as the molecular weight of the VOCs increase, while the polymer/air partition coefficients generally increase as the vapor pressure of the compounds decrease. In addition, for two of the study carpets that have a styrene-butadiene rubber (SBR) backing, the diffusion and partition coefficients are similar to independently reported values for SBR. The results suggest that predictions of VOCs emissions from new carpets may be possible based solely on a knowledge of the physical properties of the relevant compounds and the carpet backing material. However, a more rigorous validation of the model is desirable.

  3. Modeling emissions of volatile organic compounds from new carpets

    NASA Astrophysics Data System (ADS)

    Little, John C.; Hodgson, Alfred T.; Gadgil, Ashok J.

    A simple model is proposed to account for observed emissions of volatile organic compounds (VOCs) from new carpets. The model assumes that the VOCs originate predominantly in a uniform slab of polymer backing material. Parameters for the model (the initial concentration of a VOC in the polymer, a diffusion coefficient and an equilibrium polymer/air partition coefficient) are obtained from experimental data produced by a previous chamber study. The diffusion coefficients generally decrease as the molecular weight of the VOCs increase, while the partition coefficients generally increase as the vapor pressure of the compounds decreases. In addition, for two of the study carpets that have a styrene-butadiene rubber (SBR) backing, the diffusion and partition coefficients are similar to independently reported values for SBR. The results suggest that prediction of VOC emissions from new carpets may be possible based solely on a knowledge of the physical properties of the relevant compounds and the carpet backing material. However, a more rigorous validation of the model is desirable.

  4. Coarse-grained DNA modeling: Hybridization and ionic effects

    NASA Astrophysics Data System (ADS)

    Hinckley, Daniel M.

    Deoxyribonucleic acid (DNA) is a biopolymer of enormous significance in living systems. The utility of DNA in such systems is derived from the programmable nature of DNA and its unique mechanical properties. Recently, material scientists have harnessed these properties in order to create systems that spontaneous self-assemble on the nanoscale. Both biologists and material scientists are hindered by an incomplete understanding of the physical interactions that together govern DNA's behavior. Computer simulations, especially those at the coarse-grained (CG) level, can potentially complete this understanding by resolving details indiscernible with current experimental techniques. In this thesis, we advance the state-of-the-art of DNA CG simulations by first reviewing the relevant theory and the evolution of CG DNA models since their inception. Then we present 3SPN.2, an improved CG model for DNA that should provide new insights into biological and nanotechnological systems which incorporate DNA. We perform forward flux sampling simulations in order to examine the effect of sequence, oligomer length, and ionic strength on DNA oligomer hybridization. Due to the limitations inherent in continuum treatments of electrostatic interactions in biological systems, we generate a CG model of biological ions for use with 3SPN.2 and other CG models. Lastly, we illustrate the potential of 3SPN.2 and CG ions by using the models in simulations of viral capsid packaging experiments. The models and results described in this thesis will be useful in future modeling efforts that seek to identify the fundamental physics that govern behavior such as nucleosome positioning, DNA hybridization, and DNA nanoassembly.

  5. A mathematical model and numerical method for thermoelectric DNA sequencing

    NASA Astrophysics Data System (ADS)

    Shi, Liwei; Guilbeau, Eric J.; Nestorova, Gergana; Dai, Weizhong

    2014-05-01

    Single nucleotide polymorphisms (SNPs) are single base pair variations within the genome that are important indicators of genetic predisposition towards specific diseases. This study explores the feasibility of SNP detection using a thermoelectric sequencing method that measures the heat released when DNA polymerase inserts a deoxyribonucleoside triphosphate into a DNA strand. We propose a three-dimensional mathematical model that governs the DNA sequencing device with a reaction zone that contains DNA template/primer complex immobilized to the surface of the lower channel wall. The model is then solved numerically. Concentrations of reactants and the temperature distribution are obtained. Results indicate that when the nucleoside is complementary to the next base in the DNA template, polymerization occurs lengthening the complementary polymer and releasing thermal energy with a measurable temperature change, implying that the thermoelectric conceptual device for sequencing DNA may be feasible for identifying specific genes in individuals.

  6. A Signal Detection Model of Compound Decision Tasks

    DTIC Science & Technology

    2006-12-01

    A signal detection model of compound decision tasks Matthew Duncan Defence R& D Canada Technical Report DRDC Toronto TR 2006-256 December 2006...tasks Matthew Duncan Defence R& D Canada – Toronto Technical Report DRDC Toronto TR 2006-256 December 2006 Author Original approved by...la prise de décision, il faut une méthode formelle pour distinguer (clarifier) les effets des divers facteurs, et pour simplifier l’évaluation des

  7. A coarse-grained DNA model for the prediction of current signals in DNA translocation experiments

    NASA Astrophysics Data System (ADS)

    Weik, Florian; Kesselheim, Stefan; Holm, Christian

    2016-11-01

    We present an implicit solvent coarse-grained double-stranded DNA (dsDNA) model confined to an infinite cylindrical pore that reproduces the experimentally observed current modulations of a KaCl solution at various concentrations. Our model extends previous coarse-grained and mean-field approaches by incorporating a position dependent friction term on the ions, which Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] identified as an essential ingredient to correctly reproduce the experimental data of Smeets et al. [Nano Lett. 6, 89 (2006)]. Our approach reduces the computational effort by orders of magnitude compared with all-atom simulations and serves as a promising starting point for modeling the entire translocation process of dsDNA. We achieve a consistent description of the system's electrokinetics by using explicitly parameterized ions, a friction term between the DNA beads and the ions, and a lattice-Boltzmann model for the solvent.

  8. Prototype Systems Containing Human Cytochrome P450 for High-Throughput Real-Time Detection of DNA Damage by Compounds That Form DNA-Reactive Metabolites.

    PubMed

    Brito Palma, Bernardo; Fisher, Charles W; Rueff, José; Kranendonk, Michel

    2016-05-16

    The formation of reactive metabolites through biotransformation is the suspected cause of many adverse drug reactions. Testing for the propensity of a drug to form reactive metabolites has increasingly become an integral part of lead-optimization strategy in drug discovery. DNA reactivity is one undesirable facet of a drug or its metabolites and can lead to increased risk of cancer and reproductive toxicity. Many drugs are metabolized by cytochromes P450 in the liver and other tissues, and these reactions can generate hard electrophiles. These hard electrophilic reactive metabolites may react with DNA and may be detected in standard in vitro genotoxicity assays; however, the majority of these assays fall short due to the use of animal-derived organ extracts that inadequately represent human metabolism. The current study describes the development of bacterial systems that efficiently detect DNA-damaging electrophilic reactive metabolites generated by human P450 biotransformation. These assays use a GFP reporter system that detects DNA damage through induction of the SOS response and a GFP reporter to control for cytotoxicity. Two human CYP1A2-competent prototypes presented here have appropriate characteristics for the detection of DNA-damaging reactive metabolites in a high-throughput manner. The advantages of this approach include a short assay time (120-180 min) with real-time measurement, sensitivity to small amounts of compound, and adaptability to a microplate format. These systems are suitable for high-throughput assays and can serve as prototypes for the development of future enhanced versions.

  9. Linear and nonlinear optical properties of new materials based on DNA-CTMA and aromatic compounds (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Lazar, Cosmina Andreea; Kajzar, François; Rau, Ileana; Puntus, Lada N.; Manea, Ana-Maria

    2016-10-01

    In order to find eco-friendly materials for different applications an important research effort was devoted to the materials science in the last decade. A particular attention attracted the deoxyribonucleic acid (DNA). The interest is due to its versatility, biodegradability, abundance and their origin from renewable sources. DNA based new materials, functionalized with hexadecyltrimethylammonium chloride (CTMA) and aromatic compounds were prepared. Solutions with two different concentrations of aromatic compounds were obtained in butanol. The obtained, new complexes were processed into good optical quality thin films by spin coating method. Films were deposited on glass substrates and characterized for their spectroscopic, linear and nonlinear optical properties. The third-order nonlinear optical (NLO) properties of thin films were determined by the optical third-harmonic generation technique at 1 064.2 nm fundamental wavelength. The obtained materials, with improved fluorescence efficiency, present a potential interest for application in photonics.

  10. Oxidative DNA damage is prevented by extracts of olive oil, hydroxytyrosol, and other olive phenolic compounds in human blood mononuclear cells and HL60 cells.

    PubMed

    Fabiani, Roberto; Rosignoli, Patrizia; De Bartolomeo, Angelo; Fuccelli, Raffaela; Servili, Maurizio; Montedoro, Gian Francesco; Morozzi, Guido

    2008-08-01

    Our aim in this study was to provide further support to the hypothesis that phenolic compounds may play an important role in the anticarcinogenic properties of olive oil. We measured the effect of olive oil phenols on hydrogen peroxide (H(2)O(2))-induced DNA damage in human peripheral blood mononuclear cells (PBMC) and promyelocytic leukemia cells (HL60) using single-cell gel electrophoresis (comet assay). Hydroxytyrosol [3,4-dyhydroxyphenyl-ethanol (3,4-DHPEA)] and a complex mixture of phenols extracted from both virgin olive oil (OO-PE) and olive mill wastewater (WW-PE) reduced the DNA damage at concentrations as low as 1 micromol/L when coincubated in the medium with H(2)O(2) (40 micromol/L). At 10 micromol/L 3,4-DHPEA, the protection was 93% in HL60 and 89% in PBMC. A similar protective activity was also shown by the dialdehydic form of elenoic acid linked to hydroxytyrosol (3,4-DHPEA-EDA) on both kinds of cells. Other purified compounds such as isomer of oleuropein aglycon (3,4-DHPEA-EA), oleuropein, tyrosol, [p-hydroxyphenyl-ethanol (p-HPEA)] the dialdehydic form of elenoic acid linked to tyrosol, caffeic acid, and verbascoside also protected the cells against H(2)O(2)-induced DNA damage although with a lower efficacy (range of protection, 25-75%). On the other hand, when tested in a model system in which the oxidative stress was induced by phorbole 12-myristate 13-acetate-activated monocytes, p-HPEA was more effective than 3,4-DHPEA in preventing the oxidative DNA damage. Overall, these results suggest that OO-PE and WW-PE may efficiently prevent the initiation step of carcinogenesis in vivo, because the concentrations effective against the oxidative DNA damage could be easily reached with normal intake of olive oil.

  11. Genotoxicity of Tri- and Hexavalent Chromium Compounds In Vivo and Their Modes of Action on DNA Damage In Vitro

    PubMed Central

    Fang, Zhijia; Zhao, Min; Zhen, Hong; Chen, Lifeng; Shi, Ping; Huang, Zhiwei

    2014-01-01

    Chromium occurs mostly in tri- and hexavalent states in the environment. Hexavalent chromium [Cr(VI)] compounds are extensively used in diverse industries, and trivalent chromium [Cr(III)] salts are used as micronutrients and dietary supplements. In the present work, we report that they both induce genetic mutations in yeast cells. They both also cause DNA damage in both yeast and Jurkat cells and the effect of Cr(III) is greater than that of Cr(VI). We further show that Cr(III) and Cr(VI) cause DNA damage through different mechanisms. Cr(VI) intercalates DNA and Cr(III) interferes base pair stacking. Based on our results, we conclude that Cr(III) can directly cause genotoxicity in vivo. PMID:25111056

  12. Easy DNA Modeling and More with GraphiteLifeExplorer

    PubMed Central

    Hornus, Samuel; Lévy, Bruno; Larivière, Damien; Fourmentin, Eric

    2013-01-01

    The GraphiteLifeExplorer tool enables biologists to reconstruct 3D cellular complexes built from proteins and DNA molecules. Models of DNA molecules can be drawn in an intuitive way and assembled to proteins or others globular structures. Real time navigation and immersion offer a unique view to the reconstructed biological machinery. PMID:23308263

  13. Causal Network Models for Predicting Compound Targets and Driving Pathways in Cancer.

    PubMed

    Jaeger, Savina; Min, Junxia; Nigsch, Florian; Camargo, Miguel; Hutz, Janna; Cornett, Allen; Cleaver, Stephen; Buckler, Alan; Jenkins, Jeremy L

    2014-06-01

    Gene-expression data are often used to infer pathways regulating transcriptional responses. For example, differentially expressed genes (DEGs) induced by compound treatment can help characterize hits from phenotypic screens, either by correlation with known drug signatures or by pathway enrichment. Pathway enrichment is, however, typically computed with DEGs rather than "upstream" nodes that are potentially causal of "downstream" changes. Here, we present graph-based models to predict causal targets from compound-microarray data. We test several approaches to traversing network topology, and show that a consensus minimum-rank score (SigNet) beat individual methods and could highly rank compound targets among all network nodes. In addition, larger, less canonical networks outperformed linear canonical interactions. Importantly, pathway enrichment using causal nodes rather than DEGs recovers relevant pathways more often. To further validate our approach, we used integrated data sets from the Cancer Genome Atlas to identify driving pathways in triple-negative breast cancer. Critical pathways were uncovered, including the epidermal growth factor receptor 2-phosphatidylinositide 3-kinase-AKT-MAPK growth pathway andATR-p53-BRCA DNA damage pathway, in addition to unexpected pathways, such as TGF-WNT cytoskeleton remodeling, IL12-induced interferon gamma production, and TNFR-IAP (inhibitor of apoptosis) apoptosis; the latter was validated by pooled small hairpin RNA profiling in cancer cells. Overall, our approach can bridge transcriptional profiles to compound targets and driving pathways in cancer.

  14. Capstan Friction Model for DNA Ejection from Bacteriophages

    NASA Astrophysics Data System (ADS)

    Ghosal, Sandip

    2012-12-01

    Bacteriophages infect cells by attaching to the outer membrane and injecting their DNA into the cell. The phage DNA is then transcribed by the cell’s transcription machinery. A number of physical mechanisms by which DNA can be translocated from the phage capsid into the cell have been identified. A fast ejection driven by the elastic and electrostatic potential energy of the compacted DNA within the viral capsid appears to be used by most phages, at least to initiate infection. In recent in vitro experiments, the speed of DNA translocation from a λ phage capsid has been measured as a function of ejected length over the entire duration of the event. Here, a mechanical model is proposed that is able to explain the observed dependence of exit velocity on ejected length, and that is also consistent with the accepted picture of the geometric arrangement of DNA within the viral capsid.

  15. DNA base excision repair nanosystem engineering: model development.

    PubMed

    Sokhansanj, B A

    2005-01-01

    DNA base damage results from a combination of endogenous sources, (normal metabolism, increased metabolism due to obesity, stress from diseases such as arthritis and diabetes, and ischemia) and the environment (ingested toxins, ionizing radiation, etc.). If unrepaired DNA base damage can lead to diminished cell function, and potentially diseases and eventually mutations that lead to cancer. Sophisticated DNA repair mechanisms have evolved in all living cells to preserve the integrity of inherited genetic information and transcriptional control. Understanding a system like DNA repair is greatly enhanced by using engineering methods, in particular modeling interactions and using predictive simulation to analyze the impact of perturbations. We describe the use of such a "nanosystem engineering" approach to analyze the DNA base excision repair pathway in human cells, and use simulation to predict the impact of varying enzyme concentration on DNA repair capacity.

  16. Modeling chain folding in protein-constrained circular DNA.

    PubMed Central

    Martino, J A; Olson, W K

    1998-01-01

    An efficient method for sampling equilibrium configurations of DNA chains binding one or more DNA-bending proteins is presented. The technique is applied to obtain the tertiary structures of minimal bending energy for a selection of dinucleosomal minichromosomes that differ in degree of protein-DNA interaction, protein spacing along the DNA chain contour, and ring size. The protein-bound portions of the DNA chains are represented by tight, left-handed supercoils of fixed geometry. The protein-free regions are modeled individually as elastic rods. For each random spatial arrangement of the two nucleosomes assumed during a stochastic search for the global minimum, the paths of the flexible connecting DNA segments are determined through a numerical solution of the equations of equilibrium for torsionally relaxed elastic rods. The minimal energy forms reveal how protein binding and spacing and plasmid size differentially affect folding and offer new insights into experimental minichromosome systems. PMID:9591675

  17. A compound compensation method for car-following model

    NASA Astrophysics Data System (ADS)

    Zhu, Wen-Xing; Jun, Du; Zhang, Li-Dong

    2016-10-01

    A compound compensation mechanism was introduced into the car-following system. Two basic compensation methods were combined to generate a compound control strategy to improve the performance of the traffic flow system. The compensation effect was analyzed with unit step response in time domain and bode diagram in frequency domain, respectively. Two lemmas and one theorem were proved with the use of Routh criteria and small gain theorem. Numerical simulations were conducted in two situations under three types of condition. The simulation results verify the truth that with the increasing compensation parameters the stability of the car-following system is strengthened. It is shown that numerical results are in accordance with analytical results. In general, the performance of car-following model can be improved with an exterior control method.

  18. Lindley frailty model for a class of compound Poisson processes

    NASA Astrophysics Data System (ADS)

    Kadilar, Gamze Özel; Ata, Nihal

    2013-10-01

    The Lindley distribution gain importance in survival analysis for the similarity of exponential distribution and allowance for the different shapes of hazard function. Frailty models provide an alternative to proportional hazards model where misspecified or omitted covariates are described by an unobservable random variable. Despite of the distribution of the frailty is generally assumed to be continuous, it is appropriate to consider discrete frailty distributions In some circumstances. In this paper, frailty models with discrete compound Poisson process for the Lindley distributed failure time are introduced. Survival functions are derived and maximum likelihood estimation procedures for the parameters are studied. Then, the fit of the models to the earthquake data set of Turkey are examined.

  19. High Temperature High Pressure Thermodynamic Measurements for Coal Model Compounds

    SciTech Connect

    John C. Chen; Vinayak N. Kabadi

    1998-11-12

    The overall objective of this project is to develop a better thermodynamic model for predicting properties of high-boiling coal derived liquids, especially the phase equilibria of different fractions at elevated temperatures and pressures. The development of such a model requires data on vapor-liquid equilibria (VLE), enthalpy, and heat capacity which would be experimentally determined for binary systems of coal model compounds and compiled into a database. The data will be used to refine existing models such as UNIQUAC and UNIFAC. The flow VLE apparatus designed and built for a previous project was upgraded and recalibrated for data measurements for thk project. The modifications include better and more accurate sampling technique and addition of a digital recorder to monitor temperature, pressure and liquid level inside the VLE cell. VLE data measurements for system benzene-ethylbenzene have been completed. The vapor and liquid samples were analysed using the Perkin-Elmer Autosystem gas chromatography.

  20. Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase

    NASA Astrophysics Data System (ADS)

    Yoo, Jakyung; Medina-Franco, José L.

    2011-06-01

    DNA methyltransferase 1 (DNMT1) is an emerging epigenetic target for the treatment of cancer and other diseases. To date, several inhibitors from different structural classes have been published. In this work, we report a comprehensive molecular modeling study of 14 established DNTM1 inhibitors with a herein developed homology model of the catalytic domain of human DNTM1. The geometry of the homology model was in agreement with the proposed mechanism of DNA methylation. Docking results revealed that all inhibitors studied in this work have hydrogen bond interactions with a glutamic acid and arginine residues that play a central role in the mechanism of cytosine DNA methylation. The binding models of compounds such as curcumin and parthenolide suggest that these natural products are covalent blockers of the catalytic site. A pharmacophore model was also developed for all DNMT1 inhibitors considered in this work using the most favorable binding conformations and energetic terms of the docked poses. To the best of our knowledge, this is the first pharmacophore model proposed for compounds with inhibitory activity of DNMT1. The results presented in this work represent a conceptual advance for understanding the protein-ligand interactions and mechanism of action of DNMT1 inhibitors. The insights obtained in this work can be used for the structure-based design and virtual screening for novel inhibitors targeting DNMT1.

  1. QSPR Modeling of Bioconcentration Factors of Nonionic Organic Compounds

    PubMed Central

    Deeb, Omar; Khadikar, Padmakar V.; Goodarzi, Mohammad

    2010-01-01

    The terms bioaccumulation and bioconcentration refer to the uptake and build-up of chemicals that can occur in living organisms. Experimental measurement of bioconcentration is time-consuming and expensive, and is not feasible for a large number of chemicals of potential regulatory concern. A highly effective tool depending on a quantitative structure-property relationship (QSPR) can be utilized to describe the tendency of chemical concentration organisms represented by, the important ecotoxicological parameter, the logarithm of Bio Concentration Factor (log BCF) with molecular descriptors for a large set of non-ionic organic compounds. QSPR models were developed using multiple linear regression, partial least squares and neural networks analyses. Linear and non-linear QSPR models to predict log BCF of the compounds developed for the relevant descriptors. The results obtained offer good regression models having good prediction ability. The descriptors used in these models depend on the volume, connectivity, molar refractivity, surface tension and the presence of atoms accepting H-bonds. PMID:20706622

  2. Melatonin and a spin-trap compound block radiofrequency electromagnetic radiation-induced DNA strand breaks in rat brain cells.

    PubMed

    Lai, H; Singh, N P

    1997-01-01

    Effects of in vivo microwave exposure on DNA strand breaks, a form of DNA damage, were investigated in rat brain cells. In previous research, we have found that acute (2 hours) exposure to pulsed (2 microseconds pulses, 500 pps) 2450-MHz radiofrequency electromagnetic radiation (RFR) (power density 2 mW/cm2, average whole body specific absorption rate 1.2 W/kg) caused an increase in DNA single- and double-strand breaks in brain cells of the rat when assayed 4 hours post exposure using a microgel electrophoresis assay. In the present study, we found that treatment of rats immediately before and after RFR exposure with either melatonin (1 mg/kg/injection, SC) or the spin-trap compound N-tert-butyl-alpha-phenylnitrone (PBN) (100 mg/kg/injection, i.p.) blocks this effects of RFR. Since both melatonin and PBN are efficient free radical scavengers it is hypothesized that free radicals are involved in RFR-induced DNA damage in the brain cells of rats. Since cumulated DNA strand breaks in brain cells can lead to neurodegenerative diseases and cancer and an excess of free radicals in cells has been suggested to be the cause of various human diseases, data from this study could have important implications for the health effects of RFR exposure.

  3. Moving Beyond Watson-Crick Models of Coarse Grained DNA

    NASA Astrophysics Data System (ADS)

    Dorfman, Kevin; Linak, Margaret; Tourdot, Richard

    2012-02-01

    DNA structure possesses several levels of complexity, ranging from the sequence of bases (primary structure) to base pairing (secondary structure) to its three-dimensional shape (tertiary structure) and can produce a wide variety of conformations in addition to canonical double stranded DNA. By including non-Watson-Crick interactions in a coarse-grained model, we developed a system that not only can capture the traditional B-form double helix, but also can adopt a wide variety of other DNA conformations. In our experimentally parameterized, coarse-grained DNA model we are able to reproduce the microscopic features of double-stranded DNA without the need for explicit constraints and capture experimental melting curves for a number of short DNA hairpins. We demonstrate the utility of the model by simulating more complex tertiary structures such as the folding of the thrombin aptamer, which includes G-quartets, and strand invasion during triplex formation. Our results highlight the importance of non-canonical interactions in DNA coarse- grained models.

  4. Theory and modeling of particles with DNA-mediated interactions

    NASA Astrophysics Data System (ADS)

    Licata, Nicholas A.

    2008-05-01

    In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors and nanoparticle based drug delivery platforms. In Chapter I we introduce the system, which generically consists of colloidal particles functionalized with specially designed DNA markers. The sequence of bases on the DNA markers determines the particle type. Due to the hybridization between complementary single-stranded DNA, specific, type-dependent interactions can be introduced between particles by choosing the appropriate DNA marker sequences. In Chapter II we develop a statistical mechanical description of the aggregation and melting behavior of particles with DNA-mediated interactions. In Chapter III a model is proposed to describe the dynamical departure and diffusion of particles which form reversible key-lock connections. In Chapter IV we propose a method to self-assemble nanoparticle clusters using DNA scaffolds. A natural extension is discussed in Chapter V, the programmable self-assembly of nanoparticle clusters where the desired cluster geometry is encoded using DNA-mediated interactions. In Chapter VI we consider a nanoparticle based drug delivery platform for targeted, cell specific chemotherapy. In Chapter VII we present prospects for future research: the connection between DNA-mediated colloidal crystallization and jamming, and the inverse problem in self-assembly.

  5. Neurotoxicity in Preclinical Models of Occupational Exposure to Organophosphorus Compounds

    PubMed Central

    Voorhees, Jaymie R.; Rohlman, Diane S.; Lein, Pamela J.; Pieper, Andrew A.

    2017-01-01

    Organophosphorus (OPs) compounds are widely used as insecticides, plasticizers, and fuel additives. These compounds potently inhibit acetylcholinesterase (AChE), the enzyme that inactivates acetylcholine at neuronal synapses, and acute exposure to high OP levels can cause cholinergic crisis in humans and animals. Evidence further suggests that repeated exposure to lower OP levels insufficient to cause cholinergic crisis, frequently encountered in the occupational setting, also pose serious risks to people. For example, multiple epidemiological studies have identified associations between occupational OP exposure and neurodegenerative disease, psychiatric illness, and sensorimotor deficits. Rigorous scientific investigation of the basic science mechanisms underlying these epidemiological findings requires valid preclinical models in which tightly-regulated exposure paradigms can be correlated with neurotoxicity. Here, we review the experimental models of occupational OP exposure currently used in the field. We found that animal studies simulating occupational OP exposures do indeed show evidence of neurotoxicity, and that utilization of these models is helping illuminate the mechanisms underlying OP-induced neurological sequelae. Still, further work is necessary to evaluate exposure levels, protection methods, and treatment strategies, which taken together could serve to modify guidelines for improving workplace conditions globally. PMID:28149268

  6. A COMPOUND MODEL FOR THE ORIGIN OF EARTH'S WATER

    SciTech Connect

    Izidoro, A.; Winter, O. C.; De Souza Torres, K.; Haghighipour, N.

    2013-04-10

    One of the most important subjects of debate in the formation of the solar system is the origin of Earth's water. Comets have long been considered as the most likely source of the delivery of water to Earth. However, elemental and isotopic arguments suggest a very small contribution from these objects. Other sources have also been proposed, among which local adsorption of water vapor onto dust grains in the primordial nebula and delivery through planetesimals and planetary embryos have become more prominent. However, no sole source of water provides a satisfactory explanation for Earth's water as a whole. In view of that, using numerical simulations, we have developed a compound model incorporating both the principal endogenous and exogenous theories, and investigating their implications for terrestrial planet formation and water delivery. Comets are also considered in the final analysis, as it is likely that at least some of Earth's water has cometary origin. We analyze our results comparing two different water distribution models, and complement our study using the D/H ratio, finding possible relative contributions from each source and focusing on planets formed in the habitable zone. We find that the compound model plays an important role by showing greater advantage in the amount and time of water delivery in Earth-like planets.

  7. Neurotoxicity in Preclinical Models of Occupational Exposure to Organophosphorus Compounds.

    PubMed

    Voorhees, Jaymie R; Rohlman, Diane S; Lein, Pamela J; Pieper, Andrew A

    2016-01-01

    Organophosphorus (OPs) compounds are widely used as insecticides, plasticizers, and fuel additives. These compounds potently inhibit acetylcholinesterase (AChE), the enzyme that inactivates acetylcholine at neuronal synapses, and acute exposure to high OP levels can cause cholinergic crisis in humans and animals. Evidence further suggests that repeated exposure to lower OP levels insufficient to cause cholinergic crisis, frequently encountered in the occupational setting, also pose serious risks to people. For example, multiple epidemiological studies have identified associations between occupational OP exposure and neurodegenerative disease, psychiatric illness, and sensorimotor deficits. Rigorous scientific investigation of the basic science mechanisms underlying these epidemiological findings requires valid preclinical models in which tightly-regulated exposure paradigms can be correlated with neurotoxicity. Here, we review the experimental models of occupational OP exposure currently used in the field. We found that animal studies simulating occupational OP exposures do indeed show evidence of neurotoxicity, and that utilization of these models is helping illuminate the mechanisms underlying OP-induced neurological sequelae. Still, further work is necessary to evaluate exposure levels, protection methods, and treatment strategies, which taken together could serve to modify guidelines for improving workplace conditions globally.

  8. ATOMIC AND MOLECULAR PHYSICS: Modelling of a DNA packaging motor

    NASA Astrophysics Data System (ADS)

    Qian, Jun; Xie, Ping; Xue, Xiao-Guang; Wang, Peng-Ye

    2009-11-01

    During the assembly of many viruses, a powerful molecular motor packages the genome into a preassembled capsid. The Bacillus subtilis phage phi29 is an excellent model system to investigate the DNA packaging mechanism because of its highly efficient in vitro DNA packaging activity and the development of a single-molecule packaging assay. Here we make use of structural and biochemical experimental data to build a physical model of DNA packaging by the phi29 DNA packaging motor. Based on the model, various dynamic behaviours such as the packaging rate, pause frequency and slip frequency under different ATP concentrations, ADP concentrations, external loads as well as capsid fillings are studied by using Monte Carlo simulation. Good agreement is obtained between the simulated and available experimental results. Moreover, we make testable predictions that should guide future experiments related to motor function.

  9. Aquatic pathways model to predict the fate of phenolic compounds

    SciTech Connect

    Aaberg, R.L.; Peloquin, R.A.; Strenge, D.L.; Mellinger, P.J.

    1983-04-01

    Organic materials released from energy-related activities could affect human health and the environment. To better assess possible impacts, we developed a model to predict the fate of spills or discharges of pollutants into flowing or static bodies of fresh water. A computer code, Aquatic Pathways Model (APM), was written to implement the model. The computer programs use compartmental analysis to simulate aquatic ecosystems. The APM estimates the concentrations of chemicals in fish tissue, water and sediment, and is therefore useful for assessing exposure to humans through aquatic pathways. The APM will consider any aquatic pathway for which the user has transport data. Additionally, APM will estimate transport rates from physical and chemical properties of chemicals between several key compartments. The major pathways considered are biodegradation, fish and sediment uptake, photolysis, and evaporation. The model has been implemented with parameters for distribution of phenols, an important class of compounds found in the water-soluble fractions of coal liquids. Current modeling efforts show that, in comparison with many pesticides and polyaromatic hydrocarbons (PAH), the lighter phenolics (the cresols) are not persistent in the environment. The properties of heavier molecular weight phenolics (indanols, naphthols) are not well enough understood at this time to make similar judgements. For the twelve phenolics studied, biodegradation appears to be the major pathway for elimination from aquatic environments. A pond system simulation (using APM) of a spill of solvent refined coal (SRC-II) materials indicates that phenol, cresols, and other single cyclic phenolics are degraded to 16 to 25 percent of their original concentrations within 30 hours. Adsorption of these compounds into sediments and accumulation by fish was minor.

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

    PubMed Central

    Srivastava, S.; Baptista, M. S.

    2016-01-01

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

  11. Sorption and Interfacial Rheology Study of Model Asphaltene Compounds.

    PubMed

    Pradilla, Diego; Simon, Sébastien; Sjöblom, Johan; Samaniuk, Joseph; Skrzypiec, Marta; Vermant, Jan

    2016-03-29

    The sorption and rheological properties of an acidic polyaromatic compound (C5PeC11), which can be used to further our understanding of the behavior of asphaltenes, are determined experimentally. The results show that C5PeC11 exhibits the type of pH-dependent surface activity and interfacial shear rheology observed in C6-asphaltenes with a decrease in the interfacial tension concomitant with the elastic modulus when the pH increases. Surface pressure-area (Π-A) isotherms show evidence of aggregation behavior and π-π stacking at both the air/water and oil/water interfaces. Similarly, interactions between adsorbed C5PeC11 compounds are evidenced through desorption experiments at the oil/water interface. Contrary to indigenous asphaltenes, adsorption is reversible, but desorption is slower than for noninteracting species. The reversibility enables us to create layers reproducibly, whereas the presence of interactions between the compounds enables us to mimic the key aspects of interfacial activity in asphaltenes. Shear and dilatational rheology show that C5PeC11 forms a predominantly elastic film both at the liquid/air and the liquid/liquid interfaces. Furthermore, a soft glassy rheology model (SGR) fits the data obtained at the liquid/liquid interface. However, it is shown that the effective noise temperature determined from the SGR model for C5PeC11 is higher than for indigenous asphaltenes measured under similar conditions. Finally, from a colloidal and rheological standpoint, the results highlight the importance of adequately addressing the distinction between the material functions and true elasticity extracted from a shear measurement and the apparent elasticity measured in dilatational-pendant drop setups.

  12. Synthesis of model compounds for coal liquefaction research

    SciTech Connect

    Not Available

    1991-11-01

    Coal liquefaction investigations required the availability of model compounds for mechanistic investigations. Towards this end, IITRI was funded to develop an approach for the synthesis of one of the target compound. This study was carried out in several phases as outlined here. Initial synthetic investigations on obtaining 2-tetrolol was carried out using high pressure and temperature reduction with Raney nickel catalyst. The next step consisted in incorporation of a hydroxymethyelene group at the C-3 position. This was successfully carried out utilizing 2-tetrolol, formaldehyde, and calcium oxide. An alternate improved method was developed using 3-carboxyl-2-naphthol. This required less time, gave a cheer product in higher yield. Efforts at the introduction of a chloromethylene group only yielded polymeric material or starting material in spite of protection the phenolic group by various groups. They synthesis of 3, 5-dimethyl-6- bromobenzyl chloride was successfully carried out by performing the Blank reaction of 2, 4-dimethyl bromobenzene. The product was characterized by GC/MS. Purification was not possible, as it was a complex mixture. Efforts at converting it to the acetate followed by separation to was not feasible. Unlike in the case of 2- hydroxyteralol, hydroxymetylation by established procedure yielded only the starting materials. Commercially available 4-methoxy-1- maphthaldehyde was protected as the ethylene acetal. The Wittig reagent 3-chlorobenzyl phosphonium bromide was prepared and condensed with 4-methoxy-1-napthaldehyde successfully and proved that the overall synthetic approach was proceeding in the desired direction. All the necessary intermediates have been synthesized,and we have demonstrated using model compounds, that the synthetic objective can be attained.

  13. Modeling the Sensitivity of Field Surveys for Detection of Environmental DNA (eDNA)

    PubMed Central

    Schultz, Martin T.; Lance, Richard F.

    2015-01-01

    The environmental DNA (eDNA) method is the practice of collecting environmental samples and analyzing them for the presence of a genetic marker specific to a target species. Little is known about the sensitivity of the eDNA method. Sensitivity is the probability that the target marker will be detected if it is present in the water body. Methods and tools are needed to assess the sensitivity of sampling protocols, design eDNA surveys, and interpret survey results. In this study, the sensitivity of the eDNA method is modeled as a function of ambient target marker concentration. The model accounts for five steps of sample collection and analysis, including: 1) collection of a filtered water sample from the source; 2) extraction of DNA from the filter and isolation in a purified elution; 3) removal of aliquots from the elution for use in the polymerase chain reaction (PCR) assay; 4) PCR; and 5) genetic sequencing. The model is applicable to any target species. For demonstration purposes, the model is parameterized for bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) assuming sampling protocols used in the Chicago Area Waterway System (CAWS). Simulation results show that eDNA surveys have a high false negative rate at low concentrations of the genetic marker. This is attributed to processing of water samples and division of the extraction elution in preparation for the PCR assay. Increases in field survey sensitivity can be achieved by increasing sample volume, sample number, and PCR replicates. Increasing sample volume yields the greatest increase in sensitivity. It is recommended that investigators estimate and communicate the sensitivity of eDNA surveys to help facilitate interpretation of eDNA survey results. In the absence of such information, it is difficult to evaluate the results of surveys in which no water samples test positive for the target marker. It is also recommended that invasive species managers articulate concentration

  14. Yeast as a model system to study metabolic impact of selenium compounds

    PubMed Central

    Herrero, Enrique; Wellinger, Ralf E.

    2015-01-01

    Inorganic Se forms such as selenate or selenite (the two more abundant forms in nature) can be toxic in Saccharomyces cerevisiae cells, which constitute an adequate model to study such toxicity at the molecular level and the functions participating in protection against Se compounds. Those Se forms enter the yeast cell through other oxyanion transporters. Once inside the cell, inorganic Se forms may be converted into selenide through a reductive pathway that in physiological conditions involves reduced glutathione with its consequent oxidation into diglutathione and alteration of the cellular redox buffering capacity. Selenide can subsequently be converted by molecular oxygen into elemental Se, with production of superoxide anions and other reactive oxygen species. Overall, these events result in DNA damage and dose-dependent reversible or irreversible protein oxidation, although additional oxidation of other cellular macromolecules cannot be discarded. Stress-adaptation pathways are essential for efficient Se detoxification, while activation of DNA damage checkpoint and repair pathways protects against Se-mediated genotoxicity. We propose that yeast may be used to improve our knowledge on the impact of Se on metal homeostasis, the identification of Se-targets at the DNA and protein levels, and to gain more insights into the mechanism of Se-mediated apoptosis. PMID:28357286

  15. Application of the underscreened Kondo lattice model to neptunium compounds

    NASA Astrophysics Data System (ADS)

    Thomas, Christopher; da Rosa Simoes, Acirete S.; Iglesias, J. R.; Lacroix, C.; Coqublin, B.

    2012-12-01

    The coexistence of Kondo effect and ferromagnetic order has been observed in many uranium and neptunium compounds such as UTe or Np2PdGa3. This coexistence can be described within the underscreened Anderson lattice model with two f-electrons and S = 1 spins on each site. After performing the Schrieffer-Wolff transformation on this model, we have obtained an effective Hamiltonian with a f-band term in addition to the Kondo interaction for S = 1 spins. The results indicate a coexistence of Kondo effect and ferromagnetic order, with different relative values of the Kondo TK and Curie TC temperatures. We emphasize here especially the case TK < TC where there is a Kondo behavior below TC and a clear decrease of the magnetization below TK. Such a behavior has been observed in the magnetization curves of NpNiSi2 at low temperatures.

  16. Stereodefined phosphorothioate analogues of DNA: relative thermodynamic stability of the model PS-DNA/DNA and PS-DNA/RNA complexes.

    PubMed

    Boczkowska, Małgorzata; Guga, Piotr; Stec, Wojciech J

    2002-10-15

    Thermodynamic data regarding the influence of P-chirality on stability of duplexes formed between phosphorothioate DNA oligonucleotides (of either stereo-defined all-R(P) or all-S(P) or random configuration at the P atoms) and complementary DNA or RNA strands are presented. Measured melting temperatures and calculated DeltaG(37)(o) values showed that duplexes formed by PS-DNA oligomers with DNA strands are less stable than their unmodified counterparts. However, relative stability of the duplexes ([all-R(P)]-PS-DNA/DNA vs [all-S(P)]-PS-DNA/DNA) depends on their sequential composition rather than on the absolute configuration of PS-oligos, contrary to the results of theoretical considerations and molecular modeling reported in the literature. On the other hand, for all six analyzed pairs of diastereomers, the [all-R(P)]-PS isomers form more stable duplexes with RNA templates, but the origin of stereodifferentiation depends on the sequence with more favorable entropy and enthalpy factors which correlated with dT-rich and dA/dG-rich PS-oligomers, respectively.

  17. Semi-automated high-throughput fluorescent intercalator displacement-based discovery of cytotoxic DNA binding agents from a large compound library.

    PubMed

    Glass, Lateca S; Bapat, Aditi; Kelley, Mark R; Georgiadis, Millie M; Long, Eric C

    2010-03-01

    High-throughput fluorescent intercalator displacement (HT-FID) was adapted to the semi-automated screening of a commercial compound library containing 60,000 molecules resulting in the discovery of cytotoxic DNA-targeted agents. Although commercial libraries are routinely screened in drug discovery efforts, the DNA binding potential of the compounds they contain has largely been overlooked. HT-FID led to the rapid identification of a number of compounds for which DNA binding properties were validated through demonstration of concentration-dependent DNA binding and increased thermal melting of A/T- or G/C-rich DNA sequences. Selected compounds were assayed further for cell proliferation inhibition in glioblastoma cells. Seven distinct compounds emerged from this screening procedure that represent structures unknown previously to be capable of targeting DNA leading to cell death. These agents may represent structures worthy of further modification to optimally explore their potential as cytotoxic anti-cancer agents. In addition, the general screening strategy described may find broader impact toward the rapid discovery of DNA targeted agents with biological activity.

  18. Cooperativity-based modeling of heterotypic DNA nanostructure assembly.

    PubMed

    Shapiro, Anastasia; Hozeh, Avital; Girshevitz, Olga; Abu-Horowitz, Almogit; Bachelet, Ido

    2015-07-27

    DNA origami is a robust method for the fabrication of nanoscale 2D and 3D objects with complex features and geometries. The process of DNA origami folding has been recently studied, however quantitative understanding of it is still elusive. Here, we describe a systematic quantification of the assembly process of DNA nanostructures, focusing on the heterotypic DNA junction-in which arms are unequal-as their basic building block. Using bulk fluorescence studies we tracked this process and identified multiple levels of cooperativity from the arms in a single junction to neighboring junctions in a large DNA origami object, demonstrating that cooperativity is a central underlying mechanism in the process of DNA nanostructure assembly. We show that the assembly of junctions in which the arms are consecutively ordered is more efficient than junctions with randomly-ordered components, with the latter showing assembly through several alternative trajectories as a potential mechanism explaining the lower efficiency. This highlights consecutiveness as a new design consideration that could be implemented in DNA nanotechnology CAD tools to produce more efficient and high-yield designs. Altogether, our experimental findings allowed us to devise a quantitative, cooperativity-based heuristic model for the assembly of DNA nanostructures, which is highly consistent with experimental observations.

  19. Cooperativity-based modeling of heterotypic DNA nanostructure assembly

    PubMed Central

    Shapiro, Anastasia; Hozeh, Avital; Girshevitz, Olga; Abu-Horowitz, Almogit; Bachelet, Ido

    2015-01-01

    DNA origami is a robust method for the fabrication of nanoscale 2D and 3D objects with complex features and geometries. The process of DNA origami folding has been recently studied, however quantitative understanding of it is still elusive. Here, we describe a systematic quantification of the assembly process of DNA nanostructures, focusing on the heterotypic DNA junction—in which arms are unequal—as their basic building block. Using bulk fluorescence studies we tracked this process and identified multiple levels of cooperativity from the arms in a single junction to neighboring junctions in a large DNA origami object, demonstrating that cooperativity is a central underlying mechanism in the process of DNA nanostructure assembly. We show that the assembly of junctions in which the arms are consecutively ordered is more efficient than junctions with randomly-ordered components, with the latter showing assembly through several alternative trajectories as a potential mechanism explaining the lower efficiency. This highlights consecutiveness as a new design consideration that could be implemented in DNA nanotechnology CAD tools to produce more efficient and high-yield designs. Altogether, our experimental findings allowed us to devise a quantitative, cooperativity-based heuristic model for the assembly of DNA nanostructures, which is highly consistent with experimental observations. PMID:26071955

  20. Model carcinogen adsorption dynamics of DNA gel.

    PubMed

    Tomita, Naoko; Naito, Daisuke; Rokugawa, Isamu; Yamamoto, Takao; Dobashi, Toshiaki

    2014-09-01

    We have derived theoretical equations describing the adsorption of carcinogen to gels in an immersion medium containing carcinogens. The theory was developed for a cylindrical boundary condition under the assumption of a carcinogen diffusion-limited process combined with the "moving boundary picture (Furusawa et al., 2007)". The time course of the adsorbed carcinogen layer thickness and that of the carcinogen concentration in an immersion medium were expressed by a set of scaled variables, and the asymptotic behavior in the initial stage was derived. Experiments based on the theory were performed using a DNA gel sandwiched between a set of coverglasses in a medium containing acridine orange (AO). The boundary between the AO-adsorbed gel layer and AO-nonadsorbed gel layer was traced during the immersion. The time courses of the AO-adsorbed gel layer thickness and the AO concentration in the immersion medium were well explained by the theory, and the number ratio of the total AO molecules to the adsorption sites in the DNA gel was determined.

  1. Enzymology of repair of DNA adducts produced by N-nitroso compounds

    SciTech Connect

    Setlow, R.B.; Cao, E.H.; Delihas, N.C.

    1983-01-01

    The biological effects of DNA adducts depend on their nature, and on their half-lives relative to the rates of DNA replication and transcription. Their half-lives are determined by the rates of spontaneous decay, such as depurination, and the rates of enzymatic repair of the adducts or their decay products. The principle modes of repair of methylating and ethylating agents are by glycosylase catalyzed depurination of 7-alkylguanine and 3-alkyladenine and by the dealkalation of O/sup 6/-alkylguanine. Repair by dealkylation cannot be detected by the standard methods used to measure DNA repair, but it is easy to estimate the acceptor activity in cell extracts by measuring the transfer of radioactive O/sup 6/-alkyl groups in an exogenous DNA to protein. In extracts of cells treated with alkylating agents the activity is depressed because the endogenous DNA is rapidly dealkylated, using up the acceptor activity. In many cell types the decrease in activity is followed by an increase to the normal constitutive level. In other cells there is no such adaptive response. Differences in constitutive levels of methyl accepting activity in extracts of human lymphocytes and on the acceptor activity in lung macrophages from smokers (low activity) and non-smokers (high activity) have been observed. 46 references.

  2. Phosphorus-nitrogen compounds. Part 23: Syntheses, structural investigations, biological activities, and DNA interactions of new N/O spirocyclotriphosphazenes

    NASA Astrophysics Data System (ADS)

    Asmafiliz, Nuran; Kılıç, Zeynel; Hayvalı, Zeliha; Açık, Leyla; Hökelek, Tuncer; Dal, Hakan; Öner, Yağmur

    2012-02-01

    The Schiff base compounds ( 1 and 2) are synthesized by the condensation reactions of 2-furan-2-yl-methylamine with 2-hydroxy-3-methoxy- and 2-hydroxy-5-methoxy-benzaldehydes and reduced with NaBH 4 to give the new N/O-donor-type ligands ( 3 and 4). The monospirocyclotriphosphazenes containing 1,3,2-oxazaphosphorine rings ( 5 and 6) are prepared from the reactions of N 3P 3Cl 6 with 3 and 4, respectively. The reactions of 5 and 6 with excess pyrrolidine, morpholine, and 1,4-dioxa-8-azaspiro [4,5] decane (DASD) produce tetrapyrrolidino ( 5a and 6a), morpholino ( 5b and 6b), and 1,4-dioxa-8-azaspiro [4,5] deca ( 5c and 6c) spirocyclotriphosphazenes. The structural investigations of the compounds are examined by 1H, 13C, 31P NMR, DEPT, HSQC, and HMBC techniques. The solid-state structures of 5, 5a, and 6 are determined using X-ray crystallography. The compounds 5a, 5b, 5c, 6a, 6b, and 6c are subjected to antimicrobial activity against six patojen bacteria and two yeast strains. In addition, interactions between these compounds and pBR322 plasmid DNA are presented by agarose gel electrophoresis.

  3. High-temperature pyrolysis mechanisms of coal model compounds

    SciTech Connect

    Penn, J.H.; Owens, W.H.

    1991-01-01

    The degradation of the carboxylic acid group has been examined with respect to potential pretreatment strategies for fossil fuel conversion processes. In one potential pretreatment strategy involving cation exchange of the carboxylic acid group, a series of benzoic acid and stearic acid salts have been chosen to model the tight'' carboxylic acids of immature fossil fuel feedstocks and have been pyrolyzed with an entrained flow reactor. Our preliminary results indicate that Group I and II salts yield primarily the parent acid. Benzoate salts also yield small amounts of benzene while the stearic acid salts give no other detectable products. In two alternative treatment strategies, esterification and anhydride preparation have also been accomplished with these compounds being subjected to the entrained flow reactor conditions. The benzoate esters give a number of products, such as benzaldehyde, benzene, and low MW gases. The formation of these compounds is extremely dependent on pyrolysis conditions and alkoxy chain length. A xenon flashlamp and an entrained flow reactor have been used to heat organic substrates to varying temperatures using different heating rates. Ultrarapid flashlamp pyrolysis (heating rate>10{sup 50}C/s) has been performed. Since the ultrarapid pyrolysis products differ from those observed with traditional heating techniques and differ from the products formed photochemically, the flashlamp pyrolysis products are attributed to high temperature thermal activation.

  4. Hidden Markov models from molecular dynamics simulations on DNA.

    PubMed

    Thayer, Kelly M; Beveridge, D L

    2002-06-25

    An enhanced bioinformatics tool incorporating the participation of molecular structure as well as sequence in protein DNA recognition is proposed and tested. Boltzmann probability models of sequence-dependent DNA structure from all-atom molecular dynamics simulations were obtained and incorporated into hidden Markov models (HMMs) that can recognize molecular structural signals as well as sequence in protein-DNA binding sites on a genome. The binding of catabolite activator protein (CAP) to cognate DNA sequences was used as a prototype case for implementation and testing of the method. The results indicate that even HMMs based on probabilistic roll/tilt dinucleotide models of sequence-dependent DNA structure have some capability to discriminate between known CAP binding and nonbinding sites and to predict putative CAP binding sites in unknowns. Restricting HMMs to sequence only in regions of strong consensus in which the protein makes base specific contacts with the cognate DNA further improved the discriminatory capabilities of the HMMs. Comparison of results with controls based on sequence only indicates that extending the definition of consensus from sequence to structure improves the transferability of the HMMs, and provides further supportive evidence of a role for dynamical molecular structure as well as sequence in genomic regulatory mechanisms.

  5. Testing of compounds in models of pulmonary emphysema.

    PubMed

    Gardi, Concetta; Arezzini, Beatrice; Martorana, Piero A

    2008-01-01

    There is a pressing need for the development of new therapies for emphysema, particularly as no existing treatment has been shown to reduce disease progression. Compounds with a potential activity against the pathological mechanisms postulated to play a role in the development and progression of emphysema should be tested in vivo in animal models of this disease. The choice of the model is of capital importance. While models of elastase-induced emphysema are relatively easy to execute, require low personnel capacity and provide fast results, they also have a limited clinical relevance. On the other hand, models of chronic smoke exposure are time-consuming, expensive and require high personnel capacity but have a high clinical relevance. Presently, mainly two pharmacological approaches are being considered and investigated in experimental studies. The first approach consists of pharmacological interventions designed to slow down the rate at which alveolar wall is lost in emphysema. In this approach we find anti-inflammatory agents, protease inhibitors and antioxidants. The attempt to reduce lung inflammatory cell infiltration is most appealing since such an effect would also reduce the lung burden of both proteases and oxidants. The second approach is an attempt to reverse the process of alveolar loss by inducing alveolar growth. To our knowledge here only the effects of retinoids and/or retinoid receptor agonists have been investigated. This report presents a selected review of the literature of animal studies using these pharmacological approaches.

  6. Compound dislocation models (CDMs) for volcano deformation analyses

    NASA Astrophysics Data System (ADS)

    Nikkhoo, Mehdi; Walter, Thomas R.; Lundgren, Paul R.; Prats-Iraola, Pau

    2017-02-01

    Volcanic crises are often preceded and accompanied by volcano deformation caused by magmatic and hydrothermal processes. Fast and efficient model identification and parameter estimation techniques for various sources of deformation are crucial for process understanding, volcano hazard assessment and early warning purposes. As a simple model that can be a basis for rapid inversion techniques, we present a compound dislocation model (CDM) that is composed of three mutually orthogonal rectangular dislocations (RDs). We present new RD solutions, which are free of artefact singularities and that also possess full rotational degrees of freedom. The CDM can represent both planar intrusions in the near field and volumetric sources of inflation and deflation in the far field. Therefore, this source model can be applied to shallow dikes and sills, as well as to deep planar and equidimensional sources of any geometry, including oblate, prolate and other triaxial ellipsoidal shapes. In either case the sources may possess any arbitrary orientation in space. After systematically evaluating the CDM, we apply it to the co-eruptive displacements of the 2015 Calbuco eruption observed by the Sentinel-1A satellite in both ascending and descending orbits. The results show that the deformation source is a deflating vertical lens-shaped source at an approximate depth of 8 km centred beneath Calbuco volcano. The parameters of the optimal source model clearly show that it is significantly different from an isotropic point source or a single dislocation model. The Calbuco example reflects the convenience of using the CDM for a rapid interpretation of deformation data.

  7. An effective mesoscopic model of double-stranded DNA.

    PubMed

    Jeon, Jae-Hyung; Sung, Wokyung

    2014-01-01

    Watson and Crick's epochal presentation of the double helix structure in 1953 has paved the way to intense exploration of DNA's vital functions in cells. Also, recent advances of single molecule techniques have made it possible to probe structures and mechanics of constrained DNA at length scales ranging from nanometers to microns. There have been a number of atomistic scale quantum chemical calculations or molecular level simulations, but they are too computationally demanding or analytically unfeasible to describe the DNA conformation and mechanics at mesoscopic levels. At micron scales, on the other hand, the wormlike chain model has been very instrumental in describing analytically the DNA mechanics but lacks certain molecular details that are essential in describing the hybridization, nano-scale confinement, and local denaturation. To fill this fundamental gap, we present a workable and predictive mesoscopic model of double-stranded DNA where the nucleotides beads constitute the basic degrees of freedom. With the inter-strand stacking given by an interaction between diagonally opposed monomers, the model explains with analytical simplicity the helix formation and produces a generalized wormlike chain model with the concomitant large bending modulus given in terms of the helical structure and stiffness. It also explains how the helical conformation undergoes overstretch transition to the ladder-like conformation at a force plateau, in agreement with the experiment.

  8. Analysis of a DNA simulation model through hairpin melting experiments

    PubMed Central

    Linak, Margaret C.; Dorfman, Kevin D.

    2010-01-01

    We compare the predictions of a two-bead Brownian dynamics simulation model to melting experiments of DNA hairpins with complementary AT or GC stems and noninteracting loops in buffer A. This system emphasizes the role of stacking and hydrogen bonding energies, which are characteristics of DNA, rather than backbone bending, stiffness, and excluded volume interactions, which are generic characteristics of semiflexible polymers. By comparing high throughput data on the open-close transition of various DNA hairpins to the corresponding simulation data, we (1) establish a suitable metric to compare the simulations to experiments, (2) find a conversion between the simulation and experimental temperatures, and (3) point out several limitations of the model, including the lack of G-quartets and cross stacking effects. Our approach and experimental data can be used to validate similar coarse-grained simulation models. PMID:20886965

  9. Antioxidative Dietary Compounds Modulate Gene Expression Associated with Apoptosis, DNA Repair, Inhibition of Cell Proliferation and Migration

    PubMed Central

    Wang, Likui; Gao, Shijuan; Jiang, Wei; Luo, Cheng; Xu, Maonian; Bohlin, Lars; Rosendahl, Markus; Huang, Wenlin

    2014-01-01

    Many dietary compounds are known to have health benefits owing to their antioxidative and anti-inflammatory properties. To determine the molecular mechanism of these food-derived compounds, we analyzed their effect on various genes related to cell apoptosis, DNA damage and repair, oxidation and inflammation using in vitro cell culture assays. This review further tests the hypothesis proposed previously that downstream products of COX-2 (cyclooxygenase-2) called electrophilic oxo-derivatives induce antioxidant responsive elements (ARE), which leads to cell proliferation under antioxidative conditions. Our findings support this hypothesis and show that cell proliferation was inhibited when COX-2 was down-regulated by polyphenols and polysaccharides. Flattened macrophage morphology was also observed following the induction of cytokine production by polysaccharides extracted from viili, a traditional Nordic fermented dairy product. Coix lacryma-jobi (coix) polysaccharides were found to reduce mitochondrial membrane potential and induce caspase-3- and 9-mediated apoptosis. In contrast, polyphenols from blueberries were involved in the ultraviolet-activated p53/Gadd45/MDM2 DNA repair system by restoring the cell membrane potential. Inhibition of hypoxia-inducible factor-1 by saponin extracts of ginsenoside (Ginsen) and Gynostemma and inhibition of S100A4 by coix polysaccharides inhibited cancer cell migration and invasion. These observations suggest that antioxidants and changes in cell membrane potential are the major driving forces that transfer signals through the cell membrane into the cytosol and nucleus, triggering gene expression, changes in cell proliferation and the induction of apoptosis or DNA repair. PMID:25226533

  10. Analysis of the DNA interaction of copper compounds belonging to the Casiopeínas® antitumoral series.

    PubMed

    Becco, Lorena; García-Ramos, Juan Carlos; Azuara, Lena Ruiz; Gambino, Dinorah; Garat, Beatriz

    2014-11-01

    Casiopeínas® are mixed-chelate copper complexes with antitumor tested potential. Their activity, both in vitro and in vivo, as antiproliferative, cytotoxic, and genotoxic drugs has been assessed. Biological results of these copper compounds have deserved some of them entering clinical trials. Significant efforts have been devoted to the in-depth identification of their mechanism of action. Using gel electrophoresis analysis, we have previously shown that the interaction of the Casiopeínas® Cas II-gly, [Cu(4,7-dimethyl-1,10-phenanthroline)(glycinate)]NO3 with DNA, triggers the cleavage of the biomolecule by a free radical mechanism. In this work, we further study the behavior of different complexes of the same Casiopeínas® series also including glycinate as co-ligand {Cas VI-gly (5,6 dimethyl-1,10-phenanthroline glycinato copper(II) nitrate), Cas VII-gly (1,10-phenanthroline glycinato copper(II) nitrate), and Cas IX-gly (2,2'-bipyridine glycinato copper(II) nitrate)} and of a Casiopeínas® with a different co-ligand (Cas III-Cs; 4,7-dimethyl-1,10-phenanthroline salicylaldehydato-copper(II) nitrate). While all of them produce DNA degradation, the performance in the presence of a radical scavenger suggests the existence of differences in their mechanism of interaction with DNA.

  11. DNA computation model to solve 0-1 programming problem.

    PubMed

    Zhang, Fengyue; Yin, Zhixiang; Liu, Bo; Xu, Jin

    2004-01-01

    0-1 programming problem is an important problem in opsearch with very widespread applications. In this paper, a new DNA computation model utilizing solution-based and surface-based methods is presented to solve the 0-1 programming problem. This model contains the major benefits of both solution-based and surface-based methods; including vast parallelism, extraordinary information density and ease of operation. The result, verified by biological experimentation, revealed the potential of DNA computation in solving complex programming problem.

  12. Oxidations of alkenes and lignin model compounds in aqueous dispersions

    SciTech Connect

    Zhu, Weiming.

    1991-01-01

    The objective was to develop methods to oxidize water-immiscible alkenes and lignin model compounds with polymer colloid supported transition metal catalysts. The oxidations of organic compounds were carried out in aqueous phase with several water-soluble oxidants and dioxygen. Cationic polymer latexes were prepared by the emulsion copolymerization of vinylbenzyl chloride, divinylbenzene, and vinyl octadecyl ether, or styrene, or n-decyl methacrylate, and the subsequent quaternization of copolymers with trimethylamine. The latex particles were 44 nm to 71 nm in diameter. The latex bound Mn porphyrin catalysts were formed with MnTSPP [TSPP = meso-tetrakis(2,6-dichloro-3-sulfonatophenyl)porphyrin], which catalyzed the oxidation of cyclohexene, cycloocetene, allylbenzene, and 1-octene by sodium hypochlorite (NaOCl) and potassium peroxymonosulfate (KHSO[sub 5]). The latex bound porphyrin catalysts showed higher activity than MnTSPP in solution. Oxidations of 3,4-dimethoxybenzyl alcohol (DMBA), 4-hydroxy-3-methoxytoluene (HMT), and 3,4-dimethoxytoluene (DMT) were performed with either dioxygen or hydrogen peroxide and CoPcTS (PcTS = tetrasulfonatophthalocyanine), FePcTS, CuPcTS, NiPcTS, FeTCPP [TCPP = meso-tetrakis(4-carboxyphenyl)porphyrin], and MnTSPP. CoPcTS catalyzed the autoxidation of DMBA and HMT at 70-85[degrees]C and pH [ge] 8. All catalysts were active for the oxidation of DMBA, HMT, and DMT with H[sub 2]O[sub 2]. Aqueous solutions of KHSO[sub 5] oxidized water-immiscible alkenes at room temperature in the absence of organic solvent. The acidic pH [le] 1.7 solutions of commercial 2KHSO[sub 5][center dot]K[sub 2]SO[sub 4] in water produced diols from all reactive alkenes except cyclooctene. Adjustment of initial pH to [ge]6.7 with NaHCO[sub 3] enabled selective epoxidations.

  13. Thermocatalytic treatment of biomass tar model compounds via radio frequency.

    PubMed

    Anis, Samsudin; Zainal, Z A; Bakar, M Z A

    2013-05-01

    A new effective RF tar thermocatalytic treatment process with low energy intensive has been proposed to remove tar from biomass gasification. Toluene and naphthalene as biomass tar model compounds were removed via both thermal and catalytic treatment over a wide temperature range from 850 °C to 1200 °C and 450 °C to 900 °C, respectively at residence time of 0-0.7 s. Thermal characteristics of the new technique are also described in this paper. This study clearly clarified that toluene was much easier to be removed than naphthalene. Soot was found as the final product of thermal treatment of the tar model and completely removed during catalytic treatment. Radical reactions generated by RF non-thermal effect improve the tar removal. The study showed that Y-zeolite has better catalytic activity compared to dolomite on toluene and naphthalene removal due to its acidic nature and large surface area, even at lower reaction temperature of about 550 °C.

  14. Mechanistic Study of the Acid Degradation of Lignin Model Compounds

    SciTech Connect

    Sturgeon, M.; Kim, S.; Chmely, S. C.; Foust, T. D.; Beckham, G. T.

    2012-01-01

    Lignin is a major constituent of biomass, which remains underutilized in selective biomass conversion strategies to renewable fuels and chemicals. Here we are interested in understanding the mechanisms related to the acid deconstruction of lignin with a combined theoretical and experimental approach. Two model dimers with a b-O-4 aryl ether linkage (2-phenoxy-1-phenethanol and 2-phenoxy-1-phenyl-1,3 propanediol) and model dimmers with an a-O-4 aryl ether linkage were synthesized and deconstructed in H2SO4. The major products of the acidolysis of the b-O-4 compounds consisted of phenol and two aldehydes, phenylacetaldehyde and benzaldehyde. Quantum mechanical calculations were employed to elucidate possible deconstruction mechanisms with transition state theory. To confirm proposed mechanisms several possible intermediates were studied under similar acidolysis conditions. Although the resonance time for cleavage was on the order several hours, we have shown that the cleavage of the aryl ether linkage affords phenol and aldehydes. We would next like to utilize our mechanism of aryl ether cleavage in actual lignin.

  15. Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models.

    PubMed

    Ando, Tadashi; Skolnick, Jeffrey

    2014-12-01

    DNA binding proteins efficiently search for their cognitive sites on long genomic DNA by combining 3D diffusion and 1D diffusion (sliding) along the DNA. Recent experimental results and theoretical analyses revealed that the proteins show a rotation-coupled sliding along DNA helical pitch. Here, we performed Brownian dynamics simulations using newly developed coarse-grained protein and DNA models for evaluating how hydrodynamic interactions between the protein and DNA molecules, binding affinity of the protein to DNA, and DNA fluctuations affect the one dimensional diffusion of the protein on the DNA. Our results indicate that intermolecular hydrodynamic interactions reduce 1D diffusivity by 30%. On the other hand, structural fluctuations of DNA give rise to steric collisions between the CG-proteins and DNA, resulting in faster 1D sliding of the protein. Proteins with low binding affinities consistent with experimental estimates of non-specific DNA binding show hopping along the CG-DNA. This hopping significantly increases sliding speed. These simulation studies provide additional insights into the mechanism of how DNA binding proteins find their target sites on the genome.

  16. Generalized Levy-walk model for DNA nucleotide sequences

    NASA Technical Reports Server (NTRS)

    Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Simons, M.; Stanley, H. E.

    1993-01-01

    We propose a generalized Levy walk to model fractal landscapes observed in noncoding DNA sequences. We find that this model provides a very close approximation to the empirical data and explains a number of statistical properties of genomic DNA sequences such as the distribution of strand-biased regions (those with an excess of one type of nucleotide) as well as local changes in the slope of the correlation exponent alpha. The generalized Levy-walk model simultaneously accounts for the long-range correlations in noncoding DNA sequences and for the apparently paradoxical finding of long subregions of biased random walks (length lj) within these correlated sequences. In the generalized Levy-walk model, the lj are chosen from a power-law distribution P(lj) varies as lj(-mu). The correlation exponent alpha is related to mu through alpha = 2-mu/2 if 2 < mu < 3. The model is consistent with the finding of "repetitive elements" of variable length interspersed within noncoding DNA.

  17. DNA for crime investigation: European co-operation model.

    PubMed

    Fiodorova, Anna

    2014-01-01

    The article presents DNA related data exchange mechanism established within the framework of the European Union for the transnational crime investigation. First of all, it provides with the comprehensive overview of legal and practical state of play, pointing out that approved legal basis seeks to ensure legality and reliability in this area by establishing information exchange purposes and competent authorities involved, setting up technical requirements for the DNA analysis and DNA data bases, laying down provisions on accreditation of forensic service providers, foreseeing at least minimum common data protection requirements. Secondly, it reveals that despite being the most exhaustive international regulation on DNA related data exchange among law enforcement and judicial authorities it misses effective data protection mechanism, does not harmonize neither backgrounds for DNA collection in criminal process in general nor storage requirements and that results the variation in categories of subjects related to the crime investigation and included in data bases of different Member States. These gaps make the use of data collected and stored in another Member State vulnerable from the perspective of different rules on evidences' legality within the criminal process. The article also reveals the model's weakness in terms of assessment of its efficiency as statistics gathered for the time being show only number of coincidences (hits) of searched DNA profiles, but not the impact on crime investigation and its results.

  18. Formation of DNA-damaging N-nitroso compounds from the interaction of calcium-channel blockers with nitrite.

    PubMed

    Martelli, Antonietta; Robbiano, Luigi; Grossi, Sarah; Mattioli, Francesca; Brambilla, Giovanni

    2007-09-05

    A large number of drugs have been shown to react with nitrite to give genotoxic-carcinogenic N-nitroso compounds (NOC). However, the majority of drugs remain to be examined in this respect, among which calcium-channel blockers, all theoretically nitrosatable and widely used in the therapy of hypertension and other cardiovascular diseases. In this preliminary investigation, seven calcium-channel blockers have been examined either for their in vitro nitrosation according to the procedure recommended by the WHO, or for occurrence of liver DNA fragmentation, as detected by the Comet assay, in rats given by gavage 1/2 LD50 of the drug and 80 mg/kg of sodium nitrite. After 6h incubation the yields of NOC formed in vitro from nicardipine, nifedipine, nimodipine and nitrendipine ranged from 37 to 45% of the theoretical one, whereas the yields of NOC formed from diltiazem, gallopamil and verapamil ranged from 2 to 5%. In vivo, as compared with the effect of the same dose of the drug alone, a significant increase of both tail length and tail moment, indicative of an increased frequency of DNA single-strand breaks and alkali-labile sites, was produced in rat liver DNA by the administration with nitrite of gallopamil, nifedipine, nimodipine and nitrendipine, the ratio [tail length of drug+NaNO(2)/tail length of drug alone] being 3.2 for nimodipine, 3.1 for gallopamil 2.2 for nifedipine, and 2.1 for nitrendipine. Even if present, the increase in the degree of DNA fragmentation did not reach the statistical significance in rats given with nitrite nicardipine, diltiazem and verapamil. Further studies should be performed to investigate the formation of NOC in conditions simulating those occurring in the stomach of humans treated with a therapeutic dose, and to quantitate their genotoxic potency.

  19. Maternal exposure to anti-androgenic compounds, vinclozolin, flutamide and procymidone, has no effects on spermatogenesis and DNA methylation in male rats of subsequent generations

    SciTech Connect

    Inawaka, Kunifumi Kawabe, Mayumi; Takahashi, Satoru; Doi, Yuko; Tomigahara, Yoshitaka; Tarui, Hirokazu; Abe, Jun; Kawamura, Satoshi; Shirai, Tomoyuki

    2009-06-01

    To verify whether anti-androgens cause transgenerational effects on spermatogenesis and DNA methylation in rats, gravid Crl:CD(SD) female rats (4 or 5/group, gestational day (GD) 0 = day sperm detected) were intraperitoneally treated with anti-androgenic compounds, such as vinclozolin (100 mg/kg/day), procymidone (100 mg/kg/day), or flutamide (10 mg/kg/day), from GD 8 to GD 15. Testes were collected from F1 male pups at postnatal day (PND) 6 for DNA methylation analysis of the region (210 bp including 7 CpG sites) within the lysophospholipase gene by bisulfite DNA sequencing method. F0 and F1 males underwent the sperm analysis (count, motility and morphology), followed by DNA methylation analysis of the sperm. Remaining F1 males were cohabited with untreated-females to obtain F2 male pups for subsequent DNA methylation analysis of the testes at PND 6. These analyses showed no effects on spermatogenesis and fertility in F1 males of any treatment group. DNA methylation status in testes (F1 and F2 pups at PND 6) or sperms (F1 males at 13 weeks old) of the treatment groups were comparable to the control at all observation points, although DNA methylation rates in testes were slightly lower than those in sperm. In F0 males, no abnormalities in the spermatogenesis, fertility and DNA methylation status of sperm were observed. No transgenerational abnormalities of spermatogenesis and DNA methylation status caused by anti-androgenic compounds were observed.

  20. Computational and analytical modeling of cationic lipid-DNA complexes.

    PubMed

    Farago, Oded; Grønbech-Jensen, Niels

    2007-05-01

    We present a theoretical study of the physical properties of cationic lipid-DNA (CL-DNA) complexes--a promising synthetically based nonviral carrier of DNA for gene therapy. The study is based on a coarse-grained molecular model, which is used in Monte Carlo simulations of mesoscopically large systems over timescales long enough to address experimental reality. In the present work, we focus on the statistical-mechanical behavior of lamellar complexes, which in Monte Carlo simulations self-assemble spontaneously from a disordered random initial state. We measure the DNA-interaxial spacing, d(DNA), and the local cationic area charge density, sigma(M), for a wide range of values of the parameter (c) representing the fraction of cationic lipids. For weakly charged complexes (low values of (c)), we find that d(DNA) has a linear dependence on (c)(-1), which is in excellent agreement with x-ray diffraction experimental data. We also observe, in qualitative agreement with previous Poisson-Boltzmann calculations of the system, large fluctuations in the local area charge density with a pronounced minimum of sigma(M) halfway between adjacent DNA molecules. For highly-charged complexes (large (c)), we find moderate charge density fluctuations and observe deviations from linear dependence of d(DNA) on (c)(-1). This last result, together with other findings such as the decrease in the effective stretching modulus of the complex and the increased rate at which pores are formed in the complex membranes, are indicative of the gradual loss of mechanical stability of the complex, which occurs when (c) becomes large. We suggest that this may be the origin of the recently observed enhanced transfection efficiency of lamellar CL-DNA complexes at high charge densities, because the completion of the transfection process requires the disassembly of the complex and the release of the DNA into the cytoplasm. Some of the structural properties of the system are also predicted by a continuum

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

    PubMed

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

    2002-06-01

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

  2. A Mesoscale Model of DNA and Its Renaturation

    PubMed Central

    Sambriski, E.J.; Schwartz, D.C.; de Pablo, J.J.

    2009-01-01

    A mesoscale model of DNA is presented (3SPN.1), extending the scheme previously developed by our group. Each nucleotide is mapped onto three interaction sites. Solvent is accounted for implicitly through a medium-effective dielectric constant and electrostatic interactions are treated at the level of Debye-Hückel theory. The force field includes a weak, solvent-induced attraction, which helps mediate the renaturation of DNA. Model parameterization is accomplished through replica exchange molecular dynamics simulations of short oligonucleotide sequences over a range of composition and chain length. The model describes the melting temperature of DNA as a function of composition as well as ionic strength, and is consistent with heat capacity profiles from experiments. The dependence of persistence length on ionic strength is also captured by the force field. The proposed model is used to examine the renaturation of DNA. It is found that a typical renaturation event occurs through a nucleation step, whereby an interplay between repulsive electrostatic interactions and colloidal-like attractions allows the system to undergo a series of rearrangements before complete molecular reassociation occurs. PMID:19254530

  3. Feruloylacetone as the model compound of half-curcumin: synthesis and antioxidant properties.

    PubMed

    Feng, Jian-Ying; Liu, Zai-Qun

    2011-04-01

    In order to clarify the contribution of phenolic and enolic hydroxyl group to the antioxidant capacity of feruloylacetone, a model compound of half-curcumin, 6-(p-hydroxy-m-methoxyphenyl)-5-hexene-2,4-dione (FT), 6-(p-benzyloxy-m-methoxyphenyl)-5-hexene-2,4-dione (BMFT), 6-(m,p-dihydroxyphenyl)-5-hexene-2,4-dione (DDFT), 6-(p-hydroxy-m-methoxyphenyl)hexane-2,4-dione (DHFT), 6-(p-hydroxy-m-methoxyphenyl)-5-hexene-2,4-diol (THFT), and ethyl 2-(p-hydroxy-m-methoxybenzylidene)-3-oxobutanoate (EOFT) were synthesized. The radical-scavenging abilities of these compounds were tested by trapping 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonate) cationic radical (ABTS(+·)), 2,2'-diphenyl-1-picrylhydrazyl (DPPH), and galvinoxyl radicals. The reductive capacities were screened by quenching singlet oxygen and by inhibiting the oxidation of linoleic acid. They were also employed to inhibit the oxidation of DNA mediated by hydroxyl radical and 2,2'-azobis(2-amidinopropane hydrochloride) (AAPH). In addition, they were applied to protect erythrocytes against AAPH- and hemin-induced hemolysis. The obtained results revealed that the antioxidant capacity of half-curcumin was derived from the phenolic-OH and the conjugated linkage between phenolic and enolic-OH. The enolic-OH itself cannot trap radicals.

  4. Drosophila Mcm10 Is Required for DNA Replication and Differentiation in the Compound Eye

    PubMed Central

    Vo, Nicole; Taga, Ayano; Inaba, Yasuhiro; Yoshida, Hideki; Cotterill, Sue; Yamaguchi, Masamitsu

    2014-01-01

    Mini chromosome maintenance 10 (Mcm10) is an essential protein, which is conserved from S. cerevisiae to Drosophila and human, and is required for the initiation of DNA replication. Knockdown of Drosophila Mcm10 (dMcm10) by RNA interference in eye imaginal discs induces abnormal eye morphology (rough eye phenotype), and the number of ommatidia is decreased in adult eyes. We also observed a delay in the S phase and M phase in eye discs of dMcm10 knockdown fly lines. These results show important roles for dMcm10 in the progression of S and M phases. Furthermore, genome damage and apoptosis were induced by dMcm10 knockdown in eye imaginal discs. Surprisingly, when we used deadpan-lacZ and klingon-lacZ enhancer trap lines to monitor the photoreceptor cells in eye discs, knockdown of dMcm10 by the GMR-GAL4 driver reduced the signals of R7 photoreceptor cells. These data suggest an involvement of dMcm10 in R7 cell differentiation. This involvement appears to be independent of the apoptosis induced by dMcm10 knockdown. Together, these results suggest that dMcm10 knockdown has an effect on DNA replication and R7 cell differentiation. PMID:24686397

  5. Drosophila Mcm10 is required for DNA replication and differentiation in the compound eye.

    PubMed

    Vo, Nicole; Taga, Ayano; Inaba, Yasuhiro; Yoshida, Hideki; Cotterill, Sue; Yamaguchi, Masamitsu

    2014-01-01

    Mini chromosome maintenance 10 (Mcm10) is an essential protein, which is conserved from S. cerevisiae to Drosophila and human, and is required for the initiation of DNA replication. Knockdown of Drosophila Mcm10 (dMcm10) by RNA interference in eye imaginal discs induces abnormal eye morphology (rough eye phenotype), and the number of ommatidia is decreased in adult eyes. We also observed a delay in the S phase and M phase in eye discs of dMcm10 knockdown fly lines. These results show important roles for dMcm10 in the progression of S and M phases. Furthermore, genome damage and apoptosis were induced by dMcm10 knockdown in eye imaginal discs. Surprisingly, when we used deadpan-lacZ and klingon-lacZ enhancer trap lines to monitor the photoreceptor cells in eye discs, knockdown of dMcm10 by the GMR-GAL4 driver reduced the signals of R7 photoreceptor cells. These data suggest an involvement of dMcm10 in R7 cell differentiation. This involvement appears to be independent of the apoptosis induced by dMcm10 knockdown. Together, these results suggest that dMcm10 knockdown has an effect on DNA replication and R7 cell differentiation.

  6. Modeling 3D facial shape from DNA.

    PubMed

    Claes, Peter; Liberton, Denise K; Daniels, Katleen; Rosana, Kerri Matthes; Quillen, Ellen E; Pearson, Laurel N; McEvoy, Brian; Bauchet, Marc; Zaidi, Arslan A; Yao, Wei; Tang, Hua; Barsh, Gregory S; Absher, Devin M; Puts, David A; Rocha, Jorge; Beleza, Sandra; Pereira, Rinaldo W; Baynam, Gareth; Suetens, Paul; Vandermeulen, Dirk; Wagner, Jennifer K; Boster, James S; Shriver, Mark D

    2014-03-01

    Human facial diversity is substantial, complex, and largely scientifically unexplained. We used spatially dense quasi-landmarks to measure face shape in population samples with mixed West African and European ancestry from three locations (United States, Brazil, and Cape Verde). Using bootstrapped response-based imputation modeling (BRIM), we uncover the relationships between facial variation and the effects of sex, genomic ancestry, and a subset of craniofacial candidate genes. The facial effects of these variables are summarized as response-based imputed predictor (RIP) variables, which are validated using self-reported sex, genomic ancestry, and observer-based facial ratings (femininity and proportional ancestry) and judgments (sex and population group). By jointly modeling sex, genomic ancestry, and genotype, the independent effects of particular alleles on facial features can be uncovered. Results on a set of 20 genes showing significant effects on facial features provide support for this approach as a novel means to identify genes affecting normal-range facial features and for approximating the appearance of a face from genetic markers.

  7. Modeling 3D Facial Shape from DNA

    PubMed Central

    Claes, Peter; Liberton, Denise K.; Daniels, Katleen; Rosana, Kerri Matthes; Quillen, Ellen E.; Pearson, Laurel N.; McEvoy, Brian; Bauchet, Marc; Zaidi, Arslan A.; Yao, Wei; Tang, Hua; Barsh, Gregory S.; Absher, Devin M.; Puts, David A.; Rocha, Jorge; Beleza, Sandra; Pereira, Rinaldo W.; Baynam, Gareth; Suetens, Paul; Vandermeulen, Dirk; Wagner, Jennifer K.; Boster, James S.; Shriver, Mark D.

    2014-01-01

    Human facial diversity is substantial, complex, and largely scientifically unexplained. We used spatially dense quasi-landmarks to measure face shape in population samples with mixed West African and European ancestry from three locations (United States, Brazil, and Cape Verde). Using bootstrapped response-based imputation modeling (BRIM), we uncover the relationships between facial variation and the effects of sex, genomic ancestry, and a subset of craniofacial candidate genes. The facial effects of these variables are summarized as response-based imputed predictor (RIP) variables, which are validated using self-reported sex, genomic ancestry, and observer-based facial ratings (femininity and proportional ancestry) and judgments (sex and population group). By jointly modeling sex, genomic ancestry, and genotype, the independent effects of particular alleles on facial features can be uncovered. Results on a set of 20 genes showing significant effects on facial features provide support for this approach as a novel means to identify genes affecting normal-range facial features and for approximating the appearance of a face from genetic markers. PMID:24651127

  8. Source apportionment modeling of volatile organic compounds in streams

    USGS Publications Warehouse

    Pankow, J.F.; Asher, W.E.; Zogorski, J.S.

    2006-01-01

    It often is of interest to understand the relative importance of the different sources contributing to the concentration cw of a contaminant in a stream; the portions related to sources 1, 2, 3, etc. are denoted cw,1, cw,2, cw,3, etc. Like c w, 'he fractions ??1, = cw,1/c w, ??2 = cw,2/cw, ??3 = cw,3/cw, etc. depend on location and time. Volatile organic compounds (VOCs) can undergo absorption from the atmosphere into stream water or loss from stream water to the atmosphere, causing complexities affecting the source apportionment (SA) of VOCs in streams. Two SA rules are elaborated. Rule 1: VOC entering a stream across the air/water interface exclusively is assigned to the atmospheric portion of cw. Rule 2: VOC loss by volatilization, flow loss to groundwater, in-stream degradation, etc. is distributed over cw,1 cw,2, c w,3, etc. in proportion to their corresponding ?? values. How the two SA rules are applied, as well as the nature of the SA output for a given case, will depend on whether transport across the air/water interface is handled using the net flux F convention or using the individual fluxes J convention. Four hypothetical stream cases involving acetone, methyl-tert-butyl ether (MTBE), benzene, chloroform, and perchloroethylene (PCE) are considered. Acetone and MTBE are sufficiently water soluble from air for a domestic atmospheric source to be capable of yielding cw values approaching the common water quality guideline range of 1 to 10 ??g/L. For most other VOCs, such levels cause net outgassing (F > 0). When F > 0 in a given section of stream, in the net flux convention, all of the ??j, for the compound remain unchanged over that section while cw decreases. A characteristic time ??d can be calculated to predict when there will be differences between SA results obtained by the net flux convention versus the individual fluxes convention. Source apportionment modeling provides the framework necessary for comparing different strategies for mitigating

  9. Coarse-grained modeling of protein unspecifically bound to DNA

    NASA Astrophysics Data System (ADS)

    Guardiani, Carlo; Cencini, Massimo; Cecconi, Fabio

    2014-04-01

    There is now a certain consensus that transcription factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D diffusion in solution (jumps), 1D diffusion along DNA (sliding), and small jumps (hopping), achieving association rates higher than for 3D diffusion alone. We investigate the FD phenomenology through molecular dynamics simulations in the framework of coarse-grained modeling. We show that, despite the crude approximations, the model generates, upon varying the equilibrium distance of the DNA-TF interaction, a phenomenology matching a number of experimental and numerical results obtained with more refined models. In particular, focusing on the kinematics of the process, we characterize the geometrical properties of TF trajectories during sliding. We find that sliding occurs via helical paths around the DNA helix, leading to a coupling of translation along the DNA axis with rotation around it. The 1D diffusion constant measured in simulations is found to be interwoven with the geometrical properties of sliding and we develop a simple argument that can be used to quantitatively reproduce the measured values.

  10. An unenumerative DNA computing model for vertex coloring problem.

    PubMed

    Xu, Jin; Qiang, Xiaoli; Yang, Yan; Wang, Baoju; Yang, Dongliang; Luo, Liang; Pan, Linqiang; Wang, Shudong

    2011-06-01

    The solution space exponential explosion caused by the enumeration of the candidate solutions maybe is the biggest obstacle in DNA computing. In the paper, a new unenumerative DNA computing model for graph vertex coloring problem is presented based on two techniques: 1) ordering the vertex sequence for a given graph in such a way that any two consecutive labeled vertices i and i+1 should be adjacent in the graph as much as possible; 2) reducing the number of encodings representing colors according to the construture of the given graph. A graph with 12 vertices without triangles is solved and its initial solution space includes only 283 DNA strands, which is 0.0532 of 3(12) (the worst complexity).

  11. An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations

    NASA Astrophysics Data System (ADS)

    Bernal, M. A.; Sikansi, D.; Cavalcante, F.; Incerti, S.; Champion, C.; Ivanchenko, V.; Francis, Z.

    2013-12-01

    In this paper, an atomistic geometrical model for the B-DNA configuration is explained. This model accounts for five organization levels of the DNA, up to the 30 nm chromatin fiber. However, fragments of this fiber can be used to construct the whole genome. The algorithm developed in this work is capable to determine which is the closest atom with respect to an arbitrary point in space. It can be used in any application in which a DNA geometrical model is needed, for instance, in investigations related to the effects of ionizing radiations on the human genetic material. Successful consistency checks were carried out to test the proposed model. Catalogue identifier: AEPZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1245 No. of bytes in distributed program, including test data, etc.: 6574 Distribution format: tar.gz Programming language: FORTRAN. Computer: Any. Operating system: Multi-platform. RAM: 2 Gb Classification: 3. Nature of problem: The Monte Carlo method is used to simulate the interaction of ionizing radiation with the human genetic material in order to determine DNA damage yields per unit absorbed dose. To accomplish this task, an algorithm to determine if a given energy deposition lies within a given target is needed. This target can be an atom or any other structure of the genetic material. Solution method: This is a stand-alone subroutine describing an atomic-resolution geometrical model of the B-DNA configuration. It is able to determine the closest atom to an arbitrary point in space. This model accounts for five organization levels of the human genetic material, from the nucleotide pair up to the 30 nm chromatin fiber. This subroutine carries out a series of coordinate transformations

  12. Novel compound heterozygous DNA ligase IV mutations in an adolescent with a slowly-progressing radiosensitive-severe combined immunodeficiency.

    PubMed

    Tamura, Shinobu; Higuchi, Kohei; Tamaki, Masaharu; Inoue, Chizuko; Awazawa, Ryoko; Mitsuki, Noriko; Nakazawa, Yuka; Mishima, Hiroyuki; Takahashi, Kenzo; Kondo, Osamu; Imai, Kohsuke; Morio, Tomohiro; Ohara, Osamu; Ogi, Tomoo; Furukawa, Fukumi; Inoue, Masami; Yoshiura, Koh-ichiro; Kanazawa, Nobuo

    2015-10-01

    We herein describe a case of a 17-year-old boy with intractable common warts, short stature, microcephaly and slowly-progressing pancytopenia. Simultaneous quantification of T-cell receptor recombination excision circles (TREC) and immunoglobulin κ-deleting recombination excision circles (KREC) suggested very poor generation of both T-cells and B-cells. By whole exome sequencing, novel compound heterozygous mutations were identified in the patient's DNA ligase IV (LIG4) gene. The diagnosis of LIG4 syndrome was confirmed by delayed DNA double-strand break repair kinetics in γ-irradiated fibroblasts from the patient and their restoration by an introduction of wild-type LIG4. Although the patient received allogeneic hematopoietic stem cell transplantation from his haploidentical mother, he unfortunately expired due to an insufficiently reconstructed immune system. An earlier definitive diagnosis using TREC/KREC quantification and whole exome sequencing would thereby allow earlier intervention, which would be essential for improving long-term survival in similar cases with slowly-progressing LIG4 syndrome masked in adolescents.

  13. Mechanistic Modelling of DNA Repair and Cellular Survival Following Radiation-Induced DNA Damage

    NASA Astrophysics Data System (ADS)

    McMahon, Stephen J.; Schuemann, Jan; Paganetti, Harald; Prise, Kevin M.

    2016-09-01

    Characterising and predicting the effects of ionising radiation on cells remains challenging, with the lack of robust models of the underlying mechanism of radiation responses providing a significant limitation to the development of personalised radiotherapy. In this paper we present a mechanistic model of cellular response to radiation that incorporates the kinetics of different DNA repair processes, the spatial distribution of double strand breaks and the resulting probability and severity of misrepair. This model enables predictions to be made of a range of key biological endpoints (DNA repair kinetics, chromosome aberration and mutation formation, survival) across a range of cell types based on a set of 11 mechanistic fitting parameters that are common across all cells. Applying this model to cellular survival showed its capacity to stratify the radiosensitivity of cells based on aspects of their phenotype and experimental conditions such as cell cycle phase and plating delay (correlation between modelled and observed Mean Inactivation Doses R2 > 0.9). By explicitly incorporating underlying mechanistic factors, this model can integrate knowledge from a wide range of biological studies to provide robust predictions and may act as a foundation for future calculations of individualised radiosensitivity.

  14. Model identification for DNA sequence-structure relationships.

    PubMed

    Hawley, Stephen Dwyer; Chiu, Anita; Chizeck, Howard Jay

    2006-11-01

    We investigate the use of algebraic state-space models for the sequence dependent properties of DNA. By considering the DNA sequence as an input signal, rather than using an all atom physical model, computational efficiency is achieved. A challenge in deriving this type of model is obtaining its structure and estimating its parameters. Here we present two candidate model structures for the sequence dependent structural property Slide and a method of encoding the models so that a recursive least squares algorithm can be applied for parameter estimation. These models are based on the assumption that the value of Slide at a base-step is determined by the surrounding tetranucleotide sequence. The first model takes the four bases individually as inputs and has a median root mean square deviation of 0.90 A. The second model takes the four bases pairwise and has a median root mean square deviation of 0.88 A. These values indicate that the accuracy of these models is within the useful range for structure prediction. Performance is comparable to published predictions of a more physically derived model, at significantly less computational cost.

  15. Differentiation of yeasts growing on dry-cured Iberian ham by mitochondrial DNA restriction analysis, RAPD-PCR and their volatile compounds production.

    PubMed

    Andrade, M J; Rodríguez, M; Casado, E M; Bermúdez, E; Córdoba, J J

    2009-09-01

    The efficiency of mitochondrial DNA (mtDNA) restriction analysis, RAPD-PCR and volatile compounds analysis to differentiate yeast biotypes involved in flavour development of dry-cured Iberian ham throughout the ripening process is evaluated. For this purpose, 86 yeasts isolated from Iberian hams in the main ripening stages at different industries of the four Protected Designations of Origin of this product, were used. The combination of mtDNA restriction analysis and RAPD-PCR using the primer (GACA)4 showed a higher variability in the yeast species detected than obtained using only mtDNA restriction analysis. Only two species, Debaryomyces hansenii and Candida zeylanoides, were identified throughout the whole ripening process and a wide diversity of biotypes was found in these two species, with those of D. hansenii predominating. Clear differences between biotypes were detected in the generation of volatile compounds, with the biotype C2-2 of D. hansenii showing the highest concentrations of volatiles. The combined use of mtDNA restriction analysis and RAPD-PCR distinguishes yeast biotypes with different production of volatile compounds. In addition, analysis of the production profile of volatile compounds is needed to differentiate yeast strains of the same biotype recovered at different stages of ripening. Thus, the combination of these three methods could be very useful to select or monitor yeasts as starter cultures in dry-cured meat products.

  16. Probabilistic models for semisupervised discriminative motif discovery in DNA sequences.

    PubMed

    Kim, Jong Kyoung; Choi, Seungjin

    2011-01-01

    Methods for discriminative motif discovery in DNA sequences identify transcription factor binding sites (TFBSs), searching only for patterns that differentiate two sets (positive and negative sets) of sequences. On one hand, discriminative methods increase the sensitivity and specificity of motif discovery, compared to generative models. On the other hand, generative models can easily exploit unlabeled sequences to better detect functional motifs when labeled training samples are limited. In this paper, we develop a hybrid generative/discriminative model which enables us to make use of unlabeled sequences in the framework of discriminative motif discovery, leading to semisupervised discriminative motif discovery. Numerical experiments on yeast ChIP-chip data for discovering DNA motifs demonstrate that the best performance is obtained between the purely-generative and the purely-discriminative and the semisupervised learning improves the performance when labeled sequences are limited.

  17. New bimetallic dicyanidoargentate(I)-based coordination compounds: Synthesis, characterization, biological activities and DNA-BSA binding affinities

    NASA Astrophysics Data System (ADS)

    Korkmaz, Nesrin; Aydın, Ali; Karadağ, Ahmet; Yanar, Yusuf; Maaşoğlu, Yelis; Şahin, Ertan; Tekin, Şaban

    2017-02-01

    Four compounds -two (2 and 3) completely new- of composition [Ni(edbea)Ag3(CN)5] (1), [Cu(edbea)Ag2(CN)4]·H2O (2), [Cd(edbea)Ag3(CN)5]·H2O (3) and [Cd(edbea)2] [Ag(CN)2]2·H2O (4) {edbea; 2,2‧-(ethylenedioxy)bis (ethylamine)}, were synthesized and characterized using elemental, FT-IR, X-Ray (4), thermal, variable temperature magnetic measurement (1 and 2) and biological techniques. The DNA/BSA binding affinities of 2 and 3 were evaluated by UV-Vis spectrophotometric titrations, ethidium bromide exchange experiments and electrophoretic mobility measurements. Compounds 1 and 4 have previously been characterized and shown to reduce the proliferation and migration of tumor cells. For the sake of clarity, 1 precise mechanism of action on microbial organisms and temperature magnetic measurement were determined. The crystallographic analyses showed that 4 was built up of [Cd(edbea)2]II cations and [Ag2(CN)4]II anions. Complexes demonstrated a remarkable antibacterial (1-4), antifungal (1-4) and antiproliferative activities (2 and 3) to ten human bacterial pathogens, four plant pathogenic fungi or three tumor cells (HeLa, HT29, and C6), respectively. Therefore, our results strongly confirm that cell proliferation, cell morphology, Bcl-2, P53 changes and apoptosis can be related to the pharmacological effects of the complexes as suitable candidate for clinical trials.

  18. Modeling the Relaxation Time of DNA Confined in a Nanochannel

    NASA Astrophysics Data System (ADS)

    Wang, Yanwei; Tree, Douglas R.; Dorfman, Kevin D.

    2014-03-01

    Using a mapping between a dumbbell model and fine-grained Monte Carlo simulations, we have computed the relaxation time of λ-DNA in a high ionic strength buffer confined in a nanochannel (Tree et al., Biomicrofluidics 2013, 7, 054118). The relaxation time thus obtained agrees quantitatively with experimental data (Reisner et al., PRL 2005, 94, 196101) using only a single O(1) fitting parameter to account for the uncertainty in model parameters. In addition to validating our mapping, this agreement supports our previous estimates of the friction coefficient of DNA confined in a nanochannel (Tree et al., PRL 2012, 108, 228105), which have been difficult to validate due to the lack of direct experimental data. Furthermore, our calculation shows that as the channel size passes below ~100 nm (or roughly the Kuhn length of DNA) there is a dramatic drop in the relaxation time. Inasmuch as the chain friction rises with decreasing channel size, the reduction in the relaxation time can be solely attributed to the sharp decline in the fluctuations of the chain extension. Practically, the low variance in the observed DNA extension in such small channels has important implications for genome mapping. This work was supported by the NIH (R01-HG005216 and R01-HG006851) and the NSFC (21204061) and was carried out in part using computing resources at the University of Minnesota Supercomputing Institute.

  19. Modeling the Study of DNA Damage Responses in Mice

    PubMed Central

    Specks, Julia; Nieto-Soler, Maria; Lopez-Contreras, Andres J; Fernandez-Capetillo, Oscar

    2016-01-01

    Summary Damaged DNA has a profound impact on mammalian health and overall survival. In addition to being the source of mutations that initiate cancer, the accumulation of toxic amounts of DNA damage can cause severe developmental diseases and accelerate ageing. Therefore, understanding how cells respond to DNA damage has become one of the most intense areas of biomedical research in the recent years. However, whereas most mechanistic studies derive from in vitro or in cellulo work, the impact of a given mutation on a living organism is largely unpredictable. For instance, why BRCA1 mutations preferentially lead to breast cancer whereas mutations compromising mismatch repair drive colon cancer is still not understood. In this context, evaluating the specific physiological impact of mutations that compromise genome integrity has become crucial for a better dimensioning of our knowledge. We here describe the various technologies that can be used for modeling mutations in mice, and provide a review of the genes and pathways that have been modeled so far in the context of DNA damage responses. PMID:25636482

  20. CRISPR-Cas9-based target validation for p53-reactivating model compounds

    PubMed Central

    Wanzel, Michael; Vischedyk, Jonas B; Gittler, Miriam P; Gremke, Niklas; Seiz, Julia R; Hefter, Mirjam; Noack, Magdalena; Savai, Rajkumar; Mernberger, Marco; Charles, Joël P; Schneikert, Jean; Bretz, Anne Catherine; Nist, Andrea; Stiewe, Thorsten

    2015-01-01

    Inactivation of the p53 tumor suppressor by Mdm2 is one of the most frequent events in cancer, so compounds targeting the p53-Mdm2 interaction are promising for cancer therapy. Mechanisms conferring resistance to p53-reactivating compounds are largely unknown. Here we show using CRISPR-Cas9–based target validation in lung and colorectal cancer that the activity of nutlin, which blocks the p53-binding pocket of Mdm2, strictly depends on functional p53. In contrast, sensitivity to the drug RITA, which binds the Mdm2-interacting N terminus of p53, correlates with induction of DNA damage. Cells with primary or acquired RITA resistance display cross-resistance to DNA crosslinking compounds such as cisplatin and show increased DNA cross-link repair. Inhibition of FancD2 by RNA interference or pharmacological mTOR inhibitors restores RITA sensitivity. The therapeutic response to p53-reactivating compounds is therefore limited by compound-specific resistance mechanisms that can be resolved by CRISPR-Cas9-based target validation and should be considered when allocating patients to p53-reactivating treatments. PMID:26595461

  1. Clusters of DNA induced by ionizing radiation: formation of short DNA fragments. I. Theoretical modeling

    NASA Technical Reports Server (NTRS)

    Holley, W. R.; Chatterjee, A.

    1996-01-01

    We have developed a general theoretical model for the interaction of ionizing radiation with chromatin. Chromatin is modeled as a 30-nm-diameter solenoidal fiber comprised of 20 turns of nucleosomes, 6 nucleosomes per turn. Charged-particle tracks are modeled by partitioning the energy deposition between primary track core, resulting from glancing collisions with 100 eV or less per event, and delta rays due to knock-on collisions involving energy transfers >100 eV. A Monte Carlo simulation incorporates damages due to the following molecular mechanisms: (1) ionization of water molecules leading to the formation of OH, H, eaq, etc.; (2) OH attack on sugar molecules leading to strand breaks: (3) OH attack on bases; (4) direct ionization of the sugar molecules leading to strand breaks; (5) direct ionization of the bases. Our calculations predict significant clustering of damage both locally, over regions up to 40 bp and over regions extending to several kilobase pairs. A characteristic feature of the regional damage predicted by our model is the production of short fragments of DNA associated with multiple nearby strand breaks. The shapes of the spectra of DNA fragment lengths depend on the symmetries or approximate symmetries of the chromatin structure. Such fragments have subsequently been detected experimentally and are reported in an accompanying paper (B. Rydberg, Radiat, Res. 145, 200-209, 1996) after exposure to both high- and low-LET radiation. The overall measured yields agree well quantitatively with the theoretical predictions. Our theoretical results predict the existence of a strong peak at about 85 bp, which represents the revolution period about the nucleosome. Other peaks at multiples of about 1,000 bp correspond to the periodicity of the particular solenoid model of chromatin used in these calculations. Theoretical results in combination with experimental data on fragmentation spectra may help determine the consensus or average structure of the

  2. Nitrite curing of chicken, pork, and beef inhibits oxidation but does not affect N-nitroso compound (NOC)-specific DNA adduct formation during in vitro digestion.

    PubMed

    Van Hecke, Thomas; Vanden Bussche, Julie; Vanhaecke, Lynn; Vossen, Els; Van Camp, John; De Smet, Stefaan

    2014-02-26

    Uncured and nitrite-cured chicken, pork, and beef were used as low, medium, and high sources of heme-Fe, respectively, and exposed to an in vitro digestion model simulating the mouth, stomach, duodenum, and colon. With increasing content of iron compounds, up to 25-fold higher concentrations of the toxic lipid oxidation products malondialdehyde, 4-hydroxy-2-nonenal, and other volatile aldehydes were formed during digestion, together with increased protein carbonyl compounds as measurement of protein oxidation. Nitrite curing of all meats lowered lipid and protein oxidation to the level of oxidation in uncured chicken. Strongly depending on the individual fecal inoculum, colonic digestion of beef resulted in significantly higher concentrations of the NOC-specific DNA adduct O(6)-carboxymethyl-guanine compared to chicken and pork, whereas nitrite curing had no significant effect. This study confirms previously reported evidence that heme-Fe is involved in the epidemiological association between red meat consumption and colorectal cancer, but questions the role of nitrite curing in this association.

  3. A 3D Model of Double-Helical DNA Showing Variable Chemical Details

    ERIC Educational Resources Information Center

    Cady, Susan G.

    2005-01-01

    Since the first DNA model was created approximately 50 years ago using molecular models, students and teachers have been building simplified DNA models from various practical materials. A 3D double-helical DNA model, made by placing beads on a wire and stringing beads through holes in plastic canvas, is described. Suggestions are given to enhance…

  4. Mathematical modeling of DNA's transcription process for the cancer study

    NASA Astrophysics Data System (ADS)

    Morales-Peñaloza, A.; Meza-López, C. D.; Godina-Nava, J. J.

    2012-10-01

    The cancer is a phenomenon caused by an anomaly in the DNA's transcription process, therefore it is necessary to known how such anomaly is generated in order to implement alternative therapies to combat it. We propose to use mathematical modeling to treat the problem. Is implemented a simulation of the process of transcription and are studied the transport properties in the heterogeneous case using nonlinear dynamics.

  5. Modeling the Biodegradability of Chemical Compounds Using the Online CHEmical Modeling Environment (OCHEM)

    PubMed Central

    Vorberg, Susann

    2013-01-01

    Abstract Biodegradability describes the capacity of substances to be mineralized by free‐living bacteria. It is a crucial property in estimating a compound’s long‐term impact on the environment. The ability to reliably predict biodegradability would reduce the need for laborious experimental testing. However, this endpoint is difficult to model due to unavailability or inconsistency of experimental data. Our approach makes use of the Online Chemical Modeling Environment (OCHEM) and its rich supply of machine learning methods and descriptor sets to build classification models for ready biodegradability. These models were analyzed to determine the relationship between characteristic structural properties and biodegradation activity. The distinguishing feature of the developed models is their ability to estimate the accuracy of prediction for each individual compound. The models developed using seven individual descriptor sets were combined in a consensus model, which provided the highest accuracy. The identified overrepresented structural fragments can be used by chemists to improve the biodegradability of new chemical compounds. The consensus model, the datasets used, and the calculated structural fragments are publicly available at http://ochem.eu/article/31660. PMID:27485201

  6. Encapsulation of a model compound in pectin delays its release from a biobased polymeric material

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A model compound was encapsulated in pectin and then extruded with thermoplastic starch to form a composite. The intended product was a food-contact tray made of biobased polymers infused with an anti-microbial agent; however, caffeine was used as the model compound in the preliminary work. The mode...

  7. Modeling emissions of volatile organic compounds from silage

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Photochemical smog is a major air pollution problem and a significant cause of premature death in the U.S. Smog forms in the presence of volatile organic compounds (VOCs), which are emitted primarily from industry and motor vehicles in the U.S. However, dairy farms may be an important source in so...

  8. MICROBIAL VOLATILE ORGANIC COMPOUND EMISSION RATES AND EXPOSURE MODEL

    EPA Science Inventory

    This paper presents the results from a study that examined microbial volatile organic compound (MVOC) emissions from six fungi and one bacterial species (Streptomyces spp.) commonly found in indoor environments. Data are presented on peak emission rates from inoculated agar plate...

  9. Thinner inhalation effects on oxidative stress and DNA repair in a rat model of abuse.

    PubMed

    Martínez-Alfaro, Minerva; Cárabez-Trejo, Alfonso; Gallegos-Corona, Marco-Antonio; Pedraza-Aboytes, Gustavo; Hernández-Chan, Nancy Georgina; Leo-Amador, Guillermo Enrique

    2010-04-01

    Humans can come into contact with thinner by occupational exposure or by intentional inhalation abuse. Numerous studies of workers for genotoxic effects of thinner exposure have yielded conflicting results, perhaps because co-exposure to variable other compounds cannot be avoided in workplace exposure studies. In contrast, there is no data concerning the genotoxic effects of intentional inhalation abuse. The aim of this project was to examine the genotoxic effects of thinner inhalation in an animal model of thinner abuse (rats exposed to 3000 ppm toluene, a high solvent concentration over a very short, 15 min time period, twice a day for 6 weeks). The data presented here provides evidence that thinner inhalation in our experimental conditions is able to induce weight loss, lung abnormalities and oxidative stress. This oxidative stress induces oxidative DNA damage that is not a characteristic feature of genotoxic damage. No significant difference in DNA damage and DNA repair (biomarkers of genotoxicity) in lymphocytes from thinner-treated and control rats was found. Lead treatment was used as a positive control in these assays. Finally, bone marrow was evaluated as a biomarker of cellular alteration associated with thinner inhalation. The observed absence of hemopoietic and genetic toxicity could be explained in part by the absence of benzene, the only carcinogenic component of thinner; however, benzene is no longer a common component of thinner. In conclusion, thinner did not cause genotoxic effects in an experimental model of intentional abuse despite the fact that thinner inhalation induces oxidative stress.

  10. SCID mice containing muscle with human mitochondrial DNA mutations. An animal model for mitochondrial DNA defects.

    PubMed Central

    Clark, K M; Watt, D J; Lightowlers, R N; Johnson, M A; Relvas, J B; Taanman, J W; Turnbull, D M

    1998-01-01

    Defects of the mitochondrial genome are important causes of disease. Despite major advances in our investigation of patients, there is no effective therapy. Progress in this area is limited by the absence of any animal models in which we can evaluate treatment. To develop such a model we have injected human myoblasts into the tibialis anterior of SCID mice after inducing necrosis. After injection of normal human myoblasts, regenerating fibers expressed human beta-spectrin, confirming they were derived from fusion of human myoblasts. The stability of the muscle fibers was inferred by demonstrating the formation of motor end plates on the regenerating fibers. In addition, we show the presence of human cytochrome c oxidase subunit II, which is encoded by the mitochondrial genome, in the regenerated fibers. After injection of human myoblasts containing either the A8344G or the T8993C heteroplasmic mitochondrial DNA mutations, human beta-spectrin positive fibers were found to contain the mutation at a similar level to the injected myoblasts. These studies highlight the potential value of this model for the study of mitochondrial DNA defects. PMID:9854044

  11. Structural modeling for DNA binding to antioxidants resveratrol, genistein and curcumin.

    PubMed

    N'soukpoé-Kossi, C N; Bourassa, P; Mandeville, J S; Bekale, L; Tajmir-Riahi, H A

    2015-10-01

    Several models are presented here for the bindings of the antioxidant polyphenols resveratrol, genistein and curcumin with DNA in aqueous solution at physiological conditions. Multiple spectroscopic methods and molecular modeling were used to locate the binding sites of these polyphenols with DNA duplex. Structural models showed that intercalation is more stable for resveratrol and genistein than groove bindings, while curcumin interaction is via DNA grooves. Docking showed more stable complexes formed with resveratrol and genistein than curcumin with the free binding energies of -4.62 for resveratrol-DNA (intercalation), -4.28 for resveratrol-DNA (groove binding), -4.54 for genistein-DNA (intercalation), -4.38 for genistein-DNA (groove binding) and -3.84 kcal/mol for curcumin-DNA (groove binding). The free binding energies show polyphenol-DNA complexation is spontaneous at room temperature. At high polyphenol concentration a major DNA aggregation occurred, while biopolymer remained in B-family structure.

  12. DNA.

    ERIC Educational Resources Information Center

    Felsenfeld, Gary

    1985-01-01

    Structural form, bonding scheme, and chromatin structure of and gene-modification experiments with deoxyribonucleic acid (DNA) are described. Indicates that DNA's double helix is variable and also flexible as it interacts with regulatory and other molecules to transfer hereditary messages. (DH)

  13. DNA Cleavage, Cytotoxic Activities, and Antimicrobial Studies of Ternary Copper(II) Complexes of Isoxazole Schiff Base and Heterocyclic Compounds

    PubMed Central

    Chityala, Vijay Kumar; Sathish Kumar, K.; Macha, Ramesh; Tigulla, Parthasarathy; Shivaraj

    2014-01-01

    Novel mixed ligand bivalent copper complexes [Cu. L. A. ClO4] and [Cu. L. A] where “L” is Schiff bases, namely 2-((3,4-dimethylisoxazol-5-ylimino)methyl)-4-bromophenol (DMIIMBP)/2-((3,4-dimethylisoxazol-5-ylimino)methyl)-4-chlorophenol (DMIIMCP), and “A” is heterocyclic compound, such as 1,10-phenanthroline (phen)/2,21-bipyridyl (bipy)/8-hydroxyquinoline (oxine)/5-chloro-8-hydroxyquinoline (5-Cl-oxine), have been synthesized. These complexes have been characterized by IR, UV-Vis, ESR, elemental analysis, magnetic moments, TG, and DTA. On the basis of spectral studies and analytical data, five-coordinated square pyramidal/four-coordinated square planar geometry is assigned to all complexes. The ligands and their ternary complexes with Cu(II) have been screened for antimicrobial activity against bacteria and fungi by paper disc method. The antimicrobial studies of Schiff bases and their metal complexes showed significant activity and further it is observed that the metal complexes showed more activity than corresponding Schiff bases. In vitro antitumor activity of Cu(II) complexes was assayed against human cervical carcinoma (HeLa) cancer cells and it was observed that few complexes exhibit good antitumor activity on HeLa cell lines. The DNA cleavage studies have also been carried out on pBR 322 and it is observed that these Cu(II) complexes are capable of cleaving supercoiled plasmid DNA in the presence of H2O2 and UV light. PMID:24895493

  14. Reference-based gene model prediction on DNA contigs

    SciTech Connect

    Xu, Y.; Uberbacher, E.C.

    1997-01-01

    This paper presents an algorithm for constructing multiple gene models on a set of contigs of a large genomic clone. The algorithm first uses pattern recognition-based methods to locate exons or partial exons in each contig, and then applies protein homology or EST information from the databases, as reference models, to parse the predicted exons into gene models. In the phase of gene model construction, the algorithm uses a unified framework for genes ranging from situation with homologous proteins/ESTs to no homologous protein/EST in the database. By exploiting protein homology or EST information, the algorithm is able to (1) parse exons into multiple gene models over a set of DNA contigs (possibly unoriented and unordered); (2) remove falsely predicted exons; and (3) identify and locate exons missed by the initial exon prediction.

  15. Altered DNA Binding and Amplification of Human Breast Cancer Suppressor Gene BRCA1 Induced by a Novel Antitumor Compound, [Ru(η6-p-phenylethacrynate)Cl2(pta)

    PubMed Central

    Chakree, Korawan; Ovatlarnporn, Chitchamai; Dyson, Paul J.; Ratanaphan, Adisorn

    2012-01-01

    The ruthenium-based complex [Ru(η6-p-phenylethacrynate)Cl2(pta)] (pta = 1,3,5-triaza-7-phosphatricyclo-[3.3.1.1]decane), termed ethaRAPTA, is an interesting antitumor compound. The elucidation of the molecular mechanism of drug activity is central to the drug development program. To this end, we have characterized the ethaRAPTA interaction with DNA, including probing the sequence specific modified DNA structural stability and DNA amplification using the breast cancer suppressor gene 1 (BRCA1) of human breast and colon adenocarcinoma cell lines as models. The preference of ethaRAPTA base binding is in the order A > G > T > C. Once modified, the ethaRAPTA-induced BRCA1 structure has higher thermal stability than the modified equivalents of its related compound, RAPTA-C. EthaRAPTA exhibits a higher efficiency than RAPTA-C in inhibiting BRCA1 amplification. With respect to both compounds, the inhibition of BRCA1 amplification is more effective in an isolated system than in cell lines. These data provide evidence that will help to understand the process of elucidating the pathways involved in the response induced by ethaRAPTA. PMID:23202946

  16. Misfit layer compounds and ferecrystals: Model systems for thermoelectric nanocomposites

    DOE PAGES

    Merrill, Devin R.; Moore, Daniel B.; Bauers, Sage R.; ...

    2015-04-22

    A basic summary of thermoelectric principles is presented in a historical context, following the evolution of the field from initial discovery to modern day high-zT materials. A specific focus is placed on nanocomposite materials as a means to solve the challenges presented by the contradictory material requirements necessary for efficient thermal energy harvest. Misfit layer compounds are highlighted as an example of a highly ordered anisotropic nanocomposite system. Their layered structure provides the opportunity to use multiple constituents for improved thermoelectric performance, through both enhanced phonon scattering at interfaces and through electronic interactions between the constituents. Recently, a class ofmore » metastable, turbostratically-disordered misfit layer compounds has been synthesized using a kinetically controlled approach with low reaction temperatures. The kinetically stabilized structures can be prepared with a variety of constituent ratios and layering schemes, providing an avenue to systematically understand structure-function relationships not possible in the thermodynamic compounds. We summarize the work that has been done to date on these materials. The observed turbostratic disorder has been shown to result in extremely low cross plane thermal conductivity and in plane thermal conductivities that are also very small, suggesting the structural motif could be attractive as thermoelectric materials if the power factor could be improved. The first 10 compounds in the [(PbSe)1+δ]m(TiSe₂)n family (m, n ≤ 3) are reported as a case study. As n increases, the magnitude of the Seebeck coefficient is significantly increased without a simultaneous decrease in the in-plane electrical conductivity, resulting in an improved thermoelectric power factor.« less

  17. Misfit layer compounds and ferecrystals: Model systems for thermoelectric nanocomposites

    SciTech Connect

    Merrill, Devin R.; Moore, Daniel B.; Bauers, Sage R.; Falmbigl, Matthias; Johnson, David C.

    2015-04-22

    A basic summary of thermoelectric principles is presented in a historical context, following the evolution of the field from initial discovery to modern day high-zT materials. A specific focus is placed on nanocomposite materials as a means to solve the challenges presented by the contradictory material requirements necessary for efficient thermal energy harvest. Misfit layer compounds are highlighted as an example of a highly ordered anisotropic nanocomposite system. Their layered structure provides the opportunity to use multiple constituents for improved thermoelectric performance, through both enhanced phonon scattering at interfaces and through electronic interactions between the constituents. Recently, a class of metastable, turbostratically-disordered misfit layer compounds has been synthesized using a kinetically controlled approach with low reaction temperatures. The kinetically stabilized structures can be prepared with a variety of constituent ratios and layering schemes, providing an avenue to systematically understand structure-function relationships not possible in the thermodynamic compounds. We summarize the work that has been done to date on these materials. The observed turbostratic disorder has been shown to result in extremely low cross plane thermal conductivity and in plane thermal conductivities that are also very small, suggesting the structural motif could be attractive as thermoelectric materials if the power factor could be improved. The first 10 compounds in the [(PbSe)1+δ]m(TiSe₂)n family (m, n ≤ 3) are reported as a case study. As n increases, the magnitude of the Seebeck coefficient is significantly increased without a simultaneous decrease in the in-plane electrical conductivity, resulting in an improved thermoelectric power factor.

  18. Clusters of DNA damage induced by ionizing radiation: Formation of short DNA fragments. I. Theoretical modeling

    SciTech Connect

    Holley, W.R.; Chatterjee, A.

    1996-02-01

    We have developed a general theoretical model for the interaction of ionizing radiation with chromatin. Chromatin is modeled as a 30-nm-diameter solenoidal fiber composed of 20 turns of nucleosomes, 6 nucleosomes per turn. Charged-particle tracks are modeled by partitioning the energy deposition between primary track core, resulting from glancing collisions with 100 eV or less per event, and {delta} rays due to knock-on collisions involving energy transfers > 100 eV. A Monte Carlo simulation incorporates damages due to the following molecular mechanisms: (1) ionization of water molecules leading to the formation of {circ}OH, {circ}H, e{sub aq}, etc.; {circ}OH attack on sugar molecules leading to strand breaks; {circ}OH attack on bases; direct ionization of the sugar molecules leading to strand breaks; direct ionization of the bases. Our calculations predict significant clustering of damage both locally, over regions up to 40 hp and over regions extending to several kilobase pairs. A characteristic feature of the regional damage predicted by our model is the production of short fragments of DNA associated with multiple nearby strand breaks. Such fragments have subsequently been detected experimentally and are reported in an accompanying paper after exposure to both high- and low-LET radiation. The overall measured yields agree well quantitatively with the theoretical predictions. Our theoretical results predict the existence of a strong peak at about 85 bp, which represents the revolution period about the nucleosome. Other peaks at multiples of about 1,000 bp correspond to the periodicity of the particular solenoid model of chromatin used in these calculations. Theoretical results in combination with experimental data on fragmentation spectra may help determine the consensus or average structure of the chromatin fibers in mammalian DNA. 27 refs., 7 figs.

  19. Phi29 Connector-DNA Interactions Govern DNA Crunching and Rotation, Supporting the Check-Valve Model

    PubMed Central

    Kumar, Rajendra; Grubmüller, Helmut

    2016-01-01

    During replication of the ϕ29 bacteriophage inside a bacterial host cell, a DNA packaging motor transports the viral DNA into the procapsid against a pressure difference of up to 40 ± 20 atm. Several models have been proposed for the underlying molecular mechanism. Here we have used molecular dynamics simulations to examine the role of the connector part of the motor, and specifically the one-way revolution and the push-roll model. We have focused at the structure and intermolecular interactions between the DNA and the connector, for which a near-complete structure is available. The connector is found to induce considerable DNA deformations with respect to its canonical B-form. We further assessed by force-probe simulations to which extent the connector is able to prevent DNA leakage and found that the connector can act as a partial one-way valve by a check-valve mechanism via its mobile loops. Analysis of the geometry, flexibility, and energetics of channel lysine residues suggested that this arrangement of residues is incompatible with the observed DNA packaging step-size of ∼2.5 bp, such that the step-size is probably determined by the other components of the motor. Previously proposed DNA revolution and rolling motions inside the connector channel are both found implausible due to structural entanglement between the DNA and connector loops that have not been resolved in the crystal structure. Rather, in the simulations, the connector facilitates minor DNA rotation during the packaging process compatible with recent optical-tweezers experiments. Combined with the available experimental data, our simulation results suggest that the connector acts as a check-valve that prevents DNA leakage and induces DNA compression and rotation during DNA packaging. PMID:26789768

  20. A sequence-dependent rigid-base model of DNA

    NASA Astrophysics Data System (ADS)

    Gonzalez, O.; Petkevičiutė, D.; Maddocks, J. H.

    2013-02-01

    A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can

  1. Compound prioritization methods increase rates of chemical probe discovery in model organisms

    PubMed Central

    Wallace, Iain M; Urbanus, Malene L; Luciani, Genna M; Burns, Andrew R; Han, Mitchell KL; Wang, Hao; Arora, Kriti; Heisler, Lawrence E; Proctor, Michael; St. Onge, Robert P; Roemer, Terry; Roy, Peter J; Cummins, Carolyn L; Bader, Gary D; Nislow, Corey; Giaever, Guri

    2011-01-01

    SUMMARY Pre-selection of compounds that are more likely to induce a phenotype can increase the efficiency and reduce the costs for model organism screening. To identify such molecules, we screened ~81,000 compounds in S. cerevisiae and identified ~7,500 that inhibit cell growth. Screening these growth-inhibitory molecules across a diverse panel of model organisms resulted in an increased phenotypic hit-rate. This data was used to build a model to predict compounds that inhibit yeast growth. Empirical and in silico application of the model enriched the discovery of bioactive compounds in diverse model organisms. To demonstrate the potential of these molecules as lead chemical probes we used chemogenomic profiling in yeast and identified specific inhibitors of lanosterol synthase and of stearoyl-CoA 9-desaturase. As community resources, the ~7,500 growth-inhibitory molecules has been made commercially available and the computational model and filter used are provided. PMID:22035796

  2. Modelling DNA origami self-assembly at the domain level

    SciTech Connect

    Dannenberg, Frits; Kwiatkowska, Marta; Dunn, Katherine E.; Bath, Jonathan; Turberfield, Andrew J.; Ouldridge, Thomas E.

    2015-10-28

    We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

  3. Modelling DNA origami self-assembly at the domain level

    NASA Astrophysics Data System (ADS)

    Dannenberg, Frits; Dunn, Katherine E.; Bath, Jonathan; Kwiatkowska, Marta; Turberfield, Andrew J.; Ouldridge, Thomas E.

    2015-10-01

    We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

  4. The S=1 Underscreened Anderson Lattice model for Uranium compounds

    NASA Astrophysics Data System (ADS)

    Thomas, C.; Simões, A. S. R.; Iglesias, J. R.; Lacroix, C.; Perkins, N. B.; Coqblin, B.

    2011-01-01

    Magnetic properties of uranium and neptunium compounds showing coexistence of the Kondo effect and ferromagnetic order are investigated within the degenerate Anderson Lattice Hamiltonian, describing a 5f2 electronic configuration with S = 1 spins. Through the Schrieffer-Wolff transformation, both an exchange Kondo interaction for the S = 1 f-spins and an effective f-band term are obtained, allowing to describe the coexistence of Kondo effect and ferromagnetic ordering and a weak delocalization of the 5f-electrons. We calculate the Kondo and Curie temperatures and we can account for the pressure dependence of the Curie temperature of UTe.

  5. Model-based prediction of human hair color using DNA variants.

    PubMed

    Branicki, Wojciech; Liu, Fan; van Duijn, Kate; Draus-Barini, Jolanta; Pośpiech, Ewelina; Walsh, Susan; Kupiec, Tomasz; Wojas-Pelc, Anna; Kayser, Manfred

    2011-04-01

    Predicting complex human phenotypes from genotypes is the central concept of widely advocated personalized medicine, but so far has rarely led to high accuracies limiting practical applications. One notable exception, although less relevant for medical but important for forensic purposes, is human eye color, for which it has been recently demonstrated that highly accurate prediction is feasible from a small number of DNA variants. Here, we demonstrate that human hair color is predictable from DNA variants with similarly high accuracies. We analyzed in Polish Europeans with single-observer hair color grading 45 single nucleotide polymorphisms (SNPs) from 12 genes previously associated with human hair color variation. We found that a model based on a subset of 13 single or compound genetic markers from 11 genes predicted red hair color with over 0.9, black hair color with almost 0.9, as well as blond, and brown hair color with over 0.8 prevalence-adjusted accuracy expressed by the area under the receiver characteristic operating curves (AUC). The identified genetic predictors also differentiate reasonably well between similar hair colors, such as between red and blond-red, as well as between blond and dark-blond, highlighting the value of the identified DNA variants for accurate hair color prediction.

  6. Homology modeling of NAD+-dependent DNA ligase of the Wolbachia endosymbiont of Brugia malayi and its drug target potential using dispiro-cycloalkanones.

    PubMed

    Shrivastava, Nidhi; Nag, Jeetendra K; Pandey, Jyoti; Tripathi, Rama Pati; Shah, Priyanka; Siddiqi, Mohammad Imran; Misra-Bhattacharya, Shailja

    2015-07-01

    Lymphatic filarial nematodes maintain a mutualistic relationship with the endosymbiont Wolbachia. Depletion of Wolbachia produces profound defects in nematode development, fertility, and viability and thus has great promise as a novel approach for treating filarial diseases. NAD(+)-dependent DNA ligase is an essential enzyme of DNA replication, repair, and recombination. Therefore, in the present study, the antifilarial drug target potential of the NAD(+)-dependent DNA ligase of the Wolbachia symbiont of Brugia malayi (wBm-LigA) was investigated using dispiro-cycloalkanone compounds. Dispiro-cycloalkanone specifically inhibited the nick-closing and cohesive-end ligation activities of the enzyme without inhibiting human or T4 DNA ligase. The mode of inhibition was competitive with the NAD(+) cofactor. Docking studies also revealed the interaction of these compounds with the active site of the target enzyme. The adverse effects of these inhibitors were observed on adult and microfilarial stages of B. malayi in vitro, and the most active compounds were further monitored in vivo in jirds and mastomys rodent models. Compounds 1, 2, and 5 had severe adverse effects in vitro on the motility of both adult worms and microfilariae at low concentrations. Compound 2 was the best inhibitor, with the lowest 50% inhibitory concentration (IC50) (1.02 μM), followed by compound 5 (IC50, 2.3 μM) and compound 1 (IC50, 2.9 μM). These compounds also exhibited the same adverse effect on adult worms and microfilariae in vivo (P < 0.05). These compounds also tremendously reduced the wolbachial load, as evident by quantitative real-time PCR (P < 0.05). wBm-LigA thus shows great promise as an antifilarial drug target, and dispiro-cycloalkanone compounds show great promise as antifilarial lead candidates.

  7. Homology Modeling of NAD+-Dependent DNA Ligase of the Wolbachia Endosymbiont of Brugia malayi and Its Drug Target Potential Using Dispiro-Cycloalkanones

    PubMed Central

    Shrivastava, Nidhi; Nag, Jeetendra K.; Pandey, Jyoti; Tripathi, Rama Pati; Shah, Priyanka; Siddiqi, Mohammad Imran

    2015-01-01

    Lymphatic filarial nematodes maintain a mutualistic relationship with the endosymbiont Wolbachia. Depletion of Wolbachia produces profound defects in nematode development, fertility, and viability and thus has great promise as a novel approach for treating filarial diseases. NAD+-dependent DNA ligase is an essential enzyme of DNA replication, repair, and recombination. Therefore, in the present study, the antifilarial drug target potential of the NAD+-dependent DNA ligase of the Wolbachia symbiont of Brugia malayi (wBm-LigA) was investigated using dispiro-cycloalkanone compounds. Dispiro-cycloalkanone specifically inhibited the nick-closing and cohesive-end ligation activities of the enzyme without inhibiting human or T4 DNA ligase. The mode of inhibition was competitive with the NAD+ cofactor. Docking studies also revealed the interaction of these compounds with the active site of the target enzyme. The adverse effects of these inhibitors were observed on adult and microfilarial stages of B. malayi in vitro, and the most active compounds were further monitored in vivo in jirds and mastomys rodent models. Compounds 1, 2, and 5 had severe adverse effects in vitro on the motility of both adult worms and microfilariae at low concentrations. Compound 2 was the best inhibitor, with the lowest 50% inhibitory concentration (IC50) (1.02 μM), followed by compound 5 (IC50, 2.3 μM) and compound 1 (IC50, 2.9 μM). These compounds also exhibited the same adverse effect on adult worms and microfilariae in vivo (P < 0.05). These compounds also tremendously reduced the wolbachial load, as evident by quantitative real-time PCR (P < 0.05). wBm-LigA thus shows great promise as an antifilarial drug target, and dispiro-cycloalkanone compounds show great promise as antifilarial lead candidates. PMID:25845868

  8. Long-range electron transfer in a model for DNA

    NASA Astrophysics Data System (ADS)

    Endres, R. G.; Cox, D. L.

    2001-03-01

    Long-range electron transfer (ET) between well separated donor (D) and acceptor (A) sites through quantum mechanical tunneling is essential to many biological processes like respiration, photosynthesis and possibly DNA repair and damage. We are investigating the distance dependence of the electronic transition matrix element H_DA and hence of the electron transfer rate in a model for DNA. Fluorescence quenching in DNA at D-A distances of 40 Åand more suggests ET with an unusually high decay length β-1 of order 10 Å (S.O.Kelley and J.K.Barton, in:Metal Ions in Biological Systems), A.Sigel and H.Sigel, Eds., Marcel Dekker, New York, Vol.36, 1999. Assuming strong electron interactions on the D complex and suitable energetics, this could be explained by formation of a many electron Kondo boundstate. We obtain H_DA from the splitting between the two lowest adiabatic electronic eigenenergies, which constitute the potential energy surfaces (PES) of the nuclear motion in lowest order Born-Oppenheimer approximation. The PES are constructed by coupling D and A to local breathing modes and by making a semi-analytical variational ansatz for the adiabatic eigenstates. The results from the PES are compared with results from the Mulliken-Hush algorithm.

  9. Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights.

    PubMed

    Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji

    2016-12-13

    Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

  10. DNA methylation in an engineered heart tissue model of cardiac hypertrophy: common signatures and effects of DNA methylation inhibitors.

    PubMed

    Stenzig, Justus; Hirt, Marc N; Löser, Alexandra; Bartholdt, Lena M; Hensel, Jan-Tobias; Werner, Tessa R; Riemenschneider, Mona; Indenbirken, Daniela; Guenther, Thomas; Müller, Christian; Hübner, Norbert; Stoll, Monika; Eschenhagen, Thomas

    2016-01-01

    DNA methylation affects transcriptional regulation and constitutes a drug target in cancer biology. In cardiac hypertrophy, DNA methylation may control the fetal gene program. We therefore investigated DNA methylation signatures and their dynamics in an in vitro model of cardiac hypertrophy based on engineered heart tissue (EHT). We exposed EHTs from neonatal rat cardiomyocytes to a 12-fold increased afterload (AE) or to phenylephrine (PE 20 µM) and compared DNA methylation signatures to control EHT by pull-down assay and DNA methylation microarray. A 7-day intervention sufficed to induce contractile dysfunction and significantly decrease promoter methylation of hypertrophy-associated upregulated genes such as Nppa (encoding ANP) and Acta1 (α-skeletal actin) in both intervention groups. To evaluate whether pathological consequences of AE are affected by inhibiting de novo DNA methylation we applied AE in the absence and presence of DNA methyltransferase (DNMT) inhibitors: 5-aza-2'-deoxycytidine (aza, 100 µM, nucleosidic inhibitor), RG108 (60 µM, non-nucleosidic) or methylene disalicylic acid (MDSA, 25 µM, non-nucleosidic). Aza had no effect on EHT function, but RG108 and MDSA partially prevented the detrimental consequences of AE on force, contraction and relaxation velocity. RG108 reduced AE-induced Atp2a2 (SERCA2a) promoter methylation. The results provide evidence for dynamic DNA methylation in cardiac hypertrophy and warrant further investigation of the potential of DNA methylation in the treatment of cardiac hypertrophy.

  11. Crystal structure of the adenovirus DNA binding protein reveals a hook-on model for cooperative DNA binding.

    PubMed Central

    Tucker, P A; Tsernoglou, D; Tucker, A D; Coenjaerts, F E; Leenders, H; van der Vliet, P C

    1994-01-01

    The adenovirus single-stranded DNA binding protein (Ad DBP) is a multifunctional protein required, amongst other things, for DNA replication and transcription control. It binds to single- and double-stranded DNA, as well as to RNA, in a sequence-independent manner. Like other single-stranded DNA binding proteins, it binds ssDNA, cooperatively. We report the crystal structure, at 2.6 A resolution, of the nucleic acid binding domain. This domain is active in DNA replication. The protein contains two zinc atoms in different, novel coordinations. The zinc atoms appear to be required for the stability of the protein fold rather than being involved in direct contacts with the DNA. The crystal structure shows that the protein contains a 17 amino acid C-terminal extension which hooks onto a second molecule, thereby forming a protein chain. Deletion of this C-terminal arm reduces cooperativity in DNA binding, suggesting a hook-on model for cooperativity. Based on this structural work and mutant studies, we propose that DBP forms a protein core around which the single-stranded DNA winds. Images PMID:8039495

  12. Aggregation of asphaltene model compounds using a porphyrin tethered to a carboxylic acid.

    PubMed

    Schulze, Matthias; Lechner, Marc P; Stryker, Jeffrey M; Tykwinski, Rik R

    2015-07-07

    A Ni(II) porphyrin functionalized with an alkyl carboxylic acid (3) has been synthesized to model the chemical behavior of the heaviest portion of petroleum, the asphaltenes. Specifically, porphyrin 3 is used in spectroscopic studies to probe aggregation with a second asphaltene model compound containing basic nitrogen (4), designed to mimic asphaltene behavior. NMR spectroscopy documents self-association of the porphyrin and aggregation with the second model compound in solution, and a Job's plot suggests a 1 : 2 stoichiometry for compounds 3 and 4.

  13. Insights into DNA-mediated interparticle interactions from a coarse-grained model

    NASA Astrophysics Data System (ADS)

    Ding, Yajun; Mittal, Jeetain

    2014-11-01

    DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA-functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions.

  14. ESTIMATING TRANSPORT AND DEPOSITION OF A SEMI-VOLATILE COMPOUND WITH A REGIONAL PHOTOCHEMICAL MODEL

    EPA Science Inventory

    To simulate the fate of compounds that are considered semi-volatile and toxic, we have modified a model for regional particulate matter. Our changes introduce a semi-volatile compound into the atmosphere as gaseous emissions from an area source. Once emitted, the gas can transf...

  15. Development of Novel Repellents Using Structure - Activity Modeling of Compounds in the USDA Archival Database

    DTIC Science & Technology

    2011-01-01

    used in efforts to develop QSAR models. Measurement of Repellent Efficacy Screening for Repellency of Compounds with Unknown Toxicology In screening...CPT) were used to develop Quantitative Structure Activity Relationship ( QSAR ) models to predict repellency. Successful prediction of novel...acylpiperidine QSAR models employed 4 descriptors to describe the relationship between structure and repellent duration. The ANN model of the carboxamides did not

  16. Nonlinear Model of the Specificity of DNA-Protein Interactions and Its Stability

    NASA Astrophysics Data System (ADS)

    Dwiputra, D.; Hidayat, W.; Khairani, R.; Zen, F. P.

    2016-08-01

    Specific DNA-protein interactions are fundamental processes of living cells. We propose a new model of DNA-protein interactions to explain the site specificity of the interactions. The hydrogen bonds between DNA base pairs and between DNA-protein peptide groups play a significant role in determination of the specific binding site. We adopt the Morse potential with coupling terms to construct the Hamiltonian of coupled oscillators representing the hydrogen bonds in which the depth of the potentials vary in the DNA chain. In this paper we investigate the stability of the model to determine the conditions satisfying the biological circumstances of the DNA-protein interactions.

  17. Solute transport model for trace organic neutral and charged compounds through nanofiltration and reverse osmosis membranes.

    PubMed

    Kim, Tae-Uk; Drewes, Jörg E; Scott Summers, R; Amy, Gary L

    2007-09-01

    Rejection of trace organic compounds, including disinfection by-products (DBPs) and pharmaceutical active compounds (PhACs), by high-pressure membranes has become a focus of public interest internationally in both drinking water treatment and wastewater reclamation/reuse. The ability to simulate, or even predict, the rejection of these compounds by high-pressure membranes, encompassing nanofiltration (NF) and reverse osmosis (RO), will improve process economics and expand membrane applications. The objective of this research is to develop a membrane transport model to account for diffusive and convective contributions to solute transport and rejection. After completion of cross-flow tests and diffusion cell tests with target compounds, modeling efforts were performed in accordance with a non-equilibrium thermodynamic transport equation. Comparing the percentages of convection and diffusion contributions to transport, convection is dominant for most compounds, but diffusion is important for more hydrophobic non-polar compounds. Convection is also more dominant for looser membranes (i.e., NF). In addition, higher initial compound concentrations and greater J(0)/k ratios contribute to solute fluxes more dominated by convection. Given the treatment objective of compound rejection, compound transport and rejection trends are inversely related.

  18. Performance of a new atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations

    NASA Astrophysics Data System (ADS)

    Bernal, M. A.; Sikansi, D.; Cavalcante, F.; Incerti, S.; Champion, C.; Ivanchenko, V.; Francis, Z.; Karamitros, M.

    2014-03-01

    We have recently developed an atomistic model of the B-DNA configuration, up to the 30-nm chromatin fiber. This model is intended to be used in Monte Carlo simulations of the DNA-radiation interaction, specifically in conjunction with the Geant4-DNA extension of the Geant4 Monte Carlo toolkit. In this work, 11449 parallel chromatin fibers have been arranged within a cube mimicking a cell nucleus containing about 6.5×109 base pairs. Each atom in the model is represented by a sphere with the corresponding van der Waals radius. Direct single, double and total DNA strand break yields due to the impact of protons and alpha particles with LET ranging from 4.57 to 207.1 keV/μm have been determined. Also, the corresponding site-hit probabilities have been calculated.

  19. Hands on Group Work Paper Model for Teaching DNA Structure, Central Dogma and Recombinant DNA

    ERIC Educational Resources Information Center

    Altiparmak, Melek; Nakiboglu Tezer, Mahmure

    2009-01-01

    Understanding life on a molecular level is greatly enhanced when students are given the opportunity to visualize the molecules. Especially understanding DNA structure and function is essential for understanding key concepts of molecular biology such as DNA, central dogma and the manipulation of DNA. Researches have shown that undergraduate…

  20. Energetics of hydrogen bonding in proteins: a model compound study.

    PubMed Central

    Habermann, S. M.; Murphy, K. P.

    1996-01-01

    Differences in the energetics of amide-amide and amide-hydroxyl hydrogen bonds in proteins have been explored from the effect of hydroxyl groups on the structure and dissolution energetics of a series of crystalline cyclic dipeptides. The calorimetrically determined energetics are interpreted in light of the crystal structures of the studied compounds. Our results indicate that the amide-amide and amide-hydroxyl hydrogen bonds both provide considerable enthalpic stability, but that the amide-amide hydrogen bond is about twice that of the amide-hydroxyl. Additionally, the interaction of the hydroxyl group with water is seen most readily in its contributions to entropy and heat capacity changes. Surprisingly, the hydroxyl group shows weakly hydrophobic behavior in terms of these contributions. These results can be used to understand the effects of mutations on the stability of globular proteins. PMID:8819156

  1. Double-stranded DNA organization in bacteriophage heads: An alternative toroid-based model

    SciTech Connect

    Hud, N.V.

    1995-10-01

    Studies of the organization of double-stranded DNA within bacteriophage heads during the past four decades have produced a wealth of data. However, despite the presentation of numerous models, the true organization of DNA within phage heads remains unresolved. The observations of toroidal DNA structures in electron micrographs of phage lysates have long been cited as support for the organization of DNA in a spool-like fashion. This particular model, like all other models, has not been found to be consistent with all available data. Recently, the authors proposed that DNA within toroidal condensates produced in vitro is organized in a manner significantly different from that suggested by the spool model. This new toroid model has allowed the development of an alternative model for DNA organization within bacteriophage heads that is consistent with a wide range of biophysical data. Here the authors propose that bacteriophage DNA is packaged in a toroid that is folded into a highly compact structure.

  2. MODELING VOLATILE ORGANIC COMPOUND PHARMACOKINETICS IN RAT PUPS

    EPA Science Inventory

    PBPK model predictions of internal dosimetry in young rats were compared to adult animals for benzene, chloroform (CHL), methylene chloride, methyl ethly ketone (MEK), perchloroethylene, and trichloroethylene.

  3. Identifying developmental vascular disruptor compounds using a predictive signature and alternative toxicity models

    EPA Science Inventory

    Identifying Developmental Vascular Disruptor Compounds Using a Predictive Signature and Alternative Toxicity Models Presenting Author: Tamara Tal Affiliation: U.S. EPA/ORD/ISTD, RTP, NC, USA Chemically induced vascular toxicity during embryonic development can result in a wide...

  4. Indoor Residence Times of Semivolatile Organic Compounds: Model Estimation and Field Evaluation

    EPA Science Inventory

    Indoor residence times of semivolatile organic compounds (SVOCs) are a major and mostly unavailable input for residential exposure assessment. We calculated residence times for a suite of SVOCs using a fugacity model applied to residential environments. Residence times depend on...

  5. Molecular modeling and spectroscopic studies of semustine binding with DNA and its comparison with lomustine-DNA adduct formation.

    PubMed

    Agarwal, Shweta; Chadha, Deepti; Mehrotra, Ranjana

    2015-01-01

    Chloroethyl nitrosoureas constitute an important family of cancer chemotherapeutic agents, used in the treatment of various types of cancer. They exert antitumor activity by inducing DNA interstrand cross-links. Semustine, a chloroethyl nitrosourea, is a 4-methyl derivative of lomustine. There exist some interesting reports dealing with DNA-binding properties of chloroethyl nitrosoureas; however, underlying mechanism of cytotoxicity caused by semustine has not been precisely and completely delineated. The present work focuses on understanding semustine-DNA interaction to comprehend its anti-proliferative action at molecular level using various spectroscopic techniques. Attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy is used to determine the binding site of semustine on DNA. Conformational transition in DNA after semustine complexation is investigated using circular dichroism (CD) spectroscopy. Stability of semustine-DNA complexes is determined using absorption spectroscopy. Results of the present study demonstrate that semustine performs major-groove-directed DNA alkylation at guanine residues in an incubation-time-drug-concentration-dependent manner. CD spectral outcomes suggest partial transition of DNA from native B-conformation to C-form. Calculated binding constants (Ka) for semustine and lomustine interactions with DNA are 1.53 × 10(3) M(-1) and 8.12 × 10(3) M(-1), respectively. Moreover, molecular modeling simulation is performed to predict preferential binding orientation of semustine with DNA that corroborates well with spectral outcomes. Results based on comparative study of DNA-binding properties of semustine and lomustine, presented here, may establish a correlation between molecular structure and cytotoxicity of chloroethyl nitrosoureas that may be instrumental in the designing and synthesis of new nitrosourea therapeutics possessing better efficacy and fewer side effects.

  6. From organic superconductors to DNA: Fragment orbital-based model

    NASA Astrophysics Data System (ADS)

    Castet, Frédéric; Ducasse, Laurent; Fritsch, Alain

    A semi-empirical valence bond/Hartree-Fock (VB/HF) method is developed to calculate one- and two-electron interactions between molecular fragments in conducting supramolecular stacks. This fragment orbital-based formalism allows for consistent extraction of an effective Hamiltonian defined as a "frontier orbital" model. This Hamiltonian quantitatively describes transfer and electrostatic interactions between conducting electrons, while reducing the active space so dramatically that the electronic eigenstates of very large systems may be investigated. The capabilities of the VB/HF method are illustrated on two different supramolecular stacks involving a π-π interacting fragment. In the first part of this study, the framework of the VB/HF method is used to evaluate the relative magnitude of the electronic interactions between conduction electrons in organic conductors and superconductors derived from Bechgaard salts. In the second part of this study, the VB/HF formalism is extended to derive an effective model for conduction holes along doped DNA double strands. Transferable intra- and intersite parameters were first evaluated from VB/HF calculations carried out on nucleoside pairs. From this interaction databank, the effective Hamiltonian of any type of nucleoside sequence can be defined. The thermalized charge distribution for a single hole delocalized along a DNA sequence containing 240 Watson-Crick pairs is then calculated and compared with the experimental yields of damage revealed by photocleavage experiments.

  7. Evidence for a transition state model compound of in-plane vinylic SN2 reaction.

    PubMed

    Yamaguchi, Torahiko; Yamamoto, Yohsuke; Fujiwara, Yoshihisa; Tanimoto, Yoshifumi

    2005-06-23

    [reaction: see text] To isolate a transition state model compound of an in-plane vinylic S(N)2 reaction, vinyl bromide 6 bearing a newly synthesized tridentate ligand derived from 1,8-dimethoxythioxanthen-9-one (5) was prepared as a precursor. Although irradiation of 6 gave demethylated benzofuran 12, a transient broad peak which indicates formation of the desired transition state model compound was observed in the laser flash photolytic study.

  8. Marcus model of spontaneous point mutation in DNA

    NASA Astrophysics Data System (ADS)

    Turaeva, N.; Brown-Kennerly, V.

    2015-11-01

    The theoretical model of Löwdin's mechanism of spontaneous mutation based on 2D Marcus theory of DPT has been proposed in this work. The equation for the kinetics of DPT during DNA replication has been established, and the expression for the probability of spontaneous mutation has been received. The probability of spontaneous mutation formation has been estimated for tautomeric G∗-C∗ complexes, which is in the range of experimental results. The probability of spontaneous mutation as a function of temperature, replication rate, and solvent effect has been discussed. It increases with temperature and decreases with replication rate. The solvent and pH effects on the probability of spontaneous mutation can also be discussed within the framework of the model.

  9. Hepatic 3D spheroid models for the detection and study of compounds with cholestatic liability

    PubMed Central

    Hendriks, Delilah F. G.; Fredriksson Puigvert, Lisa; Messner, Simon; Mortiz, Wolfgang; Ingelman-Sundberg, Magnus

    2016-01-01

    Drug-induced cholestasis (DIC) is poorly understood and its preclinical prediction is mainly limited to assessing the compound’s potential to inhibit the bile salt export pump (BSEP). Here, we evaluated two 3D spheroid models, one from primary human hepatocytes (PHH) and one from HepaRG cells, for the detection of compounds with cholestatic liability. By repeatedly co-exposing both models to a set of compounds with different mechanisms of hepatotoxicity and a non-toxic concentrated bile acid (BA) mixture for 8 days we observed a selective synergistic toxicity of compounds known to cause cholestatic or mixed cholestatic/hepatocellular toxicity and the BA mixture compared to exposure to the compounds alone, a phenomenon that was more pronounced after extending the exposure time to 14 days. In contrast, no such synergism was observed after both 8 and 14 days of exposure to the BA mixture for compounds that cause non-cholestatic hepatotoxicity. Mechanisms behind the toxicity of the cholestatic compound chlorpromazine were accurately detected in both spheroid models, including intracellular BA accumulation, inhibition of ABCB11 expression and disruption of the F-actin cytoskeleton. Furthermore, the observed synergistic toxicity of chlorpromazine and BA was associated with increased oxidative stress and modulation of death receptor signalling. Combined, our results demonstrate that the hepatic spheroid models presented here can be used to detect and study compounds with cholestatic liability. PMID:27759057

  10. Speciation of volatile organic compound emissions for regional air quality modeling of particulate matter and ozone

    NASA Astrophysics Data System (ADS)

    Makar, P. A.; Moran, M. D.; Scholtz, M. T.; Taylor, A.

    2003-01-01

    A new classification scheme for the speciation of organic compound emissions for use in air quality models is described. The scheme uses 81 organic compound classes to preserve both net gas-phase reactivity and particulate matter (PM) formation potential. Chemical structure, vapor pressure, hydroxyl radical (OH) reactivity, freezing point/boiling point, and solubility data were used to create the 81 compound classes. Volatile, semivolatile, and nonvolatile organic compounds are included. The new classification scheme has been used in conjunction with the Canadian Emissions Processing System (CEPS) to process 1990 gas-phase and particle-phase organic compound emissions data for summer and winter conditions for a domain covering much of eastern North America. A simple postprocessing model was used to analyze the speciated organic emissions in terms of both gas-phase reactivity and potential to form organic PM. Previously unresolved compound classes that may have a significant impact on ozone formation include biogenic high-reactivity esters and internal C6-8 alkene-alcohols and anthropogenic ethanol and propanol. Organic radical production associated with anthropogenic organic compound emissions may be 1 or more orders of magnitude more important than biogenic-associated production in northern United States and Canadian cities, and a factor of 3 more important in southern U.S. cities. Previously unresolved organic compound classes such as low vapour pressure PAHs, anthropogenic diacids, dialkyl phthalates, and high carbon number alkanes may have a significant impact on organic particle formation. Primary organic particles (poorly characterized in national emissions databases) dominate total organic particle concentrations, followed by secondary formation and primary gas-particle partitioning. The influence of the assumed initial aerosol water concentration on subsequent thermodynamic calculations suggests that hydrophobic and hydrophilic compounds may form external

  11. A New Fractal Model of Chromosome and DNA Processes

    NASA Astrophysics Data System (ADS)

    Bouallegue, K.

    Dynamic chromosome structure remains unknown. Can fractals and chaos be used as new tools to model, identify and generate a structure of chromosomes?Fractals and chaos offer a rich environment for exploring and modeling the complexity of nature. In a sense, fractal geometry is used to describe, model, and analyze the complex forms found in nature. Fractals have also been widely not only in biology but also in medicine. To this effect, a fractal is considered an object that displays self-similarity under magnification and can be constructed using a simple motif (an image repeated on ever-reduced scales).It is worth noting that the problem of identifying a chromosome has become a challenge to find out which one of the models it belongs to. Nevertheless, the several different models (a hierarchical coiling, a folded fiber, and radial loop) have been proposed for mitotic chromosome but have not reached a dynamic model yet.This paper is an attempt to solve topological problems involved in the model of chromosome and DNA processes. By combining the fractal Julia process and the numerical dynamical system, we have finally found out four main points. First, we have developed not only a model of chromosome but also a model of mitosis and one of meiosis. Equally important, we have identified the centromere position through the numerical model captured below. More importantly, in this paper, we have discovered the processes of the cell divisions of both mitosis and meiosis. All in all, the results show that this work could have a strong impact on the welfare of humanity and can lead to a cure of genetic diseases.

  12. DNA

    ERIC Educational Resources Information Center

    Stent, Gunther S.

    1970-01-01

    This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)

  13. Investigation of membrane fouling in ultrafiltration using model organic compounds.

    PubMed

    Kweon, J H; Lawler, D F

    2005-01-01

    Natural organic matter (NOM) is known to be the worst foulant in the membrane processes, but the complexities of NOM make it difficult to determine its effects on membrane fouling. Therefore, simple organic compounds (surrogates for NOM) were used in this research to investigate the fouling mechanisms in ultrafiltration. Previous research on NOM components in membrane processes indicated that polysaccharides formed an important part of the fouling cake. Three polysaccharides (dextran, alginic acid, and polygalacturonic acid) and a smaller carbohydrate (tannic acid) were evaluated for their removal in softening (the treatment process in the City of Austin). Two polysaccharides (dextran and alginic acid) were selected and further investigated for their effects on membrane fouling. The two raw organic waters (4 mg/L C) showed quite different patterns of flux decline indicating different fouling mechanisms. Softening pretreatment was effective to reduce flux decline of both waters. The SEM images of the fouled membrane clearly showed the shapes of deposited foulants. The high resolution results of the XPS spectra showed substantially different spectra of carbon, C(1s), in the membrane fouled by two raw organic waters. The XPS was beneficial in determining the relative composition of each fouling material on the membrane surface.

  14. Modeling and predicting competitive sorption of organic compounds in soil.

    PubMed

    Faria, Isabel R; Young, Thomas M

    2010-12-01

    Binary systems consisting of 1,2-dichlorobenzene (12DCB) + competitor were investigated over a range of concentrations of competitor in three natural sorbents with distinct characteristics. Two models, the ideal adsorbed solution theory (IAST) and the potential theory (Polanyi-based multisolute model), widely used in the prediction of multisolute sorption equilibrium from single-solute data, were used to simulate competitive sorption in our systems. The goal was to determine which multisolute model best represented the experimentally obtained multisolute data in natural sorbents of varied properties. Results suggested that for the sorbents and sorbates studied, the IAST model provided much better results. On average, the IAST model provided lower errors (23%) than the potential model (45%). The effect of competitor structure on the degree of competition was also investigated to identify any relationships between competition and structure using molecular descriptors. The competitors chlorobenzene, naphthalene, 1,4-dichlorobenzene, 1,2,4-trichlorobenzene all showed very similar degrees of competition, while benzene, phenanthrene, and pyrene were the least effective competitors toward 12DCB across all sorbents. Different sorption sites or sorption mechanisms might be involved in the sorption of these molecules leading to a lack of competitive behavior. A significant relationship between competitor structure and the degree of competition was observed at environmentally relevant sorbed competitor concentrations for the soil containing the highest fraction of hard carbon (Forbes soil).

  15. Modeling and predicting competitive sorption of organic compounds in soil

    PubMed Central

    Faria, Isabel R.; Young, Thomas M.

    2011-01-01

    Binary systems consisting of 1,2-dichlorobenzene (12DCB) + competitor were investigated over a range of concentrations of competitor in three natural sorbents with distinct characteristics. Two models, the ideal adsorbed solution theory (IAST) and the Potential theory (Polanyi based multi-solute model), widely used in the prediction of multi-solute sorption equilibrium from single solute data were used to simulate competitive sorption in our systems. The goal was to determine which multi-solute model best represented the experimentally obtained multi-solute data in natural sorbents of varied properties. Results suggested that for the sorbents and sorbates studied the IAST model provided much better results. On average the IAST model provided lower errors (23%) than the Potential model (45%). The effect of competitor structure on the degree of competition was also investigated to identify any relationships between competition and structure using molecular descriptors. The competitors chlorobenzene, naphthalene, 1,4-dichlorobenzene, 1,2,4-trichlorobenzene all showed very similar degrees of competition, while benzene, phenanthrene and pyrene were the least effective competitors towards 12DCB across all sorbents. Different sorption sites or sorption mechanisms might be involved in the sorption of these molecules leading to a lack of competitive behavior. A significant relationship between competitor structure and the degree of competition was observed at environmentally relevant sorbed competitor concentrations for the soil containing the highest fraction of hard carbon (Forbes). PMID:21061392

  16. Interaction between bioactive compound 11a-N-tosyl-5-deoxi-pterocarpan (LQB-223) and Calf thymus DNA: Spectroscopic approach, electrophoresis and theoretical studies.

    PubMed

    Silva, Marina M; Nascimento, Eduarda O O; Silva, Edeíldo F; Araújo, João Xavier de; Santana, Camilla C; Grillo, Luciano Aparecido M; de Oliveira, Rafaela S; R R Costa, Paulo; Buarque, Camilla D; Santos, Josué Carinhanha C; Figueiredo, Isis M

    2017-03-01

    The interaction of small molecules with DNA has been quite important, since this biomolecule is currently the major target for a wide range of drugs in clinical use or advanced clinical research phase. Thus, the present work aimed to assess the interaction process between the bioactive compound 11a-N-tosyl-5-carba-pterocarpan, (LQB-223), that presents antitumor activity, with DNA, employing spectroscopic techniques, electrophoresis, viscosity and theoretical studies. Through UV-vis and molecular fluorescence spectroscopy, it was possible to infer that the preferential quenching mechanism was static, characterized by non-fluorescent supramolecular complex formation between the LQB-223 and DNA. The binding constant was 1.94∙10(3)Lmol(-1) (30°C) and, according to the thermodynamic parameters, the main forces involved in the interaction process are hydrophobic. Potassium iodide assay, competition with ethidium bromide, fluorescence contact energy transfer and melting temperature profile of DNA were employed to evaluate the binding mode. Except for KI assay, all results obtained indicated minor groove as the preferential binding mode of LQB-223 to DNA. These observations were supported by ionic strength assay, viscosity and molecular dynamics and docking studies. Finally, electrophoresis analysis demonstrated that the interaction does not promote DNA fragmentation, but it leads to variation in the migration profile after increasing the ligand concentration.

  17. Carbonyl side-chain of catechol compounds is a key structure for the suppression of copper-associated oxidative DNA damage in vitro.

    PubMed

    Ando, Motozumi; Nishida, Hiroyuki; Nishino, Yoshihiko; Ohbayashi, Manabu; Ueda, Koji; Okamoto, Yoshinori; Kojima, Nakao

    2010-12-15

    Catechol is possibly carcinogenic to humans (International Agency for Research on Cancer, IARC). The key mechanism could include its oxidative DNA-damaging effect in combination with reductive-oxidative metals like Cu. We found that DNA damage was suppressed by introducing an α-carbonyl group to catechol at C4-position to produce carbonyl catechols. During the oxidative DNA-damaging process, catechols but not carbonyl catechols were oxidized to o-quinone; however, coexisting Cu(II) was reduced to Cu(I). Carbonyl catechols were possibly arrested at the oxidation step of semiquinones in the presence of Cu(II). Cu(I)-binding to DNA was stronger than Cu(II)-binding, on the basis of the circular dichroism spectral change. None of the carbonyl catechols induced such change, suggesting sequestration of Cu(I) from DNA. Solid-phase extraction experiments and spectrophotometric analyses showed the formation of semiquinone chelates with Cu(I). Thus, chelate formation could explain the suppression mechanism of the Cu-catechol-dependent DNA damage by terminating the reduction-oxidation cycle. Structural modifications such as introducing an α-carbonyl group to catechol at C4-position would contribute to reducing the risk and improving industrial and medical potentials of aromatic/phenolic compounds sustaining our daily lives.

  18. Modeling emissions of volatile organic compounds from silage storages and feed lanes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An initial volatile organic compound (VOC) emission model for silage sources, developed using experimental data from previous studies, was incorporated into the Integrated Farm System Model (IFSM), a whole-farm simulation model used to assess the performance, environmental impacts, and economics of ...

  19. The Dynamic Character of the BCL2 Promoter i-Motif Provides a Mechanism for Modulation of Gene Expression by Compounds That Bind Selectively to the Alternative DNA Hairpin Structure

    PubMed Central

    2015-01-01

    It is generally accepted that DNA predominantly exists in duplex form in cells. However, under torsional stress imposed by active transcription, DNA can assume nonduplex structures. The BCL2 promoter region forms two different secondary DNA structures on opposite strands called the G-quadruplex and the i-motif. The i-motif is a highly dynamic structure that exists in equilibrium with a flexible hairpin species. Here we identify a pregnanol derivative and a class of piperidine derivatives that differentially modulate gene expression by stabilizing either the i-motif or the flexible hairpin species. Stabilization of the i-motif structure results in significant upregulation of the BCL2 gene and associated protein expression; in contrast, stabilization of the flexible hairpin species lowers BCL2 levels. The BCL2 levels reduced by the hairpin-binding compound led to chemosensitization to etoposide in both in vitro and in vivo models. Furthermore, we show antagonism between the two classes of compounds in solution and in cells. For the first time, our results demonstrate the principle of small molecule targeting of i-motif structures in vitro and in vivo to modulate gene expression. PMID:24559410

  20. HIGH TEMPERATURE HIGH PRESSURE THERMODYNAMIC MEASUREMENTS FOR COAL MODEL COMPOUNDS

    SciTech Connect

    Vinayak N. Kabadi

    1999-02-20

    It is well known that the fluid phase equilibria can be represented by a number of {gamma}-models , but unfortunately most of them do not function well under high temperature. In this calculation, we mainly investigate the performance of UNIQUAC and NRTL models under high temperature, using temperature dependent parameters rather than using the original formulas. the other feature of this calculation is that we try to relate the excess Gibbs energy G{sup E}and enthalpy of mixing H{sup E}simultaneously. In other words, we will use the high temperature and pressure G{sup E} and H{sup E}data to regress the temperature dependant parameters to find out which model and what kind of temperature dependant parameters should be used.

  1. Synthesis of a naphthalene-hydroxynaphthalene polymer model compound. Final report, June 13, 1990--September 12, 1991

    SciTech Connect

    Not Available

    1991-10-02

    The objective of this project was the synthesis of one pound of a new naphthalene-hydroxynaphthalene polymer model compound for use in coal combustion studies. Since this compound was an unreported compound, this effort also required the development of a synthetic route to this compound (including routes to the unique and unreported intermediates leading to its synthesis).

  2. Ecological Niche Modelling and nDNA Sequencing Support a New, Morphologically Cryptic Beetle Species Unveiled by DNA Barcoding

    PubMed Central

    Hawlitschek, Oliver; Porch, Nick; Hendrich, Lars; Balke, Michael

    2011-01-01

    Background DNA sequencing techniques used to estimate biodiversity, such as DNA barcoding, may reveal cryptic species. However, disagreements between barcoding and morphological data have already led to controversy. Species delimitation should therefore not be based on mtDNA alone. Here, we explore the use of nDNA and bioclimatic modelling in a new species of aquatic beetle revealed by mtDNA sequence data. Methodology/Principal Findings The aquatic beetle fauna of Australia is characterised by high degrees of endemism, including local radiations such as the genus Antiporus. Antiporus femoralis was previously considered to exist in two disjunct, but morphologically indistinguishable populations in south-western and south-eastern Australia. We constructed a phylogeny of Antiporus and detected a deep split between these populations. Diagnostic characters from the highly variable nuclear protein encoding arginine kinase gene confirmed the presence of two isolated populations. We then used ecological niche modelling to examine the climatic niche characteristics of the two populations. All results support the status of the two populations as distinct species. We describe the south-western species as Antiporus occidentalis sp.n. Conclusion/Significance In addition to nDNA sequence data and extended use of mitochondrial sequences, ecological niche modelling has great potential for delineating morphologically cryptic species. PMID:21347370

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

    DOEpatents

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

    2010-05-04

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

  4. Modeling associated protein-DNA pattern discovery with unified scores.

    PubMed

    Chan, Tak-Ming; Lo, Leung-Yau; Sze-To, Ho-Yin; Leung, Kwong-Sak; Xiao, Xinshu; Wong, Man-Hon

    2013-01-01

    Understanding protein-DNA interactions, specifically transcription factor (TF) and transcription factor binding site (TFBS) bindings, is crucial in deciphering gene regulation. The recent associated TF-TFBS pattern discovery combines one-sided motif discovery on both the TF and the TFBS sides. Using sequences only, it identifies the short protein-DNA binding cores available only in high-resolution 3D structures. The discovered patterns lead to promising subtype and disease analysis applications. While the related studies use either association rule mining or existing TFBS annotations, none has proposed any formal unified (both-sided) model to prioritize the top verifiable associated patterns. We propose the unified scores and develop an effective pipeline for associated TF-TFBS pattern discovery. Our stringent instance-level evaluations show that the patterns with the top unified scores match with the binding cores in 3D structures considerably better than the previous works, where up to 90 percent of the top 20 scored patterns are verified. We also introduce extended verification from literature surveys, where the high unified scores correspond to even higher verification percentage. The top scored patterns are confirmed to match the known WRKY binding cores with no available 3D structures and agree well with the top binding affinities of in vivo experiments.

  5. Solubility Prediction of Active Pharmaceutical Compounds with the UNIFAC Model

    NASA Astrophysics Data System (ADS)

    Nouar, Abderrahim; Benmessaoud, Ibtissem; Koutchoukali, Ouahiba; Koutchoukali, Mohamed Salah

    2016-03-01

    The crystallization from solution of an active pharmaceutical ingredient requires the knowledge of the solubility in the entire temperature range investigated during the process. However, during the development of a new active ingredient, these data are missing. Its experimental determination is possible, but tedious. UNIFAC Group contribution method Fredenslund et al. (Vapor-liquid equilibria using UNIFAC: a group contribution method, 1977; AIChE J 21:1086, 1975) can be used to predict this physical property. Several modifications on this model have been proposed since its development in 1977, modified UNIFAC of Dortmund Weidlich et al. (Ind Eng Chem Res 26:1372, 1987), Gmehling et al. (Ind Eng Chem Res 32:178, 1993), Pharma-modified UNIFAC Diedrichs et al. (Evaluation und Erweiterung thermodynamischer Modelle zur Vorhersage von Wirkstofflöslichkeiten, PhD Thesis, 2010), KT-UNIFAC Kang et al. (Ind Eng Chem Res 41:3260, 2002), ldots In this study, we used UNIFAC model by considering the linear temperature dependence of interaction parameters as in Pharma-modified UNIFAC and structural groups as defined by KT-UNIFAC first-order model. More than 100 binary datasets were involved in the estimation of interaction parameters. These new parameters were then used to calculate activity coefficient and solubility of some molecules in various solvents at different temperatures. The model gives better results than those from the original UNIFAC and shows good agreement between the experimental solubility and the calculated one.

  6. LAMMPS framework for dynamic bonding and an application modeling DNA

    NASA Astrophysics Data System (ADS)

    Svaneborg, Carsten

    2012-08-01

    We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected triplets and quartets of beads, where the interaction type is determined from the local pattern of bead and bond types. When breaking bonds, all angular and dihedral interactions involving broken bonds are removed. The framework allows chemical reactions to be modeled, and use it to simulate a simplistic, coarse-grained DNA model. The resulting DNA dynamics illustrates the power of the present framework. Catalogue identifier: AEME_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEME_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 2 243 491 No. of bytes in distributed program, including test data, etc.: 771 Distribution format: tar.gz Programming language: C++ Computer: Single and multiple core servers Operating system: Linux/Unix/Windows Has the code been vectorized or parallelized?: Yes. The code has been parallelized by the use of MPI directives. RAM: 1 Gb Classification: 16.11, 16.12 Nature of problem: Simulating coarse-grain models capable of chemistry e.g. DNA hybridization dynamics. Solution method: Extending LAMMPS to handle dynamic bonding and directional bonds. Unusual features: Allows bonds to be created and broken while angular and dihedral interactions are kept consistent. Additional comments: The distribution file for this program is approximately 36 Mbytes and therefore is not delivered directly

  7. A semiempirical model for estimating the hydration free energy of neutral nonpolar compounds

    NASA Astrophysics Data System (ADS)

    Ratkova, E. L.

    2012-10-01

    An improved semiempirical model for determining the hydration free energy of neutral nonpolar compounds is presented. The model is based on a combination of the RISM approach of the integral equation theory and empirical correlations. It is demonstrated that the developed model has high predictive ability for alkanes, alkenes, and dienes (present only in the test set of compounds). It is concluded that this semiempirical model can be applied in estimating the hydration free energy of more complicated structures based on saturated and nonsaturated aliphatic hydrocarbons.

  8. Recombinant DNA Paper Model Simulation: The Genetic Engineer.

    ERIC Educational Resources Information Center

    Wagner, Joan

    1998-01-01

    Describes a course for talented high school students that focuses on DNA science and technology. Employs Cold Spring Harbor's DNA Science laboratory manual. Engages students in performing sickle-cell anemia and thalassemia tests in rabbits. (DDR)

  9. Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models.

    PubMed

    Isakova, Alina; Berset, Yves; Hatzimanikatis, Vassily; Deplancke, Bart

    2016-05-06

    Many transcription factors (TFs) have the ability to cooperate on DNA elements as heterodimers. Despite the significance of TF heterodimerization for gene regulation, a quantitative understanding of cooperativity between various TF dimer partners and its impact on heterodimer DNA binding specificity models is still lacking. Here, we used a novel integrative approach, combining microfluidics-steered measurements of dimer-DNA assembly with mechanistic modeling of the implicated protein-protein-DNA interactions to quantitatively interrogate the cooperative DNA binding behavior of the adipogenic peroxisome proliferator-activated receptor γ (PPARγ):retinoid X receptor α (RXRα) heterodimer. Using the high throughput MITOMI (mechanically induced trapping of molecular interactions) platform, we derived equilibrium DNA binding data for PPARγ, RXRα, as well as the PPARγ:RXRα heterodimer to more than 300 target DNA sites and variants thereof. We then quantified cooperativity underlying heterodimer-DNA binding and derived an integrative heterodimer DNA binding constant. Using this cooperativity-inclusive constant, we were able to build a heterodimer-DNA binding specificity model that has superior predictive power than the one based on a regular one-site equilibrium. Our data further revealed that individual nucleotide substitutions within the target site affect the extent of cooperativity in PPARγ:RXRα-DNA binding. Our study therefore emphasizes the importance of assessing cooperativity when generating DNA binding specificity models for heterodimers.

  10. Synthesis, spectroscopic characterization and DFT calculations of β-O-4 type lignin model compounds

    NASA Astrophysics Data System (ADS)

    Mostaghni, Fatemeh; Teimouri, Abbas; Mirshokraei, Seyed Ahmad

    2013-06-01

    β-O-4 type lignin model compounds with the title of Erythro-2-(2-methoxyphenoxy)-1-(3,4,5-trimethoxyphenyl)-1,3-propanediol and Erythro-2-(2-methoxyphenoxy)-1-(4-Hydroxy-3,5-dimethoxyphenyl)-1,3-propanediol were synthesised and some modifications and improvements on them were introduced. These compounds were characterized by IR, Mass and NMR spectroscopy. Density functional theory (DFT) calculations were performed for the title compounds using the standard 6-31G* basis set. IR, 13C and 1H NMR of the title compounds were calculated at the DFT-B3LYP level of theory using the 6-31G* basis set. In this work comparison between the experimental and the theoretical results indicates that the DFT-B3LYP method is able to provide satisfactory results for predicting the properties of the considered compounds.

  11. Global emissions and models of photochemically active compounds

    SciTech Connect

    Penner, J.E.; Atherton, C.S.; Graedel, T.E.

    1993-05-20

    Anthropogenic emissions from industrial activity, fossil fuel combustion, and biomass burning are now known to be large enough (relative to natural sources) to perturb the chemistry of vast regions of the troposphere. A goal of the IGAC Global Emissions Inventory Activity (GEIA) is to provide authoritative and reliable emissions inventories on a 1{degree} {times} 1{degree} grid. When combined with atmospheric photochemical models, these high quality emissions inventories may be used to predict the concentrations of major photochemical products. Comparison of model results with measurements of pertinent species allows us to understand whether there are major shortcomings in our understanding of tropospheric photochemistry, the budgets and transport of trace species, and their effects in the atmosphere. Through this activity, we are building the capability to make confident predictions of the future consequences of anthropogenic emissions. This paper compares IGAC recommended emissions inventories for reactive nitrogen and sulfur dioxide to those that have been in use previously. We also present results from the three-dimensional LLNL atmospheric chemistry model that show how emissions of anthropogenic nitrogen oxides might potentially affect tropospheric ozone and OH concentrations and how emissions of anthropogenic sulfur increase sulfate aerosol loadings.

  12. Computational Models of the Representation of Bangla Compound Words in the Mental Lexicon.

    PubMed

    Dasgupta, Tirthankar; Sinha, Manjira; Basu, Anupam

    2016-08-01

    In this paper we aim to model the organization and processing of Bangla compound words in the mental lexicon. Our objective is to determine whether the mental lexicon access a Bangla compound word as a whole or decomposes the whole word into its constituent morphemes and then recognize them accordingly. To address this issue, we adopted two different strategies. First, we conduct a cross-modal priming experiment over a number of native speakers. Analysis of reaction time (RT) and error rates indicates that in general, Bangla compound words are accessed via partial decomposition process. That is some word follows full-listing mode of representation and some words follow the decomposition route of representation. Next, based on the collected RT data we have developed a computational model that can explain the processing phenomena of the access and representation of Bangla compound words. In order to achieve this, we first explored the individual roles of head word position, morphological complexity, orthographic transparency and semantic compositionality between the constituents and the whole compound word. Accordingly, we have developed a complexity based model by combining these features together. To a large extent we have successfully explained the possible processing phenomena of most of the Bangla compound words. Our proposed model shows an accuracy of around 83 %.

  13. Modeling forward stutter: toward increased objectivity in forensic DNA interpretation.

    PubMed

    Bright, Jo-Anne; Buckleton, John S; Taylor, Duncan; Fernando, M A C S S; Curran, James M

    2014-11-01

    Forward stutter, or over stutter, one repeat unit length larger than the parent allele (N + 1 stutter), is a relatively rare product of the PCR amplification of STRs used in forensic DNA analysis. We have investigated possible explanatory variables for the occurrence and size of forward stutter for four different autosomal multiplexes. In addition, we have investigated models used to predict the expected heights of forward stutter. For all tetra and penta-nucleotide repeats we can find no correlation between allelic peak height, marker, or longest uninterrupted sequence in the allele. The data fit a gamma distribution with no explanatory variables. For the single trinucleotide repeat present in two of the four multiplexes (D22S1045) forward stutter is much more common and the best explanatory variable appears to be back stutter height. This suggests some fundamental cocausation of high backward and forward stutter for this locus.

  14. Lessons for neurotoxicology from selected model compounds: SGOMSEC joint report.

    PubMed Central

    Rice, D C; Evangelista de Duffard, A M; Duffard, R; Iregren, A; Satoh, H; Watanabe, C

    1996-01-01

    The ability to identify potential neurotoxicants depends upon the characteristics of our test instruments. The neurotoxic properties of lead, methylmercury, polychlorinated biphenyls, and organic solvents would all have been detected at some dose level by tests in current use, provided that the doses were high enough and administered at an appropriate time such as during gestation. The adequacy of animal studies, particularly rodent studies, to predict intake levels at which human health can be protected is disappointing, however. It is unlikely that the use of advanced behavioral methodology would alleviate the apparent lack of sensitivity of the rodent model for many agents. PMID:8860323

  15. An elastic compound tube model for a single osteon.

    PubMed

    Braidotti, P; Branca, F P; Sciubba, E; Stagni, L

    1995-04-01

    A model is developed whereby the secondary osteon--the dominant microstructural component of the cortical bone tissue--is considered as an n-layered cylinder with internal stresses in linear isotropic elasticity. An exact solution is obtained for a loading condition represented by a tensile-compressive force. The lengthening, the side deformation, and the strain energy of the system are explicitly calculated. The behavior of the main elastic quantities is illustrated by graphs. In particular, the important role played by the parity of the number of lamellae is revealed.

  16. Modeling Scalable Pattern Generation in DNA Reaction Networks

    PubMed Central

    Allen, Peter B.; Chen, Xi; Simpson, Zack B.; Ellington, Andrew D.

    2013-01-01

    We have developed a theoretical framework for developing patterns in multiple dimensions using controllable diffusion and designed reactions implemented in DNA. This includes so-called strand displacement reactions in which one single-stranded DNA hybridizes to a hemi-duplex DNA and displaces another single-stranded DNA, reversibly or irreversibly. These reactions can be designed to proceed with designed rate and molecular specificity. By also controlling diffusion by partial complementarity to a stationary, cross-linked DNA, we can generate predictable patterns. We demonstrate this with several simulations showing deterministic, predictable shapes in space. PMID:25506295

  17. HIGH TEMPERATURE HIGH PRESSURE THERMODYNAMIC MEASUREMENTS FOR COAL MODEL COMPOUNDS

    SciTech Connect

    Vinayak N. Kabadi

    1999-02-24

    The enthalpy of a fluid measured with respect to some reference temperature and pressure (enthalpy increment or Cp) is required for many engineering designs. Different techniques for determining enthalpy increments include direct measurement, integration of heat capacity as a function of temperature at constant pressure, and calculation from accurate density measurements as a function of temperature and pressure with ideal-gas enthalpies. Techniques have been developed for measurement of heat capacities using differential scanning calorimeters, but routine measurements with a precision better than 3% are rare. For thermodynamic model development, excess enthalpies or enthalpies of mixing of binary and ternary systems are generally required. Although these data can be calculated from measured values of incremental enthalpies of mixtures and corresponding pure components, the method of calculation involves subtraction of large numbers, and it is impossible to obtain accurate results from relatively accurate incremental enthalpy data. Directly measured heats of mixing provide better data for model development. In what follows, we give a brief literature survey of experimental methods available for measurement of incremental enthalpies as well as heats of mixing.

  18. Transalkylation reactions in fossil fuels and related model compounds

    SciTech Connect

    Farcasiu, M.; Forbus, T.R.; LaPierre, R.B.

    1983-02-01

    The alkyl substituents of high molecular weight polycyclic aromatic constituents of petroleum residues are transferable to exogenous monocyclic aromatics (benzene, toluene, o-xylene, etc.) by acid catalyzed (CF/sub 3/SO/sub 3/H) Friedel Crafts transalkylation. Analysis (GC-MS) of the volatile alkylated monocyclic aromatic products provides a method for the determination of the alkyl group content/structure of the starting fossil fuel mixture. Both model systems, using alkylated naphthalenes, phenanthrenes, pyrenes and dibenzothiophenes and demineralized shale oil or petroleum resid were studied. The model studies (alkyl chain length 2-10 carbons) revealed the following reaction pathways to predominate: (1) transalkylation rates/equilibria are independent of chain length; (2) n-alkyl groups are transfered without rearrangement or fragmentation; (3) reaction rate depends upon the aromatic moiety; (4) formation of dixylylmethanes via benzyl carbenium ions is significant (12 to 25% of product; and (5) significant minor products at longer reaction times are alkyl tetralins, tetralins, napthalenes and alkylated acceptors having a chain length reduced by (-CH/sub 2/-)/sub 4/.

  19. DNA strand scission by the nephrotoxin [2,2'-bipyridine]-3,3',4,4'-tetrol-1,1'-dioxide and related compounds in the presence of iron.

    PubMed

    Cantin-Esnault, D; Oubrahim, H; Richard, J M

    2000-08-01

    The capacity of non-illuminated nephrotoxin orellanine ([2,2'-bipyridine]-3,3',4,4'-tetrol-1,1'-dioxide) to induce DNA damage in the presence of ferrous iron and dioxygen has been evaluated. Maximal single-strand breaks in plasmid DNA were obtained with a metal to ligand ratio 1:3. Instantaneous oxidation of Fe2+ in presence of orellanine under air was responsible for oxy-radical production concomitant to a stable ferric complex Fe(III)Or3 formation, leading to oxidative DNA breakage at physiological pH. DNA damage was lowered in the presence of SOD and catalase or DMSO, indicating a set of reactions that leads to oxy-radical generation. Iron chelators such as DTPA and EDTA had no protecting effect, Desferal slightly protected. GSH acted as an oxy-radical scavenger, whereas cysteine induced stronger damage. Closely related bipyridine compounds were also studied in presence of Fe2+ and O2 using a combination of spin-trapping and DNA-nicking experiments, none of which were able to chelate iron and induce damage at pH 7. Both catecholic moieties and aminoxide groups are required for observing breakage at physiological pH.

  20. Mouse models of DNA mismatch repair in cancer research

    PubMed Central

    Lee, Kyeryoung; Tosti, Elena; Edelmann, Winfried

    2016-01-01

    Germline mutations in DNA mismatch repair (MMR) genes are the cause of hereditary non-polyposis colorectal cancer/Lynch syndrome (HNPCC/LS) one of the most common cancer predisposition syndromes, and defects in MMR are also prevalent in sporadic colorectal cancers. In the past, the generation and analysis of mouse lines with knockout mutations in all of the known MMR genes has provided insight into how loss of individual MMR genes affects genome stability and contributes to cancer susceptibility. These studies also revealed essential functions for some of the MMR genes in B cell maturation and fertility. In this review, we will provide a brief overview of the cancer predisposition phenotypes of recently developed mouse models with targeted mutations in MutS and MutL homologs (Msh and Mlh, respectively) and their utility as preclinical models. The focus will be on mouse lines with conditional MMR mutations that have allowed more accurate modeling of human cancer syndromes in mice and that together with new technologies in gene targeting, hold great promise for the analysis of MMR-deficient intestinal tumors and other cancers which will drive the development of preventive and therapeutic treatment strategies. PMID:26708047

  1. Mouse models of DNA mismatch repair in cancer research.

    PubMed

    Lee, Kyeryoung; Tosti, Elena; Edelmann, Winfried

    2016-02-01

    Germline mutations in DNA mismatch repair (MMR) genes are the cause of hereditary non-polyposis colorectal cancer/Lynch syndrome (HNPCC/LS) one of the most common cancer predisposition syndromes, and defects in MMR are also prevalent in sporadic colorectal cancers. In the past, the generation and analysis of mouse lines with knockout mutations in all of the known MMR genes has provided insight into how loss of individual MMR genes affects genome stability and contributes to cancer susceptibility. These studies also revealed essential functions for some of the MMR genes in B cell maturation and fertility. In this review, we will provide a brief overview of the cancer predisposition phenotypes of recently developed mouse models with targeted mutations in MutS and MutL homologs (Msh and Mlh, respectively) and their utility as preclinical models. The focus will be on mouse lines with conditional MMR mutations that have allowed more accurate modeling of human cancer syndromes in mice and that together with new technologies in gene targeting, hold great promise for the analysis of MMR-deficient intestinal tumors and other cancers which will drive the development of preventive and therapeutic treatment strategies.

  2. Characterization of commercial inactive dry yeast preparations for enological use based on their ability to release soluble compounds and their behavior toward aroma compounds in model wines.

    PubMed

    Pozo-Bayón, Maria Angeles; Andujar-Ortiz, Inmaculada; Alcaide-Hidalgo, Juan María; Martín-Alvarez, Pedro J; Moreno-Arribas, M Victoria

    2009-11-25

    The characterization of commercial enological inactive dry yeast (IDY) with different applications in wine production has been carried out. This study was based on the yeast's ability to release soluble compounds (high molecular weight nitrogen, free amino nitrogen, peptidic nitrogen, free amino acids, and polysaccharides) into model wines and on its behavior toward the volatility of seven wine aroma compounds. Important differences in soluble compounds released into the model wines supplemented with commercial IDY were found, with the free amino acids being among the most released. The volatility of most of the aroma compounds was affected by the addition of IDY preparations at a concentration usually employed during winemaking. The extent of this effect was dependent on the physicochemical characteristics of the aroma compound and on the length of time the IDY preparations remained in contact with the model wines. Whereas shorter contact times (2, 4, and 6 days) mainly promoted a "salting-out" effect, longer exposure (9 and 13 days) provoked a retention effect, with the consequent reduction of aroma compounds in the headspace. The use of different commercial preparations also promoted different effects toward the aroma compounds that may be at least in part due to differences in their ability to release soluble compounds of yeast origin into the wines.

  3. Toward multiscale modeling of the chromatin fiber: a coarse grain model for DNA

    NASA Astrophysics Data System (ADS)

    Savelyev, Alexey; Papoian, Garegin

    2008-03-01

    In eukaryotic cells DNA is compacted a million-fold into a chromatin. Understanding the mechanism of chromatin folding is of great biological importance. All-atom Molecular Dynamics (MD) simulations could provide crucial insights into the electrostatic and structural mechanisms of chromatin folding. However, because of the enormous size of even short chromatin fiber segment and long folding time-scales, atomistic simulations are computationally impractical. Our long-term aim is to build an accurate coarse-grain (CG) model of the chromatin, derived systematically from all-atom simulations of its smaller parts. Here we report the development of the CG model for a linear DNA chain, playing the role of a linker DNA segment in the chromatin. We derived CG inter-DNA electrostatic potential from atomistic simulations with explicit solvent and mobile ions, instead of relying on the standard models of continuum electrostatics, which are inadequate at small intermolecular distances. In addition, we used the ideas of renormalization group theory to construct an optimization scheme for parameterizing the CG force field. This novel approach is designed to accurately reproduce correlations among various CG degrees of freedom. The implementation of these correlations was left as an open question in the prior studies of CG polymer models.

  4. Diffusion-controlled reactions modeling in Geant4-DNA

    SciTech Connect

    Karamitros, M.; Luan, S.; Bernal, M.A.; Allison, J.; Baldacchino, G.; Davidkova, M.; Francis, Z.; Friedland, W.; Ivantchenko, V.; Ivantchenko, A.; Mantero, A.; Nieminem, P.; Santin, G.; Tran, H.N.; Stepan, V.; Incerti, S.

    2014-10-01

    Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k–d tree data structure for quickly locating, for a given molecule, its closest reactants. The

  5. Diffusion-controlled reactions modeling in Geant4-DNA

    NASA Astrophysics Data System (ADS)

    Karamitros, M.; Luan, S.; Bernal, M. A.; Allison, J.; Baldacchino, G.; Davidkova, M.; Francis, Z.; Friedland, W.; Ivantchenko, V.; Ivantchenko, A.; Mantero, A.; Nieminem, P.; Santin, G.; Tran, H. N.; Stepan, V.; Incerti, S.

    2014-10-01

    Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k-d tree data structure for quickly locating, for a given molecule, its closest reactants. The

  6. Catalytic conversion of lignin pyrolysis model compound- guaiacol and its kinetic model including coke formation

    PubMed Central

    Zhang, Huiyan; Wang, Yun; Shao, Shanshan; Xiao, Rui

    2016-01-01

    Lignin is the most difficult to be converted and most easy coking component in biomass catalytic pyrolysis to high-value liquid fuels and chemicals. Catalytic conversion of guaiacol as a lignin model compound was conducted in a fixed-bed reactor over ZSM-5 to investigate its conversion and coking behaviors. The effects of temperature, weight hourly space velocity (WHSV) and partial pressure on product distribution were studied. The results show the maximum aromatic carbon yield of 28.55% was obtained at temperature of 650 °C, WHSV of 8 h−1 and partial pressure of 2.38 kPa, while the coke carbon yield was 19.55%. The reaction pathway was speculated to be removing methoxy group to form phenols with further aromatization to form aromatics. The amount of coke increased with increasing reaction time. The surface area and acidity of catalysts declined as coke formed on the acid sites and blocked the pore channels, which led to the decrease of aromatic yields. Finally, a kinetic model of guaiacol catalytic conversion considering coke deposition was built based on the above reaction pathway to properly predict product distribution. The experimental and model predicting data agreed well. The correlation coefficient of all equations were all higher than 0.90. PMID:27869228

  7. Catalytic conversion of lignin pyrolysis model compound- guaiacol and its kinetic model including coke formation

    NASA Astrophysics Data System (ADS)

    Zhang, Huiyan; Wang, Yun; Shao, Shanshan; Xiao, Rui

    2016-11-01

    Lignin is the most difficult to be converted and most easy coking component in biomass catalytic pyrolysis to high-value liquid fuels and chemicals. Catalytic conversion of guaiacol as a lignin model compound was conducted in a fixed-bed reactor over ZSM-5 to investigate its conversion and coking behaviors. The effects of temperature, weight hourly space velocity (WHSV) and partial pressure on product distribution were studied. The results show the maximum aromatic carbon yield of 28.55% was obtained at temperature of 650 °C, WHSV of 8 h‑1 and partial pressure of 2.38 kPa, while the coke carbon yield was 19.55%. The reaction pathway was speculated to be removing methoxy group to form phenols with further aromatization to form aromatics. The amount of coke increased with increasing reaction time. The surface area and acidity of catalysts declined as coke formed on the acid sites and blocked the pore channels, which led to the decrease of aromatic yields. Finally, a kinetic model of guaiacol catalytic conversion considering coke deposition was built based on the above reaction pathway to properly predict product distribution. The experimental and model predicting data agreed well. The correlation coefficient of all equations were all higher than 0.90.

  8. Space Radiation Effects on Human Cells: Modeling DNA Breakage, DNA Damage Foci Distribution, Chromosomal Aberrations and Tissue Effects

    NASA Technical Reports Server (NTRS)

    Ponomarev, A. L.; Huff, J. L.; Cucinotta, F. A.

    2011-01-01

    Future long-tem space travel will face challenges from radiation concerns as the space environment poses health risk to humans in space from radiations with high biological efficiency and adverse post-flight long-term effects. Solar particles events may dramatically affect the crew performance, while Galactic Cosmic Rays will induce a chronic exposure to high-linear-energy-transfer (LET) particles. These types of radiation, not present on the ground level, can increase the probability of a fatal cancer later in astronaut life. No feasible shielding is possible from radiation in space, especially for the heavy ion component, as suggested solutions will require a dramatic increase in the mass of the mission. Our research group focuses on fundamental research and strategic analysis leading to better shielding design and to better understanding of the biological mechanisms of radiation damage. We present our recent effort to model DNA damage and tissue damage using computational models based on the physics of heavy ion radiation, DNA structure and DNA damage and repair in human cells. Our particular area of expertise include the clustered DNA damage from high-LET radiation, the visualization of DSBs (DNA double strand breaks) via DNA damage foci, image analysis and the statistics of the foci for different experimental situations, chromosomal aberration formation through DSB misrepair, the kinetics of DSB repair leading to a model-derived spectrum of chromosomal aberrations, and, finally, the simulation of human tissue and the pattern of apoptotic cell damage. This compendium of theoretical and experimental data sheds light on the complex nature of radiation interacting with human DNA, cells and tissues, which can lead to mutagenesis and carcinogenesis later in human life after the space mission.

  9. Mathematical modeling of atmospheric fine particle-associated primary organic compound concentrations

    NASA Astrophysics Data System (ADS)

    Rogge, Wolfgang F.; Hildemann, Lynn M.; Mazurek, Monica A.; Cass, Glen R.; Simoneit, Bernd R. T.

    1996-08-01

    An atmospheric transport model has been used to explore the relationship between source emissions and ambient air quality for individual particle phase organic compounds present in primary aerosol source emissions. An inventory of fine particulate organic compound emissions was assembled for the Los Angeles area in the year 1982. Sources characterized included noncatalyst- and catalyst-equipped autos, diesel trucks, paved road dust, tire wear, brake lining dust, meat cooking operations, industrial oil-fired boilers, roofing tar pots, natural gas combustion in residential homes, cigarette smoke, fireplaces burning oak and pine wood, and plant leaf abrasion products. These primary fine particle source emissions were supplied to a computer-based model that simulates atmospheric transport, dispersion, and dry deposition based on the time series of hourly wind observations and mixing depths. Monthly average fine particle organic compound concentrations that would prevail if the primary organic aerosol were transported without chemical reaction were computed for more than 100 organic compounds within an 80 km × 80 km modeling area centered over Los Angeles. The monthly average compound concentrations predicted by the transport model were compared to atmospheric measurements made at monitoring sites within the study area during 1982. The predicted seasonal variation and absolute values of the concentrations of the more stable compounds are found to be in reasonable agreement with the ambient observations. While model predictions for the higher molecular weight polycyclic aromatic hydrocarbons (PAH) are in agreement with ambient observations, lower molecular weight PAH show much higher predicted than measured atmospheric concentrations in the particle phase, indicating atmospheric decay by chemical reactions or evaporation from the particle phase. The atmospheric concentrations of dicarboxylic acids and aromatic polycarboxylic acids greatly exceed the contributions that

  10. Chicken fetal liver DNA damage and adduct formation by activation-dependent DNA-reactive carcinogens and related compounds of several structural classes.

    PubMed

    Williams, Gary M; Duan, Jian-Dong; Brunnemann, Klaus D; Iatropoulos, Michael J; Vock, Esther; Deschl, Ulrich

    2014-09-01

    The chicken egg genotoxicity assay (CEGA), which utilizes the liver of an intact and aseptic embryo-fetal test organism, was evaluated using four activation-dependent DNA-reactive carcinogens and four structurally related less potent carcinogens or non-carcinogens. In the assay, three daily doses of test substances were administered to eggs containing 9-11-day-old fetuses and the fetal livers were assessed for two endpoints, DNA breaks using the alkaline single cell gel electrophoresis (comet) assay and DNA adducts using the (32)P-nucleotide postlabeling (NPL) assay. The effects of four carcinogens of different structures requiring distinct pathways of bioactivation, i.e., 2-acetylaminofluorene (AAF), aflatoxin B1 (AFB1), benzo[a]pyrene (B[a]P), and diethylnitrosamine (DEN), were compared with structurally related non-carcinogens fluorene (FLU) and benzo[e]pyrene (B[e]P) or weak carcinogens, aflatoxin B2 (AFB2) and N-nitrosodiethanolamine (NDELA). The four carcinogens all produced DNA breaks at microgram or low milligram total doses, whereas less potent carcinogens and non-carcinogens yielded borderline or negative results, respectively, at higher doses. AAF and B[a]P produced DNA adducts, whereas none was found with the related comparators FLU or B[e]P, consistent with comet results. DEN and NDELA were also negative for adducts, as expected in the case of DEN for an alkylating agent in the standard NPL assay. Also, AFB1 and AFB2 were negative in NPL, as expected, due to the nature of ring opened aflatoxin adducts, which are resistant to enzymatic digestion. Thus, the CEGA, using comet and NPL, is capable of detection of the genotoxicity of diverse DNA-reactive carcinogens, while not yielding false positives for non-carcinogens.

  11. Effects of structure on the interactions between five natural antimicrobial compounds and phospholipids of bacterial cell membrane on model monolayers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Monolayers composed of bacterial phospholipids were used as model membranes to study interactions of naturally occurring phenolic compounds 2,5-dihydroxybenzaldehyde, 2-hydroxy-5-methoxybenzaldehyde and the plant essential oil compounds carvacrol, cinnamaldehyde, and geraniol, previously found to be...

  12. Using the Theory of Elasticity to Model the Structure of DNA Loops

    NASA Astrophysics Data System (ADS)

    Balaeff, Alexander; Mahadevan, L.; Schulten, Klaus

    2000-03-01

    A fast computational method to study the conformation and energetics of short DNA loops is presented. The DNA is modeled as an electrically charged elastic rod. The ensemble of equilibrium conformations of the DNA loop, attainable for given boundary conditions, is generated as a set of numerical solutions to the equations of the Kirchhoff-Love theory of elasticity. The equations are augmented by electrostatic and van der Waals force terms. These modifications allow one to account for the DNA self-repulsion and to model the DNA loop interactions with other macromolecules, involved in a biomolecular system. We demonstrate the application of the method to the test system: the looped lac operon promoter of E. coli clamped by the repressor protein and stabilized by the catabolite gene activator protein. The developed coarse-grained modeling method provides the basis for multi-resolution modeling of protein-DNA complexes, e.g., in combination with all-atom molecular dynamics simulations.

  13. pH- and salt-dependent molecular combing of DNA: experiments and phenomenological model.

    PubMed

    Benke, Annegret; Mertig, Michael; Pompe, Wolfgang

    2011-01-21

    λ-DNA as well as plasmids can be successfully deposited by molecular combing on hydrophobic surfaces, for pH values ranging from 4 to 10. On polydimethylsiloxane (PDMS) substrates, the deposited DNA molecules are overstretched by about 60-100%. There is a significant influence of sodium ions (NaCl) on the surface density of the deposited DNA, with a maximum near to 100 mM NaCl for a DNA solution (28 ng µl(-1)) at pH 8. The combing process can be described by a micromechanical model including: (i) the adsorption of free moving coiled DNA at the substrate; (ii) the stretching of the coiled DNA by the preceding meniscus; (iii) the relaxation of the deposited DNA to the final length. The sticky ends of λ-DNA cause an adhesion force in the range of about 400 pN which allows a stable overstretching of the DNA by the preceding meniscus. The exposing of hidden hydrophobic bonds of the overstretched DNA leads to a stable deposition on the hydrophobic substrate. The pH-dependent density of deposited DNA as well as the observed influence of sodium ions can be explained by their screening of the negatively charged DNA backbone and sticky ends, respectively. The final DNA length can be derived from a balance of the stored elastic energy of the overstretched molecules and the energy of adhesion.

  14. Recent advances in small organic molecules as DNA intercalating agents: synthesis, activity, and modeling.

    PubMed

    Rescifina, Antonio; Zagni, Chiara; Varrica, Maria Giulia; Pistarà, Venerando; Corsaro, Antonino

    2014-03-03

    The interaction of small molecules with DNA plays an essential role in many biological processes. As DNA is often the target for majority of anticancer and antibiotic drugs, study about the interaction of drug and DNA has a key role in pharmacology. Moreover, understanding the interactions of small molecules with DNA is of prime significance in the rational design of more powerful and selective anticancer agents. Two of the most important and promising targets in cancer chemotherapy include DNA alkylating agents and DNA intercalators. For these last the DNA recognition is a critical step in their anti-tumor action and the intercalation is not only one kind of the interactions in DNA recognition but also a pivotal step of several clinically used anti-tumor drugs such as anthracyclines, acridines and anthraquinones. To push clinical cancer therapy, the discovery of new DNA intercalators has been considered a practical approach and a number of intercalators have been recently reported. The intercalative binding properties of such molecules can also be harnessed as diagnostic probes for DNA structure in addition to DNA-directed therapeutics. Moreover, the problem of intercalation site formation in the undistorted B-DNA of different length and sequence is matter of tremendous importance in molecular modeling studies and, nowadays, three models of DNA intercalation targets have been proposed that account for the binding features of intercalators. Finally, despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. Therefore, a default protocol to identify DNA binding modes which uses a modified canonical DNA as receptor is needed.

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  17. The reciprocal relationship between compounding awareness and vocabulary knowledge in Chinese: a latent growth model study.

    PubMed

    Cheng, Yahua; Li, Liping; Wu, Xinchun

    2015-01-01

    The aim of this study is to examine the developmental relationship between compounding awareness and vocabulary knowledge from grades 1 to 2 in Chinese children. In this study, 149 Chinese children were tested on compounding awareness and vocabulary knowledge from Time 1 to Time 4, with non-verbal IQ, working memory, phonological awareness, orthographical awareness, and rapid automatized naming at Time 1 as control variables. Latent growth modeling was conducted to analyze the data. Univariate models separately calculated children's initial levels and growth rates in compounding awareness and vocabulary knowledge. Bivariate model was used to examine the direction of the developmental relationships between the two variables with other cognitive and linguistic variables and the autoregression controlled. The results demonstrated that the initial level of compounding awareness predicted the growth rate of vocabulary knowledge, and the reverse relation was also found, after controlling for other cognitive and linguistic variables and the autoregression. The results suggested a reciprocal developmental relationship between children's compounding awareness and vocabulary knowledge for Chinese children, a finding that informs current models of the relationship between morphological awareness and vocabulary knowledge.

  18. Protective effects of garlic sulfur compounds against DNA damage induced by direct- and indirect-acting genotoxic agents in HepG2 cells.

    PubMed

    Belloir, C; Singh, V; Daurat, C; Siess, M H; Le Bon, A M

    2006-06-01

    The aim of this study was to assess the antigenotoxic activity of several garlic organosulfur compounds (OSC) in the human hepatoma cell line HepG2, using comet assay. The OSC selected were allicin (DADSO), diallyl sulfide (DAS), diallyl disulfide (DADS), S-allyl cysteine (SAC) and allyl mercaptan (AM). To explore their potential mechanisms of action, two approaches were performed: (i) a pre-treatment protocol which allowed study of the possible modulation of drug metabolism enzymes by OSC before treatment of the cells with the genotoxic agent; (ii) a co-treatment protocol by which the ability of OSC to scavenge direct-acting compounds was assessed. Preliminary studies showed that, over the concentration range tested (5-100 microM), the studied OSC neither affected cell viability nor induced DNA damage by themselves. In the pre-treatment protocol, aflatoxin B1 genotoxicity was significantly reduced by all the OSC tested except AM. DADS was the most efficient OSC in reducing benzo(a)pyrene genotoxicity. SAC and AM significantly decreased DNA breaks in HepG2 cells treated with dimethylnitrosamine. Additionally, all the OSC studied were shown to decrease the genotoxicity of the direct-acting compounds, hydrogen peroxide and methyl methanesulfonate. This study demonstrated that garlic OSC displayed antigenotoxic activity in human metabolically competent cells.

  19. Effect of thickeners on aroma compound behavior in a model dairy gel.

    PubMed

    Lubbers, Samuel; Decourcelle, Nicolas; Martinez, Daniel; Guichard, Elisabeth; Tromelin, Anne

    2007-06-13

    The effects of thickeners on the headspace release of aroma compounds from a model dairy gel were investigated. Starch, pectin, and locust bean gum (LBG) were introduced separately to the fat-free dairy gel via sugar syrups. The release of nine aroma compounds was analyzed by solid-phase microextraction (SPME), and the partition coefficients of retention were calculated. For an increase in starch concentration, there was an overall decrease in aroma release. Pectin concentrations in gel higher than 0.04% caused an increase in aroma release. For LBG no major effect was observed. A quantitative structure-property relationship (QSPR) approach was used to propose which types of interactions were involved between aroma molecules and thickener macromolecules in the complex foodstuff. Twenty molecular descriptors of volatile compounds appeared to be significant in correlation with the partition coefficients of retention. The surface-weighted negatively charged partial surface area seemed to play a critical role in the behavior of aroma compound.

  20. Topoisomerase inhibition, nucleolytic and electrolytic contribution on DNA binding activity exerted by biological active analogue of coordination compounds.

    PubMed

    Patel, Mohan N; Bhatt, Bhupesh S; Dosi, Promise A

    2012-04-01

    The neutral mononuclear copper complexes with the quinolone antibacterial drug ciprofloxacin and bipyridine derivatives have been synthesized and characterized. Complexes were screened for their antibacterial activity against three Gram((-)) and two Gram((+)) bacteria, and study suggests inhibition of gyrase activity by metal complexes as the possible mechanism. The nucleolytic activity of adducts was carried out on double stranded pUC19 DNA using gel electrophoresis in the presence of radical scavenging agents that suggest hydrolytic cleavage mechanism for plasmid DNA.

  1. Determination of the n-octanol/water partition coefficients of weakly ionizable basic compounds by reversed-phase high-performance liquid chromatography with neutral model compounds.

    PubMed

    Liang, Chao; Han, Shu-ying; Qiao, Jun-qin; Lian, Hong-zhen; Ge, Xin

    2014-11-01

    A strategy to utilize neutral model compounds for lipophilicity measurement of ionizable basic compounds by reversed-phase high-performance liquid chromatography is proposed in this paper. The applicability of the novel protocol was justified by theoretical derivation. Meanwhile, the linear relationships between logarithm of apparent n-octanol/water partition coefficients (logKow '') and logarithm of retention factors corresponding to the 100% aqueous fraction of mobile phase (logkw ) were established for a basic training set, a neutral training set and a mixed training set of these two. As proved in theory, the good linearity and external validation results indicated that the logKow ''-logkw relationships obtained from a neutral model training set were always reliable regardless of mobile phase pH. Afterwards, the above relationships were adopted to determine the logKow of harmaline, a weakly dissociable alkaloid. As far as we know, this is the first report on experimental logKow data for harmaline (logKow = 2.28 ± 0.08). Introducing neutral compounds into a basic model training set or using neutral model compounds alone is recommended to measure the lipophilicity of weakly ionizable basic compounds especially those with high hydrophobicity for the advantages of more suitable model compound choices and convenient mobile phase pH control.

  2. Pyrolysis reaction networks for lignin model compounds: unraveling thermal deconstruction of β-O-4 and α-O-4 compounds

    SciTech Connect

    Choi, Yong S.; Singh, Rahul; Zhang, Jing; Balasubramanian, Ganesh; Sturgeon, Matthew R.; Katahira, Rui; Chupka, Gina; Beckham, Gregg T.; Shanks, Brent H.

    2016-01-01

    Although lignin is one of the main components of biomass, its pyrolysis chemistry is not well understood due to complex heterogeneity. To gain insights into this chemistry, the pyrolysis of seven lignin model compounds (five ..beta..-O-4 and two ..alpha..-O-4 linked molecules) was investigated in a micropyrolyzer connected to GC-MS/FID. According to quantitative product mole balance for the reaction networks, concerted retro-ene fragmentation and homolytic dissociation were strongly suggested as the initial reaction step for ..beta..-O-4 compounds and ..alpha..-O-4 compounds, respectively. The difference in reaction pathway between compounds with different linkages was believed to result from thermodynamics of the radical initiation. The rate constants for the different reaction pathways were predicted from ab initio density functional theory calculations and pre-exponential literature values. The computational findings were consistent with the experiment results, further supporting the different pyrolysis mechanisms for the ..beta..-ether linked and ..alpha..-ether linked compounds. A combination of the two pathways from the dimeric model compounds was able to describe qualitatively the pyrolysis of a trimeric lignin model compound containing both ..beta..-O-4 and ..alpha..-O-4 linkages.

  3. Evidential evaluation of DNA profiles using a discrete statistical model implemented in the DNA LiRa software.

    PubMed

    Puch-Solis, Roberto; Clayton, Tim

    2014-07-01

    The high sensitivity of the technology for producing profiles means that it has become routine to produce profiles from relatively small quantities of DNA. The profiles obtained from low template DNA (LTDNA) are affected by several phenomena which must be taken into consideration when interpreting and evaluating this evidence. Furthermore, many of the same phenomena affect profiles from higher amounts of DNA (e.g. where complex mixtures has been revealed). In this article we present a statistical model, which forms the basis of software DNA LiRa, and that is able to calculate likelihood ratios where one to four donors are postulated and for any number of replicates. The model can take into account dropin and allelic dropout for different contributors, template degradation and uncertain allele designations. In this statistical model unknown parameters are treated following the Empirical Bayesian paradigm. The performance of LiRa is tested using examples and the outputs are compared with those generated using two other statistical software packages likeLTD and LRmix. The concept of ban efficiency is introduced as a measure for assessing model sensitivity.

  4. Prooxidant action of furanone compounds: implication of reactive oxygen species in the metal-dependent strand breaks and the formation of 8-hydroxy-2'-deoxyguanosine in DNA.

    PubMed

    Murakami, K; Haneda, M; Makino, T; Yoshino, M

    2007-07-01

    Prooxidant properties of furanone compounds including 2,5-furanone (furaneol, 4-hydroxy-2,5-dimethyl-furan-3-one), 4,5-furanone (4,5-dimethyl-3-hydroxy-2(5H)-furanone) (sotolone) and cyclotene (2-hydroxy-3-methyl-2-cyclopenten-1-one) were analyzed in relation to the metal-reducing activity. Only 2.5-furanone known as a "strawberry or pineapple furanone" inactivated aconitase the most sensitive enzyme to active oxygen in the presence of ferrous sulfate, suggesting the furaneol/iron-mediated generation of reactive oxygen species. 2,5-Furanone caused strand scission of pBR322 DNA in the presence of copper. Treatment of calf thymus DNA with 2,5-furanone plus copper produced 8-hydroxy-2'-deoxyguanosine in DNA. 2,5-Furanone showed a potent copper-reducing activity, and thus, DNA strand breaks and the formation of 8-hydroxy-2'-deoxyguanosine by 2,5-furanone can be initiated by the production of superoxide radical through the reduction of cupric ion to cuprous ion, resulting in the conversion to hydrogen peroxide and hydroxyl radical. However, an isomer and analog of 2,5-furanone, 4,5-furanone and cyclotene, respectively, did not show an inactivation of aconitase, DNA injuries including strand breakage and the formation of 8-hydroxy-2'-deoxyguanosine, and copper-reducing activity. Cytotoxic effect of 2,5-furanone with hydroxyketone structure can be explained by its prooxidant properties: furaneol/transition metal complex generates reactive oxygen species causing the inactivation of aconitase and the formation of DNA base damage by hydroxyl radical.

  5. DNA sensor model based on a carbon nanotube network in the degenerate limit

    NASA Astrophysics Data System (ADS)

    Abadi, H. Karimi Feiz; Webb, J. F.; Ahmadi, M. T.; Rahmani, M.; Saeidmanesh, M.; Khalid, M.; Ismail, R.

    2012-11-01

    An analytical model of a possible DNA sensor based on a carbon nanotube network that functions as a selective detector of DNA molecules is presented. The ability to implement label-free electronic detection using a DNA sensor based on a carbon nanotube network constitutes an important step towards low-cost, highly sensitive, simple and accurate molecular diagnostics. In particular, there is an urgent need for a simple method of detection of DNA molecules as this will provided a new and efficient way to diagnosis genetic or pathogenic diseases. Bio-compatibility and high sensitivity towards environmental perturbations make graphene nanomaterials a good choice for a sensing layer in an electronic DNA sensor. In this study, a conductance model of a DNA sensor based on a carbon nanotube network is suggested and the performance of the model is evaluated by calculating current-voltage characteristics.

  6. Interaction of a biguanide compound with membrane model interface systems: probing the properties of antimalaria and antidiabetic compounds.

    PubMed

    Samart, Nuttaporn; Beuning, Cheryle N; Haller, Kenneth J; Rithner, Chris D; Crans, Debbie C

    2014-07-29

    Since membrane penetration is important for drug efficacy, how antimalarial precursor material 1-phenylbiguanide (PBG) interacts with an interface was characterized using a reverse micelle (RM) model system. (1)H NMR studies show that PBG partitions across the membrane interface. Specifically, the (1)H NMR studies showed that the 1-phenylbiguanide compound in an aqueous environment changed when placed near an interface. PBG is known to affect hydrogen bonding in water, and as the size of the RMs changes, the water organization in the water pool is changed. The NOESY spectrum of PBG in AOT RM contains cross-peak signals between the PBG protons and AOT protons, which is consistent with the penetration of the PBG into the interface. At the same time, there is a cross peak between the biguanide moiety and the HOD signal. This shows that these NH protons are near the HOD protons, placing the biguanide functional group in the water pool. Preliminary differential FTIR spectroscopic studies confirmed this location. In summary, we found that PBG interacts with different regions of the interface, with the phenyl group penetrating the hydrophobic interface while the biguanide remains in the water pool.

  7. A compound memristive synapse model for statistical learning through STDP in spiking neural networks

    PubMed Central

    Bill, Johannes; Legenstein, Robert

    2014-01-01

    Memristors have recently emerged as promising circuit elements to mimic the function of biological synapses in neuromorphic computing. The fabrication of reliable nanoscale memristive synapses, that feature continuous conductance changes based on the timing of pre- and postsynaptic spikes, has however turned out to be challenging. In this article, we propose an alternative approach, the compound memristive synapse, that circumvents this problem by the use of memristors with binary memristive states. A compound memristive synapse employs multiple bistable memristors in parallel to jointly form one synapse, thereby providing a spectrum of synaptic efficacies. We investigate the computational implications of synaptic plasticity in the compound synapse by integrating the recently observed phenomenon of stochastic filament formation into an abstract model of stochastic switching. Using this abstract model, we first show how standard pulsing schemes give rise to spike-timing dependent plasticity (STDP) with a stabilizing weight dependence in compound synapses. In a next step, we study unsupervised learning with compound synapses in networks of spiking neurons organized in a winner-take-all architecture. Our theoretical analysis reveals that compound-synapse STDP implements generalized Expectation-Maximization in the spiking network. Specifically, the emergent synapse configuration represents the most salient features of the input distribution in a Mixture-of-Gaussians generative model. Furthermore, the network's spike response to spiking input streams approximates a well-defined Bayesian posterior distribution. We show in computer simulations how such networks learn to represent high-dimensional distributions over images of handwritten digits with high fidelity even in presence of substantial device variations and under severe noise conditions. Therefore, the compound memristive synapse may provide a synaptic design principle for future neuromorphic architectures. PMID

  8. Further studies toward a mouse model for biochemical assessment of neuropathic potential of organophosphorus compounds.

    PubMed

    Makhaeva, Galina F; Rudakova, Elena V; Hein, Nichole D; Serebryakova, Olga G; Kovaleva, Nadezhda V; Boltneva, Natalia P; Fink, John K; Richardson, Rudy J

    2014-12-01

    Inhibition and aging of neuropathy target esterase (NTE) by neuropathic organophosphorus (OP) compounds triggers OP compound-induced delayed neuropathy (OPIDN), whereas inhibition of acetylcholinesterase (AChE) produces cholinergic toxicity. The neuropathic potential of an OP compound is defined by its relative inhibitory potency toward NTE vs. AChE assessed by enzyme assays following dosing in vivo or after incubations of direct-acting compounds or active metabolites with enzymes in vitro. The standard animal model of OPIDN is the adult hen, but its large size and high husbandry costs make this species a burdensome model for assessing neuropathic potential. Although the mouse does not readily exhibit clinical signs of OPIDN, it displays axonal lesions and expresses brain AChE and NTE. Therefore, the present research was performed as a further test of the hypothesis that inhibition of mouse brain AChE and NTE could be used to assess neuropathic potential using mouse brain preparations in vitro or employing mouse brain assays following dosing of OP compounds in vivo. Excellent correlations were obtained for inhibition kinetics in vitro of mouse brain enzymes vs. hen brain and human recombinant enzymes. Furthermore, inhibition of mouse brain AChE and NTE after dosing with OP compounds afforded ED(50) ratios that agreed with relative inhibitory potencies assessed in vitro. Taken together, results with mouse brain enzymes demonstrated consistent correspondence between in vitro and in vivo predictors of neuropathic potential, thus adding to previous studies supporting the validity of a mouse model for biochemical assessment of the ability of OP compounds to produce OPIDN.

  9. A compound memristive synapse model for statistical learning through STDP in spiking neural networks.

    PubMed

    Bill, Johannes; Legenstein, Robert

    2014-01-01

    Memristors have recently emerged as promising circuit elements to mimic the function of biological synapses in neuromorphic computing. The fabrication of reliable nanoscale memristive synapses, that feature continuous conductance changes based on the timing of pre- and postsynaptic spikes, has however turned out to be challenging. In this article, we propose an alternative approach, the compound memristive synapse, that circumvents this problem by the use of memristors with binary memristive states. A compound memristive synapse employs multiple bistable memristors in parallel to jointly form one synapse, thereby providing a spectrum of synaptic efficacies. We investigate the computational implications of synaptic plasticity in the compound synapse by integrating the recently observed phenomenon of stochastic filament formation into an abstract model of stochastic switching. Using this abstract model, we first show how standard pulsing schemes give rise to spike-timing dependent plasticity (STDP) with a stabilizing weight dependence in compound synapses. In a next step, we study unsupervised learning with compound synapses in networks of spiking neurons organized in a winner-take-all architecture. Our theoretical analysis reveals that compound-synapse STDP implements generalized Expectation-Maximization in the spiking network. Specifically, the emergent synapse configuration represents the most salient features of the input distribution in a Mixture-of-Gaussians generative model. Furthermore, the network's spike response to spiking input streams approximates a well-defined Bayesian posterior distribution. We show in computer simulations how such networks learn to represent high-dimensional distributions over images of handwritten digits with high fidelity even in presence of substantial device variations and under severe noise conditions. Therefore, the compound memristive synapse may provide a synaptic design principle for future neuromorphic architectures.

  10. Infantile onset spinocerebellar ataxia caused by compound heterozygosity for Twinkle mutations and modeling of Twinkle mutations causing recessive disease

    PubMed Central

    Gulsuner, Suleyman; Stapleton, Gail A.; Walsh, Tom; Lee, Ming K.; Mandell, Jessica B.; Morales, Augusto; Klevit, Rachel E.; King, Mary-Claire; Rogers, R. Curtis

    2016-01-01

    Mutations in nuclear genes required for the replication and maintenance of mitochondrial DNA cause progressive multisystemic neuromuscular disorders with overlapping phenotypes. Biallelic mutations in C10orf2, encoding the Twinkle mitochondrial DNA helicase, lead to infantile-onset cerebellar ataxia (IOSCA), as well as milder and more severe phenotypes. We present a 13-year-old girl with ataxia, severe hearing loss, optic atrophy, peripheral neuropathy, and hypergonadotropic hypogonadism. Whole-exome sequencing revealed that the patient is compound heterozygous for previously unreported variants in the C10orf2 gene: a paternally inherited frameshift variant (c.333delT; p.L112Sfs*3) and a maternally inherited missense variant (c.904C>T; p.R302W). The identification of novel C10orf2 mutations extends the spectrum of mutations in the Twinkle helicase causing recessive disease, in particular the intermediate IOSCA phenotype. Structural modeling suggests that the p.R302W mutation and many other recessively inherited Twinkle mutations impact the position or interactions of the linker region, which is critical for the oligomeric ring structure and activity of the helicase. This study emphasizes the utility of whole-exome sequencing for the genetic diagnosis of a complex multisystemic disorder. PMID:27551684

  11. Effect of plasma and carboxylesterase on the stability, mutagenicity, and DNA cross-linking activity of some direct-acting N-nitroso compounds.

    PubMed

    Aukerman, S L; Brundrett, R B; Hilton, J; Hartman, P E

    1983-01-01

    The effects of mouse plasma, human plasma, and purified porcine liver carboxylesterase on nitrosourea, nitrosamide, and nitrosocarbamate chemical stability, mutagenicity, and DNA cross-linking activity were compared. These three classes of N-nitroso compounds are chemically similar but displayed different biological activities and were affected differently by plasma and carboxylesterase. Nitrosourea stability as well as mutagenicity and DNA cross-linking activity were affected negligibly by esterase or plasma. In contrast, nitrosamide and nitrosocarbamate stability, mutagenicity, and DNA cross-linking activity were rapidly decreased in the presence of plasma or carboxylesterase. For example, chemical half-lives were from 10- to 20-fold shorter for the nitrosamides and nitrosocarbamates in the presence of 5% mouse plasma. Similar decreases were seen for mutagenicity and DNA cross-linking activity. Preliminary studies indicated one active plasma component to be an enzyme, possibly an esterase. Additional factors such as sulfhydryls may also participate. Whereas some nitrosoureas are active antitumor agents, the lack of antitumor activity for analogous nitrosamides and nitrosocarbamates may reside predominantly in their rapid in vivo inactivation. These results may help to account for the high in vitro mutagenicity as compared with the low in vivo activities of nitrosamides and nitrosocarbamates.

  12. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.

    PubMed

    Saladin, Adrien; Amourda, Christopher; Poulain, Pierre; Férey, Nicolas; Baaden, Marc; Zacharias, Martin; Delalande, Olivier; Prévost, Chantal

    2010-10-01

    Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson-Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange.

  13. Interaction of zanamivir with DNA and RNA: Models for drug DNA and drug RNA bindings

    NASA Astrophysics Data System (ADS)

    Nafisi, Shohreh; Kahangi, Fatemeh Ghoreyshi; Azizi, Ebrahim; Zebarjad, Nader; Tajmir-Riahi, Heidar-Ali

    2007-03-01

    Zanamivir (ZAN) is the first of a new generation of influenza virus-specific drugs known as neuraminidase inhibitors, which acts by interfering with life cycles of influenza viruses A and B. It prevents the virus spreading infection to other cells by blocking the neuraminidase enzyme present on the surface of the virus. The aim of this study was to examine the stability and structural features of calf thymus DNA and yeast RNA complexes with zanamivir in aqueous solution, using constant DNA or RNA concentration (12.5 mM) and various zanamivir/polynucleotide ( P) ratios of 1/20, 1/10, 1/4, and 1/2. FTIR and UV-visible spectroscopy are used to determine the drug external binding modes, the binding constant and the stability of zanamivir-DNA and RNA complexes in aqueous solution. Structural analysis showed major interaction of zanamivir with G-C (major groove) and A-T (minor groove) base pairs and minor perturbations of the backbone PO 2 group with overall binding constants of Kzanamivir-DNA = 1.30 × 10 4 M -1 and Kzanamivir-RNA = 1.38 × 10 4 M -1. The drug interaction induces a partial B to A-DNA transition, while RNA remains in A-conformation.

  14. Chemopreventive activity of compounds extracted from Casearia sylvestris (Salicaceae) Sw against DNA damage induced by particulate matter emitted by sugarcane burning near Araraquara, Brazil

    SciTech Connect

    Prieto, A.M.; Santos, A.G.; Csipak, A.R.; Caliri, C.M.; Silva, I.C.; Arbex, M.A.; Silva, F.S.; Marchi, M.R.R.

    2012-12-15

    Ethanolic extract of Casearia sylvestris is thought to be antimutagenic. In this study, we attempted to determine whether this extract and casearin X (a clerodane diterpene from C. sylvestris) are protective against the harmful effects of airborne pollutants from sugarcane burning. To that end, we used the Tradescantia micronucleus test in meiotic pollen cells of Tradescantia pallida, the micronucleus test in mouse bone marrow cells, and the comet assay in mouse blood cells. The mutagenic compound was total suspended particulate (TSP) from air. For the Tradescantia micronucleus test, T. pallida cuttings were treated with the extract at 0.13, 0.25, or 0.50 mg/ml. Subsequently, TSP was added at 0.3 mg/ml, and tetrads from the inflorescences were examined for micronuclei. For the micronucleus test in mouse bone marrow cells and the comet assay in mouse blood cells, Balb/c mice were treated for 15 days with the extract—3.9, 7.5, or 15.0 mg/kg body weight (BW)—or with casearin X—0.3, 0.25, or 1.2 mg/kg BW—after which they received TSP (3.75 mg/kg BW). In T. pallida and mouse bone marrow cells, the extract was antimutagenic at all concentrations tested. In mouse blood cells, the extract was antigenotoxic at all concentrations, whereas casearin X was not antimutagenic but was antigenotoxic at all concentrations. We conclude that C. sylvestris ethanolic extract and casearin X protect DNA from damage induced by airborne pollutants from sugarcane burning. -- Highlights: ► We assessed DNA protection of C. sylvestris ethanolic extract. ► We assessed DNA protection of casearin X. ► We used Tradescantia pallida micronucleus test as screening. ► We used comet assay and micronucleus test in mice. ► The compounds protected DNA against sugar cane burning pollutants.

  15. Repeat instability during DNA repair: Insights from model systems

    PubMed Central

    Usdin, Karen; House, Nealia C. M.; Freudenreich, Catherine H.

    2015-01-01

    The expansion of repeated sequences is the cause of over 30 inherited genetic diseases, including Huntington disease, myotonic dystrophy (types 1 and 2), fragile X syndrome, many spinocerebellar ataxias, and some cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat expansions are dynamic, and disease inheritance and progression are influenced by the size and the rate of expansion. Thus, an understanding of the various cellular mechanisms that cooperate to control or promote repeat expansions is of interest to human health. In addition, the study of repeat expansion and contraction mechanisms has provided insight into how repair pathways operate in the context of structure-forming DNA, as well as insights into non-canonical roles for repair proteins. Here we review the mechanisms of repeat instability, with a special emphasis on the knowledge gained from the various model systems that have been developed to study this topic. We cover the repair pathways and proteins that operate to maintain genome stability, or in some cases cause instability, and the cross-talk and interactions between them. PMID:25608779

  16. Molecular modeling and snake venom phospholipase A2 inhibition by phenolic compounds: Structure-activity relationship.

    PubMed

    Alam, Md Iqbal; Alam, Mohammed A; Alam, Ozair; Nargotra, Amit; Taneja, Subhash Chandra; Koul, Surrinder

    2016-05-23

    In our earlier study, we have reported that a phenolic compound 2-hydroxy-4-methoxybenzaldehyde from Janakia arayalpatra root extract was active against Viper and Cobra envenomations. Based on the structure of this natural product, libraries of synthetic structurally variant phenolic compounds were studied through molecular docking on the venom protein. To validate the activity of eight selected compounds, we have tested them in in vivo and in vitro models. The compound 21 (2-hydroxy-3-methoxy benzaldehyde), 22 (2-hydroxy-4-methoxybenzaldehyde) and 35 (2-hydroxy-3-methoxybenzylalcohol) were found to be active against venom-induced pathophysiological changes. The compounds 20, 15 and 35 displayed maximum anti-hemorrhagic, anti-lethal and PLA2 inhibitory activity respectively. In terms of SAR, the presence of a formyl group in conjunction with a phenolic group was seen as a significant contributor towards increasing the antivenom activity. The above observations confirmed the anti-venom activity of the phenolic compounds which needs to be further investigated for the development of new anti-snake venom leads.

  17. Integrative modelling of tumour DNA methylation quantifies the contribution of metabolism

    PubMed Central

    Mehrmohamadi, Mahya; Mentch, Lucas K.; Clark, Andrew G.; Locasale, Jason W.

    2016-01-01

    Altered DNA methylation is common in cancer and often considered an early event in tumorigenesis. However, the sources of heterogeneity of DNA methylation among tumours remain poorly defined. Here we capitalize on the availability of multi-platform data on thousands of human tumours to build integrative models of DNA methylation. We quantify the contribution of clinical and molecular factors in explaining intertumoral variability in DNA methylation. We show that the levels of a set of metabolic genes involved in the methionine cycle is predictive of several features of DNA methylation in tumours, including the methylation of cancer genes. Finally, we demonstrate that patients whose DNA methylation can be predicted from the methionine cycle exhibited improved survival over cases where this regulation is disrupted. This study represents a comprehensive analysis of the determinants of methylation and demonstrates the surprisingly large interaction between metabolism and DNA methylation variation. Together, our results quantify links between tumour metabolism and epigenetics and outline clinical implications. PMID:27966532

  18. MODELING OF MULTICOMPONENT PERVAPORATION FOR REMOVAL OF VOLATILE ORGANIC COMPOUNDS FROM WATER

    EPA Science Inventory

    A resistance-in-series model was used to study the pervaporation of multiple volatile organic compounds (VOCs)-water mixtures. Permeation experiments were carried out for four membranes: poly(dimethylsiloxane) (PDMS), polyether-block-polyamides (PEBA), polyurethane (PUR) and sil...

  19. Adsorption of selected pharmaceuticals and an endocrine disrupting compound by granular activated carbon. 2. Model prediction

    SciTech Connect

    Yu, Z.; Peldszus, S.; Huck, P.M.

    2009-03-01

    The adsorption of two representative pharmaceutically active compounds (PhACs) naproxen and carbamazepine and one endocrine disrupting compound (EDC) nonylphenol was studied in pilot-scale granular activated carbon (GAC) adsorbers using post-sedimentation (PS) water from a full-scale drinking water treatment plant. The GAC adsorbents were coal-based Calgon Filtrasorb 400 and coconut shell-based PICA CTIF TE. Acidic naproxen broke through fastest while nonylphenol was removed best, which was consistent with the degree to which fouling affected compound removals. Model predictions and experimental data were generally in good agreement for all three compounds, which demonstrated the effectiveness and robustness of the pore and surface diffusion model (PSDM) used in combination with the time-variable parameter approach for predicting removals at environmentally relevant concentrations (i.e., ng/L range). Sensitivity analyses suggested that accurate determination of film diffusion coefficients was critical for predicting breakthrough for naproxen and carbamazepine, in particular when high removals are targeted. Model simulations demonstrated that GAC carbon usage rates (CURs) for naproxen were substantially influenced by the empty bed contact time (EBCT) at the investigated conditions. Model-based comparisons between GAC CURs and minimum CURs for powdered activated carbon (PAC) applications suggested that PAC would be most appropriate for achieving 90% removal of naproxen, whereas GAC would be more suitable for nonylphenol. 25 refs., 4 figs., 1 tab.

  20. A Connectionist Model of Stimulus Class Formation with a Yes/No Procedure and Compound Stimuli

    ERIC Educational Resources Information Center

    Tovar, Angel E.; Chavez, Alvaro Torres

    2012-01-01

    We analyzed stimulus class formation in a human study and in a connectionist model (CM) with a yes/no procedure, using compound stimuli. In the human study, the participants were six female undergraduate students; the CM was a feed-forward back-propagation network. Two 3-member stimulus classes were trained with a similar procedure in both the…

  1. Using Molecular Modeling in Teaching Group Theory Analysis of the Infrared Spectra of Organometallic Compounds

    ERIC Educational Resources Information Center

    Wang, Lihua

    2012-01-01

    A new method is introduced for teaching group theory analysis of the infrared spectra of organometallic compounds using molecular modeling. The main focus of this method is to enhance student understanding of the symmetry properties of vibrational modes and of the group theory analysis of infrared (IR) spectra by using visual aids provided by…

  2. Moving beyond Watson-Crick models of coarse grained DNA dynamics

    NASA Astrophysics Data System (ADS)

    Linak, Margaret C.; Tourdot, Richard; Dorfman, Kevin D.

    2011-11-01

    DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.

  3. Identifying Intracellular pDNA Losses From a Model of Nonviral Gene Delivery.

    PubMed

    Martin, Timothy; Wysocki, Beata; Wysocki, Tadeusz; Pannier, Angela

    2015-01-23

    Nonviral gene delivery systems are a type of nano-communication system that transmit plasmid packets (i.e. pDNA packets) that are programmed at the nanoscale to biological systems at the microscopic cellular level. This engineered nano-communication system suffers large pDNA losses during transmission of the genetically encoded information, preventing its use in biotechnological and medical applications. The pDNA losses largely remain uncharacterized, and the ramifications of reducing pDNA loss from newly designed gene delivery systems remain difficult to predict. Here, the pDNA losses during primary and secondary transmission chains were identified utilizing a MATLAB model employing queuing theory simulating delivery of pEGFPLuc transgene to HeLa cells carried by Lipofectamine 2000 nonviral DNA carrier. Minimizing pDNA loss during endosomal escape of the primary transmission process results in increased number of pDNA in the nucleus with increased transfection, but with increased probability of cell death. The number of pDNA copies in the nucleus and the amount of time the pDNAs are in the nucleus directly correlates to improved transfection efficiency. During secondary transmission, pDNAs are degraded during distribution to daughter cells. Reducing pDNA losses improves transfection, but a balance in quantity of nuclear pDNA, mitosis, and toxicity must be considered in order to achieve therapeutically relevant transfection levels.

  4. Evaluation of Models for Solubility and Volatility of Copper Compounds Under Steam Generation Conditions

    SciTech Connect

    Palmer, D.; Petrov, A.

    1999-09-12

    The loss in efficiency of power plants with mixed metallurgy, due to transport and deposition of copper and its oxides in HP turbines, has been recognized as one of the key problems to be solved in the utility industry worldwide. Within this context, the most important problem to be addressed is the solubility and volatility of copper compounds under steam generation condition. This paper presents an evaluation of different solubility end volatility models for copper compounds, and presents a comparison between the calculated and test data.

  5. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    NASA Astrophysics Data System (ADS)

    Snodin, Benedict E. K.; Randisi, Ferdinando; Mosayebi, Majid; Šulc, Petr; Schreck, John S.; Romano, Flavio; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.; Doye, Jonathan P. K.

    2015-06-01

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na+] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  6. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    SciTech Connect

    Snodin, Benedict E. K. Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; Šulc, Petr; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.

    2015-06-21

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  7. The MCRA model for probabilistic single-compound and cumulative risk assessment of pesticides.

    PubMed

    van der Voet, Hilko; de Boer, Waldo J; Kruisselbrink, Johannes W; Goedhart, Paul W; van der Heijden, Gerie W A M; Kennedy, Marc C; Boon, Polly E; van Klaveren, Jacob D

    2015-05-01

    Pesticide risk assessment is hampered by worst-case assumptions leading to overly pessimistic assessments. On the other hand, cumulative health effects of similar pesticides are often not taken into account. This paper describes models and a web-based software system developed in the European research project ACROPOLIS. The models are appropriate for both acute and chronic exposure assessments of single compounds and of multiple compounds in cumulative assessment groups. The software system MCRA (Monte Carlo Risk Assessment) is available for stakeholders in pesticide risk assessment at mcra.rivm.nl. We describe the MCRA implementation of the methods as advised in the 2012 EFSA Guidance on probabilistic modelling, as well as more refined methods developed in the ACROPOLIS project. The emphasis is on cumulative assessments. Two approaches, sample-based and compound-based, are contrasted. It is shown that additional data on agricultural use of pesticides may give more realistic risk assessments. Examples are given of model and software validation of acute and chronic assessments, using both simulated data and comparisons against the previous release of MCRA and against the standard software DEEM-FCID used by the Environmental Protection Agency in the USA. It is shown that the EFSA Guidance pessimistic model may not always give an appropriate modelling of exposure.

  8. Zalypsis: a novel marine-derived compound with potent antimyeloma activity that reveals high sensitivity of malignant plasma cells to DNA double-strand breaks.

    PubMed

    Ocio, Enrique M; Maiso, Patricia; Chen, Xi; Garayoa, Mercedes; Alvarez-Fernández, Stela; San-Segundo, Laura; Vilanova, David; López-Corral, Lucía; Montero, Juan C; Hernández-Iglesias, Teresa; de Alava, Enrique; Galmarini, Carlos; Avilés, Pablo; Cuevas, Carmen; San-Miguel, Jesús F; Pandiella, Atanasio

    2009-04-16

    Multiple myeloma (MM) remains incurable, and new drugs with novel mechanisms of action are still needed. In this report, we have analyzed the action of Zalypsis, an alkaloid analogous to certain natural marine compounds, in MM. Zalypsis turned out to be the most potent antimyeloma agent we have tested so far, with IC(50) values from picomolar to low nanomolar ranges. It also showed remarkable ex vivo potency in plasma cells from patients and in MM cells in vivo xenografted in mice. Besides the induction of apoptosis and cell cycle arrest, Zalypsis provoked DNA double-strand breaks (DSBs), evidenced by an increase in phospho-histone-H2AX and phospho-CHK2, followed by a striking overexpression of p53 in p53 wild-type cell lines. In addition, in those cell lines in which p53 was mutated, Zalypsis also provoked DSBs and induced cell death, although higher concentrations were required. Immunohistochemical studies in tumors also demonstrated histone-H2AX phosphorylation and p53 overexpression. Gene expression profile studies were concordant with these results, revealing an important deregulation of genes involved in DNA damage response. The potent in vitro and in vivo antimyeloma activity of Zalypsis uncovers the high sensitivity of tumor plasma cells to DSBs and strongly supports the use of this compound in MM patients.

  9. Measurement of unscheduled DNA synthesis and S-phase synthesis in rodent hepatocytes following in vivo treatment: Testing of 24 compounds

    SciTech Connect

    Mirsalis, J.C.; Tyson, C.K.; Steinmetz, K.L.; Loh, E.K.; Hamilton, C.M.; Bakke, J.P. ); Spalding, J.W. )

    1989-01-01

    The in vivo-in vitro hepatocyte DNA repair assay has been shown to be useful for studying genotoxic hepatocarcinogens. In addition, measurement of S-phase synthesis (SPS) provides an indirect indicator of hepatocellular proliferation, which may be an important mechanism in rodent carcinogenesis. This assay was used to examine 24 chemicals for their ability to induce unscheduled DNA synthesis (UDS) or SPS in Fischer-344 rats or B6C3F1 mice following in vivo treatment. Hepatocytes were isolated by liver perfusion and incubated with {sup 3}H-thymidine following in vivo treatment by gavage. Chemicals chosen for testing were from the National Toxicology Program (NTP) genetic toxicology testing program and most were also evaluated in long-term animal studies conducted by the NTP. Dinitrotoluene and Michler's Ketone induced positive UDS response in rat, while N-nitrosodiethanolamine and selenium sulfide induced equivocal UDS results in mouse and rat, respectively. BCMEE, bromoform, chloroform, PBB, 1,1,2-trichloroethane, and trichloroethylene were all potent inducers of SPS in mouse liver, while C.I. Solvent Yellow 14, and 1,1,2,2-tetrachloroethane yielded equivocal SPS results in rat and mouse, respectively. These results indicate that most of the test compounds do not induced UDS in the liver; however, the significant S-phase response induced by many of these compounds, especially the halogenated solvents, may be an important mechanism in their hepatocarinogenicity.

  10. Development and validation of quantitative structure-activity relationship models for compounds acting on serotoninergic receptors.

    PubMed

    Zydek, Grażyna; Brzezińska, Elżbieta

    2012-01-01

    A quantitative structure-activity relationship (QSAR) study has been made on 20 compounds with serotonin (5-HT) receptor affinity. Thin-layer chromatographic (TLC) data and physicochemical parameters were applied in this study. RP2 TLC 60F(254) plates (silanized) impregnated with solutions of propionic acid, ethylbenzene, 4-ethylphenol, and propionamide (used as analogues of the key receptor amino acids) and their mixtures (denoted as S1-S7 biochromatographic models) were used in two developing phases as a model of drug-5-HT receptor interaction. The semiempirical method AM1 (HyperChem v. 7.0 program) and ACD/Labs v. 8.0 program were employed to calculate a set of physicochemical parameters for the investigated compounds. Correlation and multiple linear regression analysis were used to search for the best QSAR equations. The correlations obtained for the compounds studied represent their interactions with the proposed biochromatographic models. The good multivariate relationships (R(2) = 0.78-0.84) obtained by means of regression analysis can be used for predicting the quantitative effect of biological activity of different compounds with 5-HT receptor affinity. "Leave-one-out" (LOO) and "leave-N-out" (LNO) cross-validation methods were used to judge the predictive power of final regression equations.

  11. Modeling of protein and phenolic compound removal from aqueous solutions by electrocoagulation.

    PubMed

    Robić, Goran; Miranda, Everson Alves

    2010-01-01

    Electrocoagulation is a technique basically applied in water and wastewater treatment, but which has a number of potential applications in polymer, protein, drug, and vaccine delivery. In this work, we correlate the current applied between the electrodes to the removal of phenolic compounds or protein from aqueous solutions, but the principle can also be applied to other biological compounds such as plant pigments and sugars. Simple and time-dependent models were developed based on the complex formation between these biological substances and the aluminium hydroxide gel phase. The models developed represent a good agreement with experimental data (R(2) as high as 0.992). Besides construction of the models, the effect of pH on the efficiency of removal of proteins and phenolic compounds was evaluated. It was found that this parameter has significant effect on the efficiency of the electrocoagulation and the maximal removal efficiency for bovine serum albumin and phenolic compound catechin was observed at pH 8.0.

  12. Temperature-dependent kinetics of grape seed phenolic compounds extraction: experiment and model.

    PubMed

    Bucić-Kojić, Ana; Sovová, Helena; Planinić, Mirela; Tomas, Srećko

    2013-02-15

    The kinetics of a batch solid-liquid extraction of total phenolic compounds (PC) from milled grape seed (Vitis vinifera L. cv. "Frankovka") using 50% ethanol at different extraction temperatures (25-80°C) was studied. The maximum yield of PC was 0.13 kg(GAE)/kg(db) after 200 min of extraction in agitated vessel at 80°C. A new model based on the assumptions of a first order kinetics mechanism for the solid-liquid extraction and a linear equilibrium at the solid-liquid interface was developed. The model involves the concept of broken and intact cells in order to describe two successive extraction periods: a very fast surface washing process followed by slow diffusion of phenolic compounds from grape seeds to the solvent. The proposed model is suited to fit experimental data and to simulate the extraction of phenolic compounds, which was confirmed by the correlation coefficient (r≥0.965), the root mean square error (RMSE≤0.003 kg(GAE)/kg(db)) and the mean relative deviation modulus (E≤2.149%). The temperature influenced both equilibrium partition coefficients of phenolic compounds and transport properties, which is manifested by a relatively high value of activation energy (23-24) kJ/mol and by values of effective diffusivity in seed particles.

  13. Skeletal muscle DNA damage precedes spinal motor neuron DNA damage in a mouse model of Spinal Muscular Atrophy (SMA).

    PubMed

    Fayzullina, Saniya; Martin, Lee J

    2014-01-01

    Spinal Muscular Atrophy (SMA) is a hereditary childhood disease that causes paralysis by progressive degeneration of skeletal muscles and spinal motor neurons. SMA is associated with reduced levels of full-length Survival of Motor Neuron (SMN) protein, due to mutations in the Survival of Motor Neuron 1 gene. The mechanisms by which lack of SMN causes SMA pathology are not known, making it very difficult to develop effective therapies. We investigated whether DNA damage is a perinatal pathological event in SMA, and whether DNA damage and cell death first occur in skeletal muscle or spinal cord of SMA mice. We used a mouse model of severe SMA to ascertain the extent of cell death and DNA damage throughout the body of prenatal and newborn mice. SMA mice at birth (postnatal day 0) exhibited internucleosomal fragmentation in genomic DNA from hindlimb skeletal muscle, but not in genomic DNA from spinal cord. SMA mice at postnatal day 5, compared with littermate controls, exhibited increased apoptotic cell death profiles in skeletal muscle, by hematoxylin and eosin, terminal deoxynucleotidyl transferase dUTP nick end labeling, and electron microscopy. SMA mice had no increased cell death, no loss of choline acetyl transferase (ChAT)-positive motor neurons, and no overt pathology in the ventral horn of the spinal cord. At embryonic days 13 and 15.5, SMA mice did not exhibit statistically significant increases in cell death profiles in spinal cord or skeletal muscle. Motor neuron numbers in the ventral horn, as identified by ChAT immunoreactivity, were comparable in SMA mice and control littermates at embryonic day 15.5 and postnatal day 5. These observations demonstrate that in SMA, disease in skeletal muscle emerges before pathology in spinal cord, including loss of motor neurons. Overall, this work identifies DNA damage and cell death in skeletal muscle as therapeutic targets for SMA.

  14. Development of Models for Predicting the Predominant Taste and Odor Compounds in Taihu Lake, China

    PubMed Central

    Sun, Xiaoxue; Deng, Xuwei; Niu, Yuan; Xie, Ping

    2012-01-01

    Taste and odor (T&O) problems, which have adversely affected the quality of water supplied to millions of residents, have repeatedly occurred in Taihu Lake (e.g., a serious odor accident occurred in 2007). Because these accidents are difficult for water resource managers to forecast in a timely manner, there is an urgent need to develop optimum models to predict these T&O problems. For this purpose, various biotic and abiotic environmental parameters were monitored monthly for one year at 30 sites across Taihu Lake. This is the first investigation of this huge lake to sample T&O compounds at the whole-lake level. Certain phytoplankton taxa were important variables in the models; for instance, the concentrations of the particle-bound 2-methylisoborneol (p-MIB) were correlated with the presence of Oscillatoria, whereas those of the p-β-cyclocitral and p-β-ionone were correlated with Microcystis levels. Abiotic factors such as nitrogen (TN, TDN, NO3-N, and NO2-N), pH, DO, COND, COD and Chl-a also contributed significantly to the T&O predictive models. The dissolved (d) T&O compounds were related to both the algal biomass and to certain abiotic environmental factors, whereas the particle-bound (p) T&O compounds were more strongly related to the algal presence. We also tested the validity of these models using an independent data set that was previously collected from Taihu Lake in 2008. In comparing the concentrations of the T&O compounds observed in 2008 with those concentrations predicted from our models, we found that most of the predicted data points fell within the 90% confidence intervals of the observed values. This result supported the validity of these models in the studied system. These models, basing on easily collected environmental data, will be of practical value to the water resource managers of Taihu Lake for evaluating the probability of T&O accidents. PMID:23284835

  15. Mathematical modeling of the role of mitochondrial fusion and fission in mitochondrial DNA maintenance.

    PubMed

    Tam, Zhi Yang; Gruber, Jan; Halliwell, Barry; Gunawan, Rudiyanto

    2013-01-01

    Accumulation of mitochondrial DNA (mtDNA) mutations has been implicated in a wide range of human pathologies, including neurodegenerative diseases, sarcopenia, and the aging process itself. In cells, mtDNA molecules are constantly turned over (i.e. replicated and degraded) and are also exchanged among mitochondria during the fusion and fission of these organelles. While the expansion of a mutant mtDNA population is believed to occur by random segregation of these molecules during turnover, the role of mitochondrial fusion-fission in this context is currently not well understood. In this study, an in silico modeling approach is taken to investigate the effects of mitochondrial fusion and fission dynamics on mutant mtDNA accumulation. Here we report model simulations suggesting that when mitochondrial fusion-fission rate is low, the slow mtDNA mixing can lead to an uneven distribution of mutant mtDNA among mitochondria in between two mitochondrial autophagic events leading to more stochasticity in the outcomes from a single random autophagic event. Consequently, slower mitochondrial fusion-fission results in higher variability in the mtDNA mutation burden among cells in a tissue over time, and mtDNA mutations have a higher propensity to clonally expand due to the increased stochasticity. When these mutations affect cellular energetics, nuclear retrograde signalling can upregulate mtDNA replication, which is expected to slow clonal expansion of these mutant mtDNA. However, our simulations suggest that the protective ability of retrograde signalling depends on the efficiency of fusion-fission process. Our results thus shed light on the interplay between mitochondrial fusion-fission and mtDNA turnover and may explain the mechanism underlying the experimentally observed increase in the accumulation of mtDNA mutations when either mitochondrial fusion or fission is inhibited.

  16. Bond cleavage of lignin model compounds into aromatic monomers using supported metal catalysts in supercritical water

    PubMed Central

    Yamaguchi, Aritomo; Mimura, Naoki; Shirai, Masayuki; Sato, Osamu

    2017-01-01

    More efficient use of lignin carbon is necessary for carbon-efficient utilization of lignocellulosic biomass. Conversion of lignin into valuable aromatic compounds requires the cleavage of C–O ether bonds and C–C bonds between lignin monomer units. The catalytic cleavage of C–O bonds is still challenging, and cleavage of C–C bonds is even more difficult. Here, we report cleavage of the aromatic C–O bonds in lignin model compounds using supported metal catalysts in supercritical water without adding hydrogen gas and without causing hydrogenation of the aromatic rings. The cleavage of the C–C bond in bibenzyl was also achieved with Rh/C as a catalyst. Use of this technique may greatly facilitate the conversion of lignin into valuable aromatic compounds. PMID:28387304

  17. Comparisons of Non-Gaussian Statistical Models in DNA Methylation Analysis

    PubMed Central

    Ma, Zhanyu; Teschendorff, Andrew E.; Yu, Hong; Taghia, Jalil; Guo, Jun

    2014-01-01

    As a key regulatory mechanism of gene expression, DNA methylation patterns are widely altered in many complex genetic diseases, including cancer. DNA methylation is naturally quantified by bounded support data; therefore, it is non-Gaussian distributed. In order to capture such properties, we introduce some non-Gaussian statistical models to perform dimension reduction on DNA methylation data. Afterwards, non-Gaussian statistical model-based unsupervised clustering strategies are applied to cluster the data. Comparisons and analysis of different dimension reduction strategies and unsupervised clustering methods are presented. Experimental results show that the non-Gaussian statistical model-based methods are superior to the conventional Gaussian distribution-based method. They are meaningful tools for DNA methylation analysis. Moreover, among several non-Gaussian methods, the one that captures the bounded nature of DNA methylation data reveals the best clustering performance. PMID:24937687

  18. Bilirubin conjugates of human bile. Nuclear-magnetic-resonance, infrared and optical spectra of model compounds

    PubMed Central

    Kuenzle, Clive C.

    1970-01-01

    N.m.r., i.r. and optical spectra of model compounds were recorded. These were to help in elucidating the structures of the phenylazo derivatives of bilirubin conjugates isolated from human bile. Model compounds included commercial and human bile bilirubin, mesobilirubin, bilirubin dimethyl ester, dimethoxybilirubin dimethyl ester and the corresponding phenylazo derivatives. The phenylazo derivative of vinylneoxanthobilirubinic acid was also investigated. All compounds were of the type IXα, and no other isomer could be detected with the spectroscopic methods employed. The compounds crystallize as the lactams, except for dimethoxybilirubin dimethyl ester and its phenylazo derivative, which are held in the lactim ether configuration. With all other compounds no tautomeric forms other than the lactams could be detected, although small proportions of bilirubin must exist as the lactim. Bilirubin does not form a betaine, a structure that has been proposed by von Dobeneck & Brunner (1965) to explain the bathochromic shift of its optical spectrum as compared with the expected position of the absorption maximum at 420nm. However, this shift to 453nm can be explained on the basis of internal hydrogen bonds occurring between the carboxylic protons and the pyrrole rings of bilirubin, as proposed by Fog & Jellum (1963), and new evidence for such a bonding has been accumulated. The bilirubin sulphate described by Watson (1958), which is formed by treatment of bilirubin with concentrated sulphuric acid and acetic anhydride, was also investigated. The main product of this reaction was isolated as its phenylazo derivative, and was shown to be 3,18-di(ethylidene sulphate)-2,7,13,17-tetramethylbiladiene-ac-8,12-dipropionic acid. The reaction leading to this compound is an addition of sulphuric acid to the vinyl side chains of bilirubin according to Markownikoff's rule. PMID:5500301

  19. Key intermediates in nitrogen transformation during microwave pyrolysis of sewage sludge: a protein model compound study.

    PubMed

    Zhang, Jun; Tian, Yu; Cui, Yanni; Zuo, Wei; Tan, Tao

    2013-03-01

    The nitrogen transformations with attention to NH3 and HCN were investigated at temperatures of 300-800°C during microwave pyrolysis of a protein model compound. The evolution of nitrogenated compounds in the char, tar and gas products were conducted. The amine-N, heterocyclic-N and nitrile-N compounds were identified as three important intermediates during the pyrolysis. NH3 and HCN were formed with comparable activation energies competed to consume the same reactive substances at temperatures of 300-800°C. The deamination and dehydrogenation of amine-N compounds from protein cracking contributed to the formation of NH3 (about 8.9% of Soy-N) and HCN (6.6%) from 300 to 500°C. The cracking of nitrile-N and heterocyclic-N compounds from the dehydrogenation and polymerization of amine-N generated HCN (13.4%) and NH3 (31.3%) between 500 and 800°C. It might be able to reduce the HCN and NH3 emissions through controlling the intermediates production at temperatures of 500-800°C.

  20. Behavior of platinum(iv) complexes in models of tumor hypoxia: cytotoxicity, compound distribution and accumulation.

    PubMed

    Schreiber-Brynzak, Ekaterina; Pichler, Verena; Heffeter, Petra; Hanson, Buck; Theiner, Sarah; Lichtscheidl-Schultz, Irene; Kornauth, Christoph; Bamonti, Luca; Dhery, Vineet; Groza, Diana; Berry, David; Berger, Walter; Galanski, Markus; Jakupec, Michael A; Keppler, Bernhard K

    2016-04-01

    Hypoxia in solid tumors remains a challenge for conventional cancer therapeutics. As a source for resistance, metastasis development and drug bioprocessing, it influences treatment results and disease outcome. Bioreductive platinum(iv) prodrugs might be advantageous over conventional metal-based therapeutics, as biotransformation in a reductive milieu, such as under hypoxia, is required for drug activation. This study deals with a two-step screening of experimental platinum(iv) prodrugs with different rates of reduction and lipophilicity with the aim of identifying the most appropriate compounds for further investigations. In the first step, the cytotoxicity of all compounds was compared in hypoxic multicellular spheroids and monolayer culture using a set of cancer cell lines with different sensitivities to platinum(ii) compounds. Secondly, two selected compounds were tested in hypoxic xenografts in SCID mouse models in comparison to satraplatin, and, additionally, (LA)-ICP-MS-based accumulation and distribution studies were performed for these compounds in hypoxic spheroids and xenografts. Our findings suggest that, while cellular uptake and cytotoxicity strongly correlate with lipophilicity, cytotoxicity under hypoxia compared to non-hypoxic conditions and antitumor activity of platinum(iv) prodrugs are dependent on their rate of reduction.

  1. Molecular Modeling and Experimental Investigations of Nonlinear Optical Compounds Monosubstituted Derivatives of Dicyanovinylbenzene

    NASA Technical Reports Server (NTRS)

    Timofeeva, Tatiana V.; Nesterov, Vladimir N.; Antipin, Mikhail Yu.; Clark, Ronald D.; Sanghadasa, Mohan; Cardelino, Beatriz H.; Moore, Craig E.; Frazier, Donald O.

    1999-01-01

    A search for potential nonlinear optical compounds was performed using the Cambridge Structure Database and molecular modeling. We investigated a series of monosubstituted derivatives of dicyanovinylbenzene, since the nonlinear optical (NLO) properties of such derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were studied earlier. The molecular geometry of these compounds was investigated with x-ray analysis and discussed along with the results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the planarity of the molecules of this series has been revealed. Two new compounds from the series studied, ortho-F and para-Cl-dicyanovinylbenzene, according to powder measurements, were found to be NLO compounds in the crystal state about 10 times more active than urea. The peculiarities of crystal structure formation in the framework of balance between van der Waals and electrostatic interactions have been discussed. The crystal shape of DIVA and two new NLO compounds have been calculated on the basis of the known crystal structure.

  2. Ribonuclease H/DNA Polymerase HIV-1 Reverse Transcriptase Dual Inhibitor: Mechanistic Studies on the Allosteric Mode of Action of Isatin-Based Compound RMNC6

    PubMed Central

    Corona, Angela; Meleddu, Rita; Esposito, Francesca; Distinto, Simona; Bianco, Giulia; Masaoka, Takashi; Maccioni, Elias; Menéndez-Arias, Luis; Alcaro, Stefano; Le Grice, Stuart F. J.; Tramontano, Enzo

    2016-01-01

    The DNA polymerase and ribonuclease H (RNase H) activities of human immunodeficiency virus type 1 (HIV-1) are needed for the replication of the viral genome and are validated drug targets. However, there are no approved drugs inhibiting RNase H and the efficiency of DNA polymerase inhibitors can be diminished by the presence of drug resistance mutations. In this context, drugs inhibiting both activities could represent a significant advance towards better anti-HIV therapies. We report on the mechanisms of allosteric inhibition of a newly synthesized isatin-based compound designated as RMNC6 that showed IC50 values of 1.4 and 9.8 μM on HIV-1 RT-associated RNase H and polymerase activities, respectively. Blind docking studies predict that RMNC6 could bind two different pockets in the RT: one in the DNA polymerase domain (partially overlapping the non-nucleoside RT inhibitor [NNRTI] binding pocket), and a second one close to the RNase H active site. Enzymatic studies showed that RMNC6 interferes with efavirenz (an approved NNRTI) in its binding to the RT polymerase domain, although NNRTI resistance-associated mutations such as K103N, Y181C and Y188L had a minor impact on RT susceptibility to RMNC6. In addition, despite being naturally resistant to NNRTIs, the polymerase activity of HIV-1 group O RT was efficiently inhibited by RMNC6. The compound was also an inhibitor of the RNase H activity of wild-type HIV-1 group O RT, although we observed a 6.5-fold increase in the IC50 in comparison with the prototypic HIV-1 group M subtype B enzyme. Mutagenesis studies showed that RT RNase H domain residues Asn474 and Tyr501, and in a lesser extent Ala502 and Ala508, are critical for RMNC6 inhibition of the endonuclease activity of the RT, without affecting its DNA polymerization activity. Our results show that RMNC6 acts as a dual inhibitor with allosteric sites in the DNA polymerase and the RNase H domains of HIV-1 RT. PMID:26800261

  3. Ribonuclease H/DNA Polymerase HIV-1 Reverse Transcriptase Dual Inhibitor: Mechanistic Studies on the Allosteric Mode of Action of Isatin-Based Compound RMNC6.

    PubMed

    Corona, Angela; Meleddu, Rita; Esposito, Francesca; Distinto, Simona; Bianco, Giulia; Masaoka, Takashi; Maccioni, Elias; Menéndez-Arias, Luis; Alcaro, Stefano; Le Grice, Stuart F J; Tramontano, Enzo

    2016-01-01

    The DNA polymerase and ribonuclease H (RNase H) activities of human immunodeficiency virus type 1 (HIV-1) are needed for the replication of the viral genome and are validated drug targets. However, there are no approved drugs inhibiting RNase H and the efficiency of DNA polymerase inhibitors can be diminished by the presence of drug resistance mutations. In this context, drugs inhibiting both activities could represent a significant advance towards better anti-HIV therapies. We report on the mechanisms of allosteric inhibition of a newly synthesized isatin-based compound designated as RMNC6 that showed IC50 values of 1.4 and 9.8 μM on HIV-1 RT-associated RNase H and polymerase activities, respectively. Blind docking studies predict that RMNC6 could bind two different pockets in the RT: one in the DNA polymerase domain (partially overlapping the non-nucleoside RT inhibitor [NNRTI] binding pocket), and a second one close to the RNase H active site. Enzymatic studies showed that RMNC6 interferes with efavirenz (an approved NNRTI) in its binding to the RT polymerase domain, although NNRTI resistance-associated mutations such as K103N, Y181C and Y188L had a minor impact on RT susceptibility to RMNC6. In addition, despite being naturally resistant to NNRTIs, the polymerase activity of HIV-1 group O RT was efficiently inhibited by RMNC6. The compound was also an inhibitor of the RNase H activity of wild-type HIV-1 group O RT, although we observed a 6.5-fold increase in the IC50 in comparison with the prototypic HIV-1 group M subtype B enzyme. Mutagenesis studies showed that RT RNase H domain residues Asn474 and Tyr501, and in a lesser extent Ala502 and Ala508, are critical for RMNC6 inhibition of the endonuclease activity of the RT, without affecting its DNA polymerization activity. Our results show that RMNC6 acts as a dual inhibitor with allosteric sites in the DNA polymerase and the RNase H domains of HIV-1 RT.

  4. A model of a nonlinear DNA-protein interaction system with Killingbeck potential and its stability

    NASA Astrophysics Data System (ADS)

    Syahroni, E.; Suparmi, A.; Cari, C.; Fuad, A.

    2016-11-01

    In this paper, we presented a model of a nonlinear DNA-protein interaction system. The interaction system consisted of a molecule of protein bound with a single chain of DNA. The interaction between DNA chain, especially adenine and thymine, and DNA-protein bound to glutamine and adenine. The forms of these bonds are adapted from the hydrogen bonds. The Killingbeack potential were used to describe both of the interactions. We proposed the Hamiltonian equation to describe the general model of interaction. The interaction model is satisfied when a protein molecule triggers pulses on a DNA chain. An initial shift in position of protein xm should trigger the shift in position of DNA ym , or alter the state. However, an initial shift in DNA, yn , should not alter the state of a rest protein (i.e. xm = 0), otherwise, the protein would not steadily bind. We also investigated the stability of the model from the DNA-protein interaction with Lyapunov function. The stability of system can be determined when we obtained the equilibrium point.

  5. Ising-model description of long-range correlations in DNA sequences.

    PubMed

    Colliva, A; Pellegrini, R; Testori, A; Caselle, M

    2015-05-01

    We model long-range correlations of nucleotides in the human DNA sequence using the long-range one-dimensional (1D) Ising model. We show that, for distances between 10(3) and 10(6) bp, the correlations show a universal behavior and may be described by the non-mean-field limit of the long-range 1D Ising model. This allows us to make some testable hypothesis on the nature of the interaction between distant portions of the DNA chain which led to the DNA structure that we observe today in higher eukaryotes.

  6. Ising-model description of long-range correlations in DNA sequences

    NASA Astrophysics Data System (ADS)

    Colliva, A.; Pellegrini, R.; Testori, A.; Caselle, M.

    2015-05-01

    We model long-range correlations of nucleotides in the human DNA sequence using the long-range one-dimensional (1D) Ising model. We show that, for distances between 103 and 106 bp, the correlations show a universal behavior and may be described by the non-mean-field limit of the long-range 1D Ising model. This allows us to make some testable hypothesis on the nature of the interaction between distant portions of the DNA chain which led to the DNA structure that we observe today in higher eukaryotes.

  7. Acquisition of a comprhensive air quality model evaluation data set for organic compounds

    SciTech Connect

    Fraser, M.P.; CAss, G.R.; Grosjean, E.; Grosjean, D.

    1995-12-01

    In previous work, photochemical airshed models have been formulated and tested that are capable of predicting the concentrations of more than 50 individual vapor-phase organic compounds that are found in the urban atmosphere. In a separate development, air quality models that account for the concentration of nearly 100 particle-phase organic compounds have been tested. The opportunity thus exists to create a combined air quality model that simultaneously tracks both gas-phase, semi-volatile, and particle-phase organic compounds that range in carbon number from C1 to about C34. Such a tool can be used both to explore the relationship between source emissions and ambient air quality, and to study gas-to-particle conversion processes for organic compounds. A major barrier to the development of such a comprehensive model for atmospheric organic air pollution is the absence of an equally comprehensive atmospheric data base against which such a model can be tested. During September, 1993, an experiment designed to acquire such an air quality model validation data set for organics was conducted in Southern California. At four urban locations and at one upwind offshore island, consecutive measurements over four hour averaging limes were made of speciated vapor phase hydrocarbons, chlorinated organics, and certain gas phase oxygenates via stainless steel canister collection followed by GC/FID and GC/MS analysis. Semi-volatile organics were collected on PUF cartridges, and particle phase organics were collected by filtration, followed by GC/MS analysis. Aldehydes were collected on DNPH impregnated cartridges, and PAN`s were measured by electron capture GC. The design and selected results of that experiment will be discussed.

  8. Highly efficient radiosensitization of human glioblastoma and lung cancer cells by a G-quadruplex DNA binding compound

    PubMed Central

    Merle, Patrick; Gueugneau, Marine; Teulade-Fichou, Marie-Paule; Müller-Barthélémy, Mélanie; Amiard, Simon; Chautard, Emmanuel; Guetta, Corinne; Dedieu, Véronique; Communal, Yves; Mergny, Jean-Louis; Gallego, Maria; White, Charles; Verrelle, Pierre; Tchirkov, Andreï

    2015-01-01

    Telomeres are nucleoprotein structures at the end of chromosomes which stabilize and protect them from nucleotidic degradation and end-to-end fusions. The G-rich telomeric single-stranded DNA overhang can adopt a four-stranded G-quadruplex DNA structure (G4). Stabilization of the G4 structure by binding of small molecule ligands enhances radiosensitivity of tumor cells, and this combined treatment represents a novel anticancer approach. We studied the effect of the platinum-derived G4-ligand, Pt-ctpy, in association with radiation on human glioblastoma (SF763 and SF767) and non-small cell lung cancer (A549 and H1299) cells in vitro and in vivo. Treatments with submicromolar concentrations of Pt-ctpy inhibited tumor proliferation in vitro with cell cycle alterations and induction of apoptosis. Non-toxic concentrations of the ligand were then combined with ionizing radiation. Pt-ctpy radiosensitized all cell lines with dose-enhancement factors between 1.32 and 1.77. The combined treatment led to increased DNA breaks. Furthermore, a significant radiosensitizing effect of Pt-ctpy in mice xenografted with glioblastoma SF763 cells was shown by delayed tumor growth and improved survival. Pt-ctpy can act in synergy with radiation for efficient killing of cancer cells at concentrations at which it has no obvious toxicity per se, opening perspectives for future therapeutic applications. PMID:26542881

  9. Toxic effects of perfluorinated compounds at human cellular level and on a model vertebrate.

    PubMed

    Rainieri, Sandra; Conlledo, Nadia; Langerholc, Tomaž; Madorran, Eneko; Sala, Martin; Barranco, Alejandro

    2017-03-09

    This work aims at deepening the understanding of the mode of action of some of the most prominent perfluorinated compounds (PFCs) by detecting in a realistic way their effects. To this end, after adjusting the exposure media taking into account the biological model employed and the physico-chemical properties of PFCs, we evaluated the toxic effects of PFOA, PFOS and PFNA in a human macrophage cell line (TLT cells) and in zebrafish embryos. We performed such evaluation on individual compounds and mixtures. Acute toxicity was greater for PFOS in zebrafish; however, it was greater for PFNA in TLT cells. PFNA was also the compound producing the greatest levels of oxidative stress, both in zebrafish and TLT cells. Additionally, in both biological systems, it showed a much stronger effect on mixtures in comparison to the others PFCs tested in this work. Mixture studies in zebrafish showed that acute toxicity depended on the concentration and that the mixture was far more toxic than the individual compounds. This study highlights the importance of studying PFCs in realistic conditions on various biological models.

  10. Predictive QSPR Modelling for the Second Virial Coefficient of the Pure Organic Compounds.

    PubMed

    Mokshyna, E; Polishchuk, P G; Nedostup, V I; Kuzmin, V E

    2015-01-01

    In this article we developed a system of the predictive models for the second virial coefficients of the pure compounds. Second virial coefficient is the property derived from the virial equation of state, and is of particular interest as it describes pair intermolecular interactions. The two-layer QSPR models were developed, which exploited the well-known physical equations and allowed us to include this information into traditional QSPR methodology. This shows some new perspectives for work with temperature-dependent properties. It was shown that 2D descriptors can be successfully used for modeling of complex thermodynamic properties like virial coefficients.

  11. Mesoscopic models for DNA stretching under force: New results and comparison with experiments.

    PubMed

    Manghi, Manoel; Destainville, Nicolas; Palmeri, John

    2012-10-01

    Single-molecule experiments on double-stranded B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity. The nature and the critical forces of these transitions depend on DNA base sequence, loading rate, salt conditions and temperature. It has been proposed that the first transition, at forces of 60-80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA, while the second one, at stronger forces, is a strand peeling resulting in single-stranded DNAs (ssDNA), similar to thermal denaturation. But due to experimental conditions these two transitions can overlap, for instance for poly(dA-dT). In an attempt to propose a coherent picture compatible with this variety of experimental observations, we derive an analytical formula using a coupled discrete worm-like chain-Ising model. Our model takes into account bending rigidity, discreteness of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit of zero force, this model simplifies into a coupled model already developed by us for studying thermal DNA melting, establishing a connection with previous fitting parameter values for denaturation profiles. Our results are summarized as follows: i) ssDNA is fitted, using an analytical formula, over a nano-Newton range with only three free parameters, the contour length, the bending modulus and the monomer size; ii) a surprisingly good fit on this force range is possible only by choosing a monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase length; iii) mesoscopic models are not able to fit B to ssDNA (or S to ss) transitions; iv) an analytical formula for fitting B to S transitions is derived in the strong force approximation and for long DNAs, which is in excellent agreement with exact transfer matrix calculations; v) this formula fits perfectly well poly(dG-dC) and λ-DNA

  12. Drosophila melanogaster as a model system for the evaluation of anti-aging compounds.

    PubMed

    Jafari, Mahtab

    2010-01-01

    Understanding the causes of aging is a complex problem due to the multiple factors that influence aging, which include genetics, environment, metabolism and reproduction, among others. These multiple factors create logistical difficulties in the evaluation of anti-aging agents. There is a need for good model systems to evaluate potential anti-aging compounds. The model systems used should represent the complexities of aging in humans, so that the findings may be extrapolated to human studies, but they should also present an opportunity to minimize the variables so that the experimental results can be accurately interpreted. In addition to positively affecting lifespan, the impact of the compound on the physiologic confounders of aging, including fecundity and the health span--the period of life where an organism is generally healthy and free from serious or chronic illness--of the model organism needs to be evaluated. Fecundity is considered a major confounder of aging in fruit flies. It is well established that female flies that are exposed to toxic substances typically reduce their dietary intake and their reproductive output and display an artifactual lifespan extension. As a result, drugs that achieve longevity benefits by reducing fecundity as a result of diminished food intake are probably not useful candidates for eventual treatment of aging in humans and should be eliminated during the screening process. Drosophila melanogaster provides a suitable model system for the screening of anti-aging compounds as D. melanogaster and humans have many conserved physiological and biological pathways. In this paper, I propose an algorithm to screen anti-aging compounds using Drosophila melanogaster as a model system.

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  15. Hydrolytic cleavage of DNA-model substrates promoted by polyoxovanadates.

    PubMed

    Steens, Nele; Ramadan, Ahmed M; Absillis, Gregory; Parac-Vogt, Tatjana N

    2010-01-14

    Hydrolysis of 4-nitrophenyl phosphate (NPP) and bis-4-nitrophenyl phosphate (BNPP), two commonly used DNA model substrates, was examined in vanadate solutions by means of (1)H, (31)P and (51)V NMR spectroscopy. The hydrolysis of the phosphoester bond in NPP at 50 degrees C and pH 5.0 proceeds with a rate constant of 1.74 x 10(-5) s(-1). The cleavage of the phosphoester bond in BNPP at 70 degrees C and pH 5.0 proceeds with a rate constant of 3.32 x 10(-6) s(-1), representing an acceleration of four orders of magnitude compared to the uncatalyzed cleavage. Inorganic phosphate and nitrophenol (NP) were the only products of hydrolysis. The NMR spectra did not show evidence of any paramagnetic species, excluding the possibility of V(V) reduction to V(IV), indicating that the cleavage of the phosphoester bond is purely hydrolytic. The pH dependence of k(obs) revealed that the hydrolysis proceeds fastest in solutions of pH 5.5. Comparison of the rate profile with the concentration profile of polyoxovanadates shows a striking overlap of the k(obs) profile with the concentration of decavanadate (V(10)). Kinetic experiments at 37 degrees C using a fixed amount of NPP and increasing amounts of V(10) permitted the calculation of catalytic (k(c) = 5.67 x 10(-6) s(-1)) and formation constants for the NPP-V(10) complex (K(f) = 71.53 M(-1)). Variable temperature (31)P NMR spectra of a reaction mixture revealed broadening and shifting of the (31)P resonance upon addition of increasing amounts of decavanadate and upon increasing temperature, implying the dynamic exchange process between free and bound NPP at higher temperatures. The origin of the hydrolytic activity of V(10) is most likely due its high lability and its dissociation into smaller fragments which may allow the attachment of NPP and BNPP into the polyoxovanadate framework.

  16. DEVELOPMENT AND VALIDATION OF AN AIR-TO-BEEF FOOD CHAIN MODEL FOR DIOXIN-LIKE COMPOUNDS

    EPA Science Inventory

    A model for predicting concentrations of dioxin-like compounds in beef is developed and tested. The key premise of the model is that concentrations of these compounds in air are the source term, or starting point, for estimating beef concentrations. Vapor-phase concentrations t...

  17. Stereoregularity of poly (lactic acid) and their model compounds as studied by NMR and quantum chemical calculations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In order to understand the origin of the tacticity splitting in the NMR spectrum of poly(lactic acid), monomer model compound and dimer model compounds (both isotactic and syndiotactic) were synthesized and their 1H and 13C NMR chemical shifts observed. Two energetically stable conformations were o...

  18. Transgenerational inheritance: Models and mechanisms of non-DNA sequence-based inheritance.

    PubMed

    Miska, Eric A; Ferguson-Smith, Anne C

    2016-10-07

    Heritability has traditionally been thought to be a characteristic feature of the genetic material of an organism-notably, its DNA. However, it is now clear that inheritance not based on DNA sequence exists in multiple organisms, with examples found in microbes, plants, and invertebrate and vertebrate animals. In mammals, the molecular mechanisms have been challenging to elucidate, in part due to difficulties in designing robust models and approaches. Here we review some of the evidence, concepts, and potential mechanisms of non-DNA sequence-based transgenerational inheritance. We highlight model systems and discuss whether phenotypes are replicated or reconstructed over successive generations, as well as whether mechanisms operate at transcriptional and/or posttranscriptional levels. Finally, we explore the short- and long-term implications of non-DNA sequence-based inheritance. Understanding the effects of non-DNA sequence-based mechanisms is key to a full appreciation of heritability in health and disease.

  19. Chapter 8: Pyrolysis Mechanisms of Lignin Model Compounds Using a Heated Micro-Reactor

    SciTech Connect

    Robichaud, David J.; Nimlos, Mark R.; Ellison, G. Barney

    2015-10-03

    Lignin is an important component of biomass, and the decomposition of its thermal deconstruction products is important in pyrolysis and gasification. In this chapter, we investigate the unimolecular pyrolysis chemistry through the use of singly and doubly substituted benzene molecules that are model compounds representative of lignin and its primary pyrolysis products. These model compounds are decomposed in a heated micro-reactor, and the products, including radicals and unstable intermediates, are measured using photoionization mass spectrometry and matrix isolation infrared spectroscopy. We show that the unimolecular chemistry can yield insight into the initial decomposition of these species. At pyrolysis and gasification severities, singly substituted benzenes typically undergo bond scission and elimination reactions to form radicals. Some require radical-driven chain reactions. For doubly substituted benzenes, proximity effects of the substituents can change the reaction pathways.

  20. Tannin structural elucidation and quantitative ³¹P NMR analysis. 1. Model compounds.

    PubMed

    Melone, Federica; Saladino, Raffaele; Lange, Heiko; Crestini, Claudia

    2013-10-02

    Tannins and flavonoids are secondary metabolites of plants that display a wide array of biological activities. This peculiarity is related to the inhibition of extracellular enzymes that occurs through the complexation of peptides by tannins. Not only the nature of these interactions, but more fundamentally also the structure of these heterogeneous polyphenolic molecules are not completely clear. This first paper describes the development of a new analytical method for the structural characterization of tannins on the basis of tannin model compounds employing an in situ labeling of all labile H groups (aliphatic OH, phenolic OH, and carboxylic acids) with a phosphorus reagent. The ³¹P NMR analysis of ³¹P-labeled samples allowed the unprecedented quantitative and qualitative structural characterization of hydrolyzable tannins, proanthocyanidins, and catechin tannin model compounds, forming the foundations for the quantitative structural elucidation of a variety of actual tannin samples described in part 2 of this series.

  1. Reaction of nitric oxide with heme proteins and model compounds of hemoglobin

    SciTech Connect

    Sharma, V.S.; Traylor, T.G.; Gardiner, R.; Mizukami, H.

    1987-06-30

    Rates for the reaction of nitric oxide with several ferric heme proteins and model compounds have been measured. The NO combination rates are markedly affected by the presence or absence of distal histidine. Elephant myoglobin in which the E7 distal histidine has been replaced by glutamine reacts with NO 500-1000 times faster than do the native hemoglobins or myoglobins. By contrast, there is not difference in the CO combination rate constants of sperm whale and elephant myoglobins. Studies on ferric model compounds for the R and T states of hemoglobin indicate that their NO combination rate constants are similar to those observed for the combination of CO with the corresponding ferro derivatives. The last observation suggests that the presence of an axial water molecule at the ligand binding site of ferric hemoglobin A prevents it from exhibiting significant cooperativity in its reactions with NO.

  2. Probing Complex Free-Radical Reaction Pathways of Fuel Model Compounds

    SciTech Connect

    Buchanan III, A C; Kidder, Michelle; Beste, Ariana; Britt, Phillip F

    2012-01-01

    Fossil (e.g. coal) and renewable (e.g. woody biomass) organic energy resources have received considerable attention as possible sources of liquid transportation fuels and commodity chemicals. Knowledge of the reactivity of these complex materials has been advanced through fundamental studies of organic compounds that model constituent substructures. In particular, an improved understanding of thermochemical reaction pathways involving free-radical intermediates has arisen from detailed experimental kinetic studies and, more recently, advanced computational investigations. In this presentation, we will discuss our recent investigations of the fundamental pyrolysis pathways of model compounds that represent key substructures in the lignin component of woody biomass with a focus on molecules representative of the dominant beta-O-4 aryl ether linkages. Additional mechanistic insights gleaned from DFT calculations on the kinetics of key elementary reaction steps will also be presented, as well as a few thoughts on the significant contributions of Jim Franz to this area of free radical chemistry.

  3. Cascade of chromosomal rearrangements caused by a heterogeneous T-DNA integration supports the double-strand break repair model for T-DNA integration.

    PubMed

    Hu, Yufei; Chen, Zhiyu; Zhuang, Chuxiong; Huang, Jilei

    2017-02-28

    Transferred DNA (T-DNA) from Agrobacterium tumefaciens can be integrated into the plant genome. The double-strand break repair (DSBR) pathway is a major model for T-DNA integration. From this model, we expect that two ends of a T-DNA molecule would invade into a single DNA double-strand break (DSB) or independent DSBs in the plant genome. We call the later phenomenon a heterogeneous T-DNA integration which has never been observed. In this work, we demonstrated it in an Arabidopsis T-DNA insertion mutant seb19. To resolve the chromosomal structural changes caused by T-DNA integration at both the nucleotide and chromosome levels, we performed inverse PCR, genome resequencing, fluorescence in situ hybridization and linkage analysis. We found, in seb19, a single T-DNA connected two different chromosomal loci and caused complex chromosomal rearrangements. The specific break-junction pattern in seb19 is consistent with the result of heterogeneous T-DNA integration but not of recombination between two T-DNA insertions. We demonstrated that, in seb19, heterogeneous T-DNA integration evoked a cascade of incorrect repair of seven DSBs on chromosome 4 and 5, and then produced translocation, inversion, duplication and deletion. Heterogeneous T-DNA integration supports the DSBR model and suggests that two ends of a T-DNA molecule could be integrated into the plant genome independently. Our results also show a new origin of chromosomal abnormalities. This article is protected by copyright. All rights reserved.

  4. Some new nano-structure zinc(II) coordination compounds of an imidazolidine Schiff base: Spectral, thermal, antimicrobial properties and DNA interaction

    NASA Astrophysics Data System (ADS)

    Montazerozohori, Morteza; Musavi, Sayed Alireza; Naghiha, Asghar; Zohour, Mostafa Montazer

    2014-08-01

    Some novel nano-sized structure zinc complexes of a new Schiff base ligand entitled as (3-nitro-benzylidene)-{2-[2-(3-nitro-phenyl)-imidazolidine-1-yl]-ethyl}-amine(L) with general formula of ZnLX2 wherein X = Cl-, Br-, I-, SCN- and N3- have been synthesized under ultrasonic conditions. The ligand and its complexes have been characterized by elemental analysis, molar conductance measurements, FT-IR, 1H and 13C NMR and UV-Visible spectroscopy. The resulting data from spectral investigation especially 1H and 13C NMR well confirmed formation of an imidazolidine ring in the ligand structure. Transmission electron microscopy (TEM) showed nano-size structures with average particle sizes of 21.80-78.10 nm for the zinc(II) Schiff base complexes. The free Schiff base and its Zn(II) complexes have been screened in vitro both for antibacterial activity against some gram-positive and gram-negative bacteria and also for antifungal activity. The metal complexes were found to be more active than the free Schiff base ligand. The results showed that ZnL(N3)2 is the most effective inhibitor against Escherichia coli, Pseudomonas aereuguinosa, Staphylococcus aureus and Candida albicans while ZnLBr2 was found to be more effective against Bacillus subtillis than other compounds. Moreover, DNA cleavage potential of all compounds with plasmid DNA was investigated. The results showed that the ligand and ZnLCl2 complex cleave DNA more efficiently than others. In final, thermal analysis of ligand and its complexes revealed that they are decomposed via 2-3 thermal steps in the range of room temperature to 1000 °C. Furthermore some activation kinetic parameters such as A, E*, ΔH*, ΔS* and ΔG* were calculated based on TG/DTA plots by use of coats - Redfern relation. Positive values of activation energy evaluated for the compounds confirmed the thermal stability of them. In addition to, the positive ΔH*, and ΔG* values suggested endothermic character for the thermal decomposition steps.

  5. Phosphorus-nitrogen compounds: Part 28. Syntheses, structural characterizations, antimicrobial and cytotoxic activities, and DNA interactions of new phosphazenes bearing vanillinato and pendant ferrocenyl groups

    NASA Astrophysics Data System (ADS)

    Tümer, Yasemin; Asmafiliz, Nuran; Kılıç, Zeynel; Hökelek, Tuncer; Yasemin Koç, L.; Açık, Leyla; Yola, Mehmet Lütfi; Solak, Ali Osman; Öner, Yağmur; Dündar, Devrim; Yavuz, Makbule

    2013-10-01

    The gradually Cl replacement reactions of spirocyclic mono (1 and 2) and bisferrocenyl cyclotriphosphazenes (3-5) with the potassium salt of 4-hydroxy-3-methoxybenzaldehyde (potassium vanillinate) gave mono (1a-5a), geminal (gem-1b-5b), non-geminal (cis-1b, cis-5b and trans-2b-5b), tri (1c-5c) and tetra-substituted phosphazenes (1d-5d). Some phosphazenes have stereogenic P-center(s). The chirality of 4c was verified using chiral HPLC column. Electrochemical behaviors were influenced only by the number of ferrocene groups, but not the length of the amine chains and the substituent(s). The structures of the new phosphazenes were determined by FTIR, MS, 1H, 13C and 31P NMR, HSQC and HMBC spectral data. The solid-state structures of cis-1b and 4d were examined by single crystal X-ray diffraction techniques. The twelve phosphazene derivatives were screened for antimicrobial activity and the compounds 5a, cis-1b and 2c exhibited the highest antibacterial activity against G(+) and G(-) bacteria. In addition, it was found that overall gem-1b inhibited the growth of Mycobacterium tuberculosis. The compounds 1d, 2d and 4d were tested in HeLa cancer cell lines. Among these compounds, 2d had cytotoxic effect on HeLa cell in the first 48 h. Moreover, interactions between compounds 2a, gem-1b, gem-2b, cis-1b, 2c, 3c, 4c, 5c, 1d, 2d and 4d, and pBR322 plasmid DNA were investigated.

  6. Protein expression from unintegrated HIV-1 DNA introduces bias in primary in vitro post-integration latency models.

    PubMed

    Bonczkowski, Pawel; De Scheerder, Marie-Angélique; Malatinkova, Eva; Borch, Alexandra; Melkova, Zora; Koenig, Renate; De Spiegelaere, Ward; Vandekerckhove, Linos

    2016-12-02

    To understand the persistence of latently HIV-1 infected cells in virally suppressed infected patients, a number of in vitro models of HIV latency have been developed. In an attempt to mimic the in vivo situation as closely as possible, several models use primary cells and replication-competent viruses in combination with antiretroviral compounds to prevent ongoing replication. Latency is subsequently measured by HIV RNA and/or protein production after cellular activation. To discriminate between pre- and post-integration latency, integrase inhibitors are routinely used, preventing novel integrations upon cellular activation. Here, we show that this choice of antiretrovirals may still cause a bias of pre-integration latency in these models, as unintegrated HIV DNA can form and directly contribute to the levels of HIV RNA and protein production. We further show that the addition of reverse transcriptase inhibitors effectively suppresses the levels of episomal HIV DNA (as measured by 2-LTR circles) and decreases the levels of HIV transcription. Consequently, we show that latency levels described in models that only use integrase inhibitors may be overestimated. The inclusion of additional control conditions, such as 2-LTR quantification and the addition of reverse transcriptase inhibitors, is crucial to fully elucidate the actual levels of post-integration latency.

  7. Protein expression from unintegrated HIV-1 DNA introduces bias in primary in vitro post-integration latency models

    PubMed Central

    Bonczkowski, Pawel; De Scheerder, Marie-Angélique; Malatinkova, Eva; Borch, Alexandra; Melkova, Zora; Koenig, Renate; De Spiegelaere, Ward; Vandekerckhove, Linos

    2016-01-01

    To understand the persistence of latently HIV-1 infected cells in virally suppressed infected patients, a number of in vitro models of HIV latency have been developed. In an attempt to mimic the in vivo situation as closely as possible, several models use primary cells and replication-competent viruses in combination with antiretroviral compounds to prevent ongoing replication. Latency is subsequently measured by HIV RNA and/or protein production after cellular activation. To discriminate between pre- and post-integration latency, integrase inhibitors are routinely used, preventing novel integrations upon cellular activation. Here, we show that this choice of antiretrovirals may still cause a bias of pre-integration latency in these models, as unintegrated HIV DNA can form and directly contribute to the levels of HIV RNA and protein production. We further show that the addition of reverse transcriptase inhibitors effectively suppresses the levels of episomal HIV DNA (as measured by 2-LTR circles) and decreases the levels of HIV transcription. Consequently, we show that latency levels described in models that only use integrase inhibitors may be overestimated. The inclusion of additional control conditions, such as 2-LTR quantification and the addition of reverse transcriptase inhibitors, is crucial to fully elucidate the actual levels of post-integration latency. PMID:27910923

  8. Volatile Organic Compounds source contributions in Paris: Measurement and modeling approaches. Focus on the traffic source

    NASA Astrophysics Data System (ADS)

    Gros, Valerie; Petetin, Hervé; Sarda-Estève, Roland; Kalogridis, Cerise; Baudic, Alexia; Bonnaire, Nicolas; Bonsang, Bernard; Xueref-Rémy, Irène; Ammoura, Lamia; Le Priol, Tiphaine; François Petit, Jean; Sanchez, Olivier; Rosso, Amandine; Perrussel, Olivier; Petit, Jean-Eudes; Sciare, Jean

    2013-04-01

    first results obtained with the CHIMERE model used both in research and air quality forecasting at local, national and European scales. The wide variety of measured compounds will allow evaluating both VOC's emission inventory and formation/consumption processes.

  9. [Computer simulation of the transcription process in the discrete model of DNA molecule].

    PubMed

    Zakir'ianov, F K; Khamzin, S R

    2011-01-01

    A mathematical model of the nonlinear dynamics of DNA has been considered, which takes into account the real sequence of the nitrous base. Soliton solutions describing the nonlinear mechanisms of the regulation of DNA transcription have been obtained. It has been shown that the soliton-like excitation may both fade in the terminator of the first gene and pass into the promotor of the second gene. Thus, transcription processes in one gene and two consecutive genes are modeled.

  10. Calibration of silicone rubber passive samplers: experimental and modeled relations between sampling rate and compound properties.

    PubMed

    Rusina, Tatsiana P; Smedes, Foppe; Koblizkova, Martina; Klanova, Jana

    2010-01-01

    Sampling rates (Rs) for silicone rubber (SR) passive samplers were measured under two different hydrodynamic conditions. Concentrations were maintained in the aqueous phase by continuous equilibration with SR sheets of a large total surface area which had been spiked with polycyclic aromatic hydrocarbons and/or polychlorinated biphenyls. Test sheets made of the same SR but of much smaller surface area were used to measure the uptake rate. Measured Rs values decreased with increasing passive sampler-water partition coefficient (Kpw) according to Rs approximately Kpw(-0.08) under both hydrodynamic conditions. This decrease is not significantly different from modeled values if the uncertainty of the diffusion coefficients in water is included. Modeling also confirmed that uptake of the test compounds under the experimental conditions was entirely controlled by diffusion in the water phase. A model using Rs approximately M(-0.47) is suggested for extrapolation of Rs estimated from the dissipation of performance reference compounds to target compounds in a higher hydrophobicity range.

  11. The Murine Intravaginal HSV-2 Challenge Model for Investigation of DNA Vaccines

    PubMed Central

    Marshak, Joshua O.; Dong, Lichun; Koelle, David M.

    2014-01-01

    DNA vaccines have been licensed in veterinary medicine and have promise for humans. This format is relatively immunogenic in mice and guinea pigs, the two principle HSV-2 animal models, permitting rapid assessment of vectors, antigens, adjuvants, and delivery systems. Limitations include the relatively poor immunogenicity of naked DNA in humans and the profound differences in HSV-2 pathogenesis between host species. Herein, we detail lessons learned over the last few years investigating candidate DNA vaccines in the progesterone-primed female mouse vaginal model of HSV-2 infection as a guide to investigators in the field. PMID:24671693

  12. A probabilistic model for risk assessment of residual host cell DNA in biological products.

    PubMed

    Yang, Harry; Zhang, Lanju; Galinski, Mark

    2010-04-26

    Biological products such as viral vaccines manufactured in cells contain residual DNA derived from host cell substrates used in production. It is theoretically possible that the residual DNA could transmit activated oncogenes and/or latent infectious viral genomes to subjects receiving the product, and induce oncogenic or infective events. A probabilistic model to estimate the risks due to residual DNA is proposed. The model takes account of enzyme inactivation process. It allows for more accurate risk assessment when compared to methods currently in use. An application of the method to determine safety factor of a vaccine product is provided.

  13. Molecular Modeling and Experimental Study of Nonlinear Optical Compounds: Mono-Substituted Derivatives of Dicyanovinylbenzene

    NASA Technical Reports Server (NTRS)

    Timofeeva, Tatyana V.; Nesterov, Vladimir N.; Antipin, Mikhael Y.; Clark, R. D.; Sanghadasa, M.; Cardelino, B. H.; Moore, C. E.; Frazier, Donald O.

    2000-01-01

    A search for potential nonlinear optical (NLO) compounds has been performed using the Cambridge Structural Database and molecular modeling. We have studied a series of mono-substituted derivatives of dicyanovinylbenzene as the NLO properties of one of its derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were described earlier. The molecular geometry in the series of the compounds studied was investigated with an X- ray analysis and discussed along with results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the molecular planarity has been revealed. Two new compounds from the series studied were found to be active for second harmonic generation (SHG) in the powder. The measurements of SHG efficiency have shown that the o-F- and p-Cl-derivatives of dicyanovinylbenzene are about 10 and 20- times more active than urea, respectively. The peculiarities of crystal structure formation in the framework of balance between the van der Waals and electrostatic interactions have been discussed. The crystal morphology of DIVA and two new SHG-active compounds have been calculated on the basis of their known crystal structures.

  14. Identification of compounds with anti-convulsant properties in a zebrafish model of epileptic seizures

    PubMed Central

    Baxendale, Sarah; Holdsworth, Celia J.; Meza Santoscoy, Paola L.; Harrison, Michael R. M.; Fox, James; Parkin, Caroline A.; Ingham, Philip W.; Cunliffe, Vincent T.

    2012-01-01

    SUMMARY The availability of animal models of epileptic seizures provides opportunities to identify novel anticonvulsants for the treatment of people with epilepsy. We found that exposure of 2-day-old zebrafish embryos to the convulsant agent pentylenetetrazole (PTZ) rapidly induces the expression of synaptic-activity-regulated genes in the CNS, and elicited vigorous episodes of calcium (Ca2+) flux in muscle cells as well as intense locomotor activity. We then screened a library of ∼2000 known bioactive small molecules and identified 46 compounds that suppressed PTZ-inducedtranscription of the synaptic-activity-regulated gene fos in 2-day-old (2 dpf) zebrafish embryos. Further analysis of a subset of these compounds, which included compounds with known and newly identified anticonvulsant properties, revealed that they exhibited concentration-dependent inhibition of both locomotor activity and PTZ-induced fos transcription, confirming their anticonvulsant characteristics. We conclude that this in situ hybridisation assay for fos transcription in the zebrafish embryonic CNS is a robust, high-throughput in vivo indicator of the neural response to convulsant treatment and lends itself well to chemical screening applications. Moreover, our results demonstrate that suppression of PTZ-induced fos expression provides a sensitive means of identifying compounds with anticonvulsant activities. PMID:22730455

  15. Variation in rDNA locus number and position among legume species and detection of 2 linked rDNA loci in the model Medicago truncatula by FISH.

    PubMed

    Abirached-Darmency, Mona; Prado-Vivant, Emilce; Chelysheva, Liudmila; Pouthier, Thomas

    2005-06-01

    Within Fabaceae, legume species have a variable genome size, chromosome number, and ploidy level. The genome distribution of ribosomal genes, easily detectable by fluorescent in situ hybridization (FISH), is a good tool for anchoring physical and genetic comparative maps. The organisation of 45S rDNA and 5S loci was analysed by FISH in the 4 closely related species: Pisum sativum, Medicago truncatula, Medicago sativa (2 diploid taxa), and Lathyrus sativus. The 2 types of rDNA arrays displayed interspecific variation in locus number and location, but little intraspecific variation was detected. In the model legume, M. truncatula, the presence of 2 adjacent 45S rDNA loci was demonstrated, and the location of the rDNA loci was independent of the general evolution of the genome DNA. The different parameters relative to clustering of the rDNA loci in specific chromosome regions and the possible basis of rDNA instability are discussed.

  16. In vivo imaging of DNA lipid nanocapsules after systemic administration in a melanoma mouse model.

    PubMed

    David, Stephanie; Carmoy, Nathalie; Resnier, Pauline; Denis, Caroline; Misery, Laurent; Pitard, Bruno; Benoit, Jean-Pierre; Passirani, Catherine; Montier, Tristan

    2012-02-14

    The biodistribution of intravenously injected DNA lipid nanocapsules (DNA LNCs), encapsulating pHSV-tk, was analysed by in vivo imaging on an orthotopic melanoma mouse model and by a subsequent treatment with ganciclovir (GCV), using the gene-directed enzyme prodrug therapy (GDEPT) approach. Luminescent melanoma cells, implanted subcutaneously in the right flank of the mice, allowed us to follow tumour growth and tumour localisation with in vivo bioluminescence imaging (BLI). In parallel, DNA LNCs or PEG DNA LNCs (DNA LNCs recovered with PEG(2000)) encapsulating a fluorescent probe, DiD, allowed us to follow their biodistribution with in vivo biofluorescence imaging (BFI). The BF-images confirmed a prolonged circulation-time for PEG DNA LNCs as was previously observed on an ectotopic model of glioma; comparison with BL-images evidenced the colocalisation of PEG DNA LNCs and melanoma cells. After these promising results, treatment with PEG DNA LNCs and GCV on a few animals was performed and the treatment efficacy measured by BLI. The first results showed tumour growth reduction tendency and, once optimised, this therapy strategy could become a new option for melanoma treatment.

  17. Aquatic Pathways Model to predict the fate of phenolic compounds. Appendixes A through D

    SciTech Connect

    Aaberg, R.L.; Peloquin, R.A.; Strenge, D.L.; Mellinger, P.L.

    1983-04-01

    Organic materials released from energy-related activities could affect human health and the environment. We have developed a model to predict the fate of spills or discharges of pollutants into flowing or static bodies of fresh water. A computer code, Aquatic Pathways Model (APM), was written to implement the model. The APM estimates the concentrations of chemicals in fish tissue, water and sediment, and is therefore useful for assessing exposure to humans through aquatic pathways. The major pathways considered are biodegradation, fish and sediment uptake, photolysis, and evaporation. The model has been implemented with parameters for the distribution of phenols, an important class of compounds found in the water-soluble fractions of coal liquids. The model was developed to estimate the fate of liquids derived from coal. Current modeling efforts show that, in comparison with many pesticides and polyaromatic hydrocarbons (PAH), the lighter phenolics (the cresols) are not persistent in the environment. For the twelve phenolics studied, biodegradation appears to be the major pathway for elimination from aquatic environments. A pond system simulation of a spill of solvent-refined coal (SRC-II) materials indicates that phenol, cresols, and other single cyclic phenolics are degraded to 16 to 25 percent of their original concentrations within 30 hours. Adsorption of these compounds into sediments and accumulation by fish was minor. Results of a simulated spill of a coal liquid (SRC-II) into a pond show that APM predicted the allocation of 12 phenolic components among six compartments at 30 hours after a small spill. The simulation indicated that most of the introduced phenolic compounds were biodegraded. The phenolics remaining in the aquatic system partitioned according to their molecular weight and structure. A substantial amount was predicted to remain in the water, with less than 0.01% distributed in sediment or fish.

  18. How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model

    NASA Astrophysics Data System (ADS)

    Reiter-Schad, Michaela; Werner, Erik; Tegenfeldt, Jonas O.; Mehlig, Bernhard; Ambjörnsson, Tobias

    2015-09-01

    When double-stranded DNA molecules are heated, or exposed to denaturing agents, the two strands are separated. The statistical physics of this process has a long history and is commonly described in terms of the Poland-Scheraga (PS) model. Crucial to this model is the configurational entropy for a melted region (compared to the entropy of an intact region of the same size), quantified by the loop factor. In this study, we investigate how confinement affects the DNA melting transition, by using the loop factor for an ideal Gaussian chain. By subsequent numerical solutions of the PS model, we demonstrate that the melting temperature depends on the persistence lengths of single-stranded and double-stranded DNA. For realistic values of the persistence lengths, the melting temperature is predicted to decrease with decreasing channel diameter. We also demonstrate that confinement broadens the melting transition. These general findings hold for the three scenarios investigated: 1. homo-DNA, i.e., identical basepairs along the DNA molecule, 2. random sequence DNA, and 3. "real" DNA, here T4 phage DNA. We show that cases 2 and 3 in general give rise to broader transitions than case 1. Case 3 exhibits a similar phase transition as case 2 provided the random sequence DNA has the same ratio of AT to GC basepairs (A - adenine, T - thymine, G - guanine, C - cytosine). A simple analytical estimate for the shift in melting temperature is provided as a function of nanochannel diameter. For homo-DNA, we also present an analytical prediction of the melting probability as a function of temperature.

  19. Equilibrium and kinetics of DNA overstretching modeled with a quartic energy landscape.

    PubMed

    Argudo, David; Purohit, Prashant K

    2014-11-04

    It is well known that the dsDNA molecule undergoes a phase transition from B-DNA into an overstretched state at high forces. For some time, the structure of the overstretched state remained unknown and highly debated, but recent advances in experimental techniques have presented evidence of more than one possible phase (or even a mixed phase) depending on ionic conditions, temperature, and basepair sequence. Here, we present a theoretical model to study the overstretching transition with the possibility that the overstretched state is a mixture of two phases: a structure with portions of inner strand separation (melted or M-DNA), and an extended phase that retains the basepair structure (S-DNA). We model the double-stranded DNA as a chain composed of n segments of length l, where the transition is studied by means of a Landau quartic potential with statistical fluctuations. The length l is a measure of cooperativity of the transition and is key to characterizing the overstretched phase. By analyzing the different values of l corresponding to a wide spectrum of experiments, we find that for a range of temperatures and ionic conditions, the overstretched form is likely to be a mix of M-DNA and S-DNA. For a transition close to a pure S-DNA state, where the change in extension is close to 1.7 times the original B-DNA length, we find l ? 25 basepairs regardless of temperature and ionic concentration. Our model is fully analytical, yet it accurately reproduces the force-extension curves, as well as the transient kinetic behavior, seen in DNA overstretching experiments.

  20. Dynamical Model for the Decay of Hot and Rotating Compound Nuclei

    SciTech Connect

    Gupta, Raj K.; Singh, Dalip; Arun, Sham K.; Niyti; Kumar, Raj

    2009-03-04

    As an alternative to the well known Hauser-Feshbach analysis and statistical fission model, a dynamical collective clusterization model, called the dynamical cluster-decay model (DCM), is developed for the decay of hot and rotating compound nuclei (CN) formed in the low-energy heavy ion reactions. The model is a non-statistical description for the decay of a CN to light particles (LPs), intermediate mass fragments (IMFs), fusion-fission (FF) and quasi-fission (QF)(equivalently, capture) processes. The model considers all decay products as dynamical mass motions of preformed fragments or clusters through the interaction barrier, thereby including structure effects of the CN, and is applicable to CN from different mass regions.

  1. Modeling of multicomponent pervaporation for removal of volatile organic compounds from water

    SciTech Connect

    Ji, W.; Sikdar, S.K.; Hwang, S.T.

    1994-01-01

    A resistance-in-series model was used to study the pervaporation of multiple volatile organic compounds (VOCs)-water mixtures. Permeation experiments were carried out for four membranes and three VOCs. The membrane permeability were calculated in terms of the resistance-in-series model. The membrane performances were then compared with each other based on the permeabilities. Both organic and water permeabilities of polyether-block-polyamides (PEBA) membrane for one VOC-water, two VOC-water, and three VOC-water mixtures were found to be comparable with each other.

  2. A DNA double-strand break kinetic rejoining model based on the local effect model.

    PubMed

    Tommasino, F; Friedrich, T; Scholz, U; Taucher-Scholz, G; Durante, M; Scholz, M

    2013-11-01

    We report here on a DNA double-strand break (DSB) kinetic rejoining model applicable to a wide range of radiation qualities based on the DNA damage pattern predicted by the local effect model (LEM). In the LEM this pattern is derived from the SSB and DSB yields after photon irradiation in combination with an amorphous track structure approach. Together with the assumption of a giant-loop organization to describe the higher order chromatin structure this allows the definition of two different classes of DSB. These classes are defined by the level of clustering on a micrometer scale, i.e., "isolated DSB" (iDSB) are characterized by a single DSB in a giant loop and "clustered DSB" (cDSB) by two or more DSB in a loop. Clustered DSB are assumed to represent a more difficult challenge for the cell repair machinery compared to isolated DSB, and we thus hypothesize here that the fraction of isolated DSB can be identified with the fast component of rejoining, whereas clustered DSB are identified with the slow component of rejoining. The resulting predicted bi-exponential decay functions nicely reproduce the experimental curves of DSB rejoining over time obtained by means of gel electrophoresis elution techniques as reported by different labs, involving different cell types and a wide spectrum of radiation qualities. New experimental data are also presented aimed at investigating the effects of the same ion species accelerated at different energies. The results presented here further support the relevance of the proposed two classes of DSB as a basis for understanding cell response to ion irradiation. Importantly the density of DSB within DNA giant loops of around 2 Mbp size, i.e., on a micrometer scale, is identified as a key parameter for the description of radiation effectiveness.

  3. DNA studies are necessary for accurate patient diagnosis in compound heterozygosity for Hb Adana (HBA2:c.179>A) with deletional or nondeletional α-thalassaemia

    PubMed Central

    Tan, Jin Ai Mary Anne; Kho, Siew Leng; Ngim, Chin Fang; Chua, Kek Heng; Goh, Ai Sim; Yeoh, Seoh Leng; George, Elizabeth

    2016-01-01

    Haemoglobin (Hb) Adana (HBA2:c.179>A) interacts with deletional and nondeletional α-thalassaemia mutations to produce HbH disorders with varying clinical manifestations from asymptomatic to severe anaemia with significant hepatosplenomegaly. Hb Adana carriers are generally asymptomatic and haemoglobin subtyping is unable to detect this highly unstable α-haemoglobin variant. This study identified 13 patients with compound heterozygosity for Hb Adana with either the 3.7 kb gene deletion (-α3.7), Hb Constant Spring (HbCS) (HBA2:c.427T>C) or Hb Paksé (HBA2:429A>T). Multiplex Amplification Refractory Mutation System was used for the detection of five deletional and six nondeletional α-thalassaemia mutations. Duplex-PCR was used to confirm Hb Paksé and HbCS. Results showed 84.6% of the Hb Adana patients were Malays. Using DNA studies, compound heterozygosity for Hb Adana and HbCS (αcodon 59α/αCSα) was confirmed in 11 patients. A novel point in this investigation was that DNA studies confirmed Hb Paksé for the first time in a Malaysian patient (αcodon 59α/αPakséα) after nine years of being misdiagnosis with Hb Adana and HbCS (αcodon 59α/αCSα). Thus, the reliance on haematology studies and Hb subtyping to detect Hb variants is inadequate in countries where thalassaemia is prevalent and caused by a wide spectrum of mutations. PMID:27271331

  4. A Bayesian Approach to Joint Modeling of Protein-DNA Binding, Gene Expression and Sequence Data

    PubMed Central

    Xie, Yang; Pan, Wei; Jeong, Kyeong S.; Xiao, Guanghua; Khodursky, Arkady B.

    2012-01-01

    The genome-wide DNA-protein binding data, DNA sequence data and gene expression data represent complementary means to deciphering global and local transcriptional regulatory circuits. Combining these different types of data can not only improve the statistical power, but also provide a more comprehensive picture of gene regulation. In this paper, we propose a novel statistical model to augment proteinDNA binding data with gene expression and DNA sequence data when available. We specify a hierarchical Bayes model and use Markov chain Monte Carlo simulations to draw inferences. Both simulation studies and an analysis of an experimental dataset show that the proposed joint modeling method can significantly improve the specificity and sensitivity of identifying target genes as compared to conventional approaches relying on a single data source. PMID:20049751

  5. Exploring the binding mechanism of phosphoramidate derivative with DNA: Spectroscopy, calorimetry and modeling

    NASA Astrophysics Data System (ADS)

    Wang, Gongke; Wu, Hongwei; Wang, Dongchao; Yan, Changling; Lu, Yan

    2013-03-01

    In this study, one of the amino phosphine ester derivatives α-(3-hydroxy-4-methoxyphenyl)-N-phenyl-α-aminophosphonate (HMPAP) was synthesized, and the molecular interaction of HMPAP with ct-DNA has been investigated by UV-Vis absorption spectra, fluorescence spectra, isothermal titration calorimetry (ITC) and molecular modeling. The binding constant (Kb) of HMPAP to ct-DNA at different temperatures were calculated from fluorescence spectra. According to the UV-Vis absorption spectra, ethidium bromide displacement studies and ITC experimental results, we can conclude that HMPAP is an intercalator. The molecular modeling results indicated that HMPAP can slide into the G-C rich region of ct-DNA. ITC data showed that ct-DNA/HMPAP binding is enthalpy controlled. Furthermore, the results obtained from molecular modeling corroborated the experimental results obtanied from spectroscopic and ITC investigations.

  6. Isoflavonoid compounds extracted from Pueraria lobata suppress alcohol preference in a pharmacogenetic rat model of alcoholism.

    PubMed

    Lin, R C; Guthrie, S; Xie, C Y; Mai, K; Lee, D Y; Lumeng, L; Li, T K

    1996-06-01

    The extract from an edible vine, Pueraria lobata, has long been used in China to lessen alcohol intoxication. We have previously shown that daidzin, one of the major components from this plant extract, is efficacious in lowering blood alcohol levels and shortens sleep time induced by alcohol ingestion. This study was conducted to test the antidipsotropic effect of daidzin and two other major isoflavonoids, daidzein and puerarin, from Pueraria lobata administered by the oral route. An alcohol-preferring rat model, the selectively-bred P line of rats, was used for the study. All three isoflavonoid compounds were effective in suppressing voluntary alcohol consumption by the P rats. When given orally to P rats at a dose of 100 mg/kg/day, daidzein, daidzin, and puerarin decreased ethanol intake by 75%, 50%, and 40%, respectively. The decrease in alcohol consumption was accompanied by an increase in water intake, so that the total fluid volume consumed daily remained unchanged. The effects of these isoflavonoid compounds on alcohol and water intake were reversible. Suppression of alcohol consumption was evident after 1 day of administration and became maximal after 2 days. Similarly, alcohol preference returned to baseline levels 2 days after discontinuation of the isoflavonoids. Rats receiving the herbal extracts ate the same amounts of food as control animals, and they gained weight normally during the experiments. When administered orally, none of these compounds affected the activities of liver alcohol dehydrogenase and aldehyde dehydrogenase. Therefore, the reversal of alcohol preference produced by these compounds may be mediated via the CNS. Data demonstrate that isoflavonoid compounds extracted from Pueraria lobata is effective in suppressing the appetite for alcohol when taken orally, raising the possibility that other constituents of edible plants may exert similar and more potent actions.

  7. Toxic volatile organic compounds in environmental tobacco smoke: Emission factors for modeling exposures of California populations

    SciTech Connect

    Daisey, J.M.; Mahanama, K.R.R.; Hodgson, A.T.

    1994-10-01

    The primary objective of this study was to measure emission factors for selected toxic air contaminants in environmental tobacco smoke (ETS) using a room-sized environmental chamber. The emissions of 23 volatile organic compounds (VOCs), including, 1,3-butadiene, three aldehydes and two vapor-phase N-nitrosamines were determined for six commercial brands of cigarettes and reference cigarette 1R4F. The commercial brands were selected to represent 62.5% of the cigarettes smoked in California. For each brand, three cigarettes were machine smoked in the chamber. The experiments were conducted over four hours to investigate the effects of aging. Emission factors of the target compounds were also determined for sidestream smoke (SS). For almost all target compounds, the ETS emission factors were significantly higher than the corresponding SS values probably due to less favorable combustion conditions and wall losses in the SS apparatus. Where valid comparisons could be made, the ETS emission factors were generally in good agreement with the literature. Therefore, the ETS emission factors, rather than the SS values, are recommended for use in models to estimate population exposures from this source. The variabilities in the emission factors ({mu}g/cigarette) of the selected toxic air contaminants among brands, expressed as coefficients of variation, were 16 to 29%. Therefore, emissions among brands were Generally similar. Differences among brands were related to the smoked lengths of the cigarettes and the masses of consumed tobacco. Mentholation and whether a cigarette was classified as light or regular did not significantly affect emissions. Aging was determined not to be a significant factor for the target compounds. There were, however, deposition losses of the less volatile compounds to chamber surfaces.

  8. Direct detection of the hydrolysis of nerve agent model compounds using a fluorescent probe.

    PubMed

    Zheng, Xueying; Okolotowicz, Karl; Wang, Beilin; Macdonald, Mary; Cashman, John R; Zhang, Jun

    2010-09-06

    Nerve agents are highly toxic organophosphorus compounds (OPs) that are used as chemical warfare agents. Developing a catalytic bioscavenger to efficiently detoxify nerve agents in the bloodstream of affected individuals has been recognized as an attractive approach to prevent nerve agent toxicity. However, the search for nerve agent catalysts has been hindered by the lack of efficient direct assays for nerve agent hydrolysis. In addition, authentic nerve agents are restricted and access to use for experiments by the general research community is prohibited. Herein we report development of a method that combines use of novel nerve agent model compounds possessing a thiocholine leaving group that reacts with the fluorescent thio-detection probe, BES-Thio, to afford detection of sub-micromolar amounts of nerve agent model compounds hydrolysis products. The detection sensitivity of BES-Thio assay was approximately 10 times better than the Ellman assay. This developed method is useful as a direct, sensitive screening method for evaluating OP hydrolysis efficiency from catalytic cholinesterases. When the assay was assembled in the presence of oxime, OP-inhibited cholinesterases that were able to be reactivated by specific oxime showed oxime-assisted enzyme-mediated OP hydrolysis. Therefore, this method is also useful to screen oxime analogs to identify novel agents that can reactivate OP-inhibited cholinesterases or to screen various enzymes to identify pseudo-catalytic bioscavengers that can be readily reactivated by clinically approved oximes.

  9. A functional [NiFe]-hydrogenase model compound that undergoes biologically relevant reversible thiolate protonation.

    PubMed

    Weber, Katharina; Krämer, Tobias; Shafaat, Hannah S; Weyhermüller, Thomas; Bill, Eckhard; van Gastel, Maurice; Neese, Frank; Lubitz, Wolfgang

    2012-12-26

    Two model compounds of the active site of [NiFe]-hydrogenases with an unusual {S(2)Ni(μ-S)(μ-CO)Fe(CO)(2)S}-coordination environment around the metals are reported. The neutral compound [Ni(xbsms)(μ-CO)(μ-S)Fe(CO)(2)('S')], (1) (H(2)xbsms = 1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) is converted to [1H][BF(4)] by reversible protonation using HBF(4)·Et(2)O. The protonation takes place at the terminal thiolate sulfur atom that is coordinated to nickel. Catalytic intermediates with a protonated terminal cysteinate were suggested for the native protein but have not yet been confirmed experimentally. [1H][BF(4)] is the first dinuclear [NiFe] model compound for such a species. Both complexes have been synthesized and characterized by X-ray crystallography, NMR-, FTIR-, and (57)Fe-Mössbauer spectroscopy as well as by electronic absorption and resonance Raman spectroscopy. The experimental results clearly show that the protonation has a significant impact on the electronic structure of the iron center, although it takes place at the nickel site. DFT calculations support the interpretation of the spectroscopic data and indicate the presence of a bonding interaction between the metal ions, which is relevant for the enzyme as well. Electrochemical experiments show that both 1 and [1H][BF(4)] are active for electrocatalytic proton reduction in aprotic solvents.

  10. Reactions of aqueous chlorine and chlorine dioxide with model food compounds

    SciTech Connect

    Fukayama, M.Y.; Tan, H.; Wheeler, W.B.; Wei, C.

    1986-11-01

    This presentation reviews published information concerning the reactions of chlorine gas (CL/sub 2/(g)), aqueous chlorine, and ClO/sub 2/ with model food compounds, the fate of chlorine during the chlorination of specific food products, and the potential toxicity of the reaction products. Fatty acids and their methyl esters react with chlorine with the degree of incorporation corresponding to their degree of unsaturation. Aqueous chlorine oxidizes and chlorinates lipids and amino acids much more readily than ClO/sub 2/. Several amino acids are highly susceptible to oxidation and chlorination by chlorine compounds. Reactions of chlorine and ClO/sub 2/ with several food products, including flour and shrimp, have also been characterized. Although significant quantities of chlorine can be incorporated into specific model compounds and food products, the health risks associated with exposure to chlorinated organic products are unknown. Preliminary studies using the Ames Salmonella/microsome mutagenicity assay indicate that the reaction products from mixtures of aqueous chlorine and various lipids or tryptophan are nonmutagenic. Nevertheless, additional studies are warranted, so that the toxicological significance of these reaction products can be understood more fully.

  11. Chemical synthesis of two series of nerve agent model compounds and their stereoselective interaction with human acetylcholinesterase and human butyrylcholinesterase.

    PubMed

    Barakat, Nora H; Zheng, Xueying; Gilley, Cynthia B; MacDonald, Mary; Okolotowicz, Karl; Cashman, John R; Vyas, Shubham; Beck, Jeremy M; Hadad, Christopher M; Zhang, Jun

    2009-10-01

    Both G and V type nerve agents possess a center of chirality about phosphorus. The S(p) enantiomers are generally more potent inhibitors than their R(p) counterparts toward acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). To develop model compounds with defined centers of chirality that mimic the target nerve agent structures, we synthesized both the S(p) and the R(p) stereoisomers of two series of G type nerve agent model compounds in enantiomerically enriched form. The two series of model compounds contained identical substituents on the phosphorus as the G type agents, except that thiomethyl (CH(3)-S-) and thiocholine [(CH(3))(3)NCH(2)CH(2)-S-] groups were used to replace the traditional nerve agent leaving groups (i.e., fluoro for GB, GF, and GD and cyano for GA). Inhibition kinetic studies of the thiomethyl- and thiocholine-substituted series of nerve agent model compounds revealed that the S(p) enantiomers of both series of compounds showed greater inhibition potency toward AChE and BChE. The level of stereoselectivity, as indicated by the ratio of the bimolecular inhibition rate constants between S(p) and R(p) enantiomers, was greatest for the GF model compounds in both series. The thiocholine analogues were much more potent than the corresponding thiomethyl analogues. With the exception of the GA model compounds, both series showed greater potency against AChE than BChE. The stereoselectivity (i.e., S(p) > R(p)), enzyme selectivity, and dynamic range of inhibition potency contributed from these two series of compounds suggest that the combined application of these model compounds will provide useful research tools for understanding interactions of nerve agents with cholinesterase and other enzymes involved in nerve agent and organophosphate pharmacology. The potential of and limitations for using these model compounds in the development of biological therapeutics against nerve agent toxicity are also discussed.

  12. A model for the control of DNA integrity by the sperm nuclear matrix

    PubMed Central

    Gawecka, Joanna E; Ribas-Maynou, Jordi; Benet, Jordi; Ward, W Steven

    2015-01-01

    The highly condensed chromatin of mammalian spermatozoa is usually considered to be biologically inert before fertilization. However, we have demonstrated that even in this compacted state, sperm chromatin is subject to degradation at open configurations associated with the nuclear matrix through a process we have termed sperm chromatin fragmentation (SCF). This suggests that a mechanism exists to monitor the health of spermatozoa during transit through the male reproductive tract and to destroy the genome of defective sperm cells. The site of DNA damage in SCF, the matrix attachment sites, are the same that we hypothesize initiate DNA synthesis in the zygote. When sperm that have damaged DNA are injected into the oocyte, the newly created zygote responds by delaying DNA synthesis in the male pronucleus and, if the damage is severe enough, arresting the embryo's development. Here we present a model for paternal DNA regulation by the nuclear matrix that begins during sperm maturation and continues through early embryonic development. PMID:25926613

  13. Organic compounds present in airborne particles stimulate superoxide production and DNA fragmentation: role of NOX and xanthine oxidase in animal tissues.

    PubMed

    Busso, Iván Tavera; Silva, Guillermo Benjamín; Carreras, Hebe Alejandra

    2016-08-01

    Suspended particulate matter trigger the production of reactive oxygen species. However, most of the studies dealing with oxidative damage of airborne particles focus on the effects of individual compounds and not real mixtures. In order to study the enzymatic superoxide production resulting from the exposition to a complex mixture, we derived organic extracts from airborne particles collected daily in an urban area and exposed kidney, liver, and heart mammal tissues. After that, we measured DNA damage employing the comet assay. We observed that in every tissue, NADPH oxidase and xanthine oxidase were involved in O2 (-) production when they were exposed to the organic extracts, as the lucigenin's chemiluminescence decays when enzymes were inhibited. The same trend was observed with the percentage of cells with comets, since DNA damage was higher when they were exposed to same experimental conditions. Our data allow us to hypothesize that these enzymes play an important role in the oxidative stress produced by PAHs and that there is a mechanism involving them in the O2 (-)generation.

  14. The traditional Chinese medical compound Rocaglamide protects nonmalignant primary cells from DNA damage-induced toxicity by inhibition of p53 expression

    PubMed Central

    Becker, M S; Schmezer, P; Breuer, R; Haas, S F; Essers, M A; Krammer, P H; Li-Weber, M

    2014-01-01

    One of the main obstacles of conventional anticancer therapy is the toxicity of chemotherapeutics to normal tissues. So far, clinical approaches that aim to specifically reduce chemotherapy-mediated toxicities are rare. Recently, a number of studies have demonstrated that herbal extracts derived from traditional Chinese medicine (TCM) may reduce chemotherapy-induced side effects. Thus, we screened a panel of published cancer-inhibiting TCM compounds for their chemoprotective potential and identified the phytochemical Rocaglamide (Roc-A) as a candidate. We show that Roc-A significantly reduces apoptotic cell death induced by DNA-damaging anticancer drugs in primary human and murine cells. Investigation of the molecular mechanism of Roc-A-mediated protection revealed that Roc-A specifically blocks DNA damage-induced upregulation of the transcription factor p53 by inhibiting its protein synthesis. The essential role of p53 in Roc-A-mediated protection was confirmed by siRNA knockdown of p53 and by comparison of the effects of Roc-A on chemoprotection of splenocytes isolated from wild-type and p53-deficient mice. Importantly, Roc-A did not protect p53-deficient or -mutated cancer cells. Our data suggest that Roc-A may be used as an adjuvant to reduce the side effects of chemotherapy in patients with p53-deficient or -mutated tumors. PMID:24434508

  15. An Analytical Model for the Distributions of Velocity and Discharge in Compound Channels with Submerged Vegetation

    PubMed Central

    Jiang, Beihan; Yang, Kejun; Cao, Shuyou

    2015-01-01

    Based on the momentum transfer theory, an analytical model is proposed for the velocity and discharge distributions in compound channels with submerged vegetation on the floodplain. The partially vegetated channel was divided into three sub-regions, i.e. the main channel region, the floodplain region with submerged vegetation and the floodplain region without vegetation. For each region, the force balance relationship was established, and the momentum transfer between different regions was presented. Verification by the experimental data and comparison with the traditional method shows that the proposed method is capable of predicting for the velocity and discharge distributions in compound channels with submerged vegetation and is superior to the conventional method. The results also show that when the momentum transfer between different regions is ignored, the computed discharge will be much lager than the measured data, and the error increases with the discharge, especially in the floodplain region. PMID:26161661

  16. X-ray diffraction study of thermotropic liquid crystalline polyesters and diester model compounds

    NASA Astrophysics Data System (ADS)

    Chin, H. H.; Azaroff, L. V.; Griffin, A. C.

    1987-10-01

    Two nematic liquid crystalline polyesters were examined by X-ray diffraction following quenching from the nematic temperature in a magnetic field of 15 tesla. It was not possible to quench an aligned nematic glass; instead a polycrystalline phase showing some preferred orientation or an unoriented nematic melt yielded monodomain nematic diffraction patterns with one resembling that of a fiber (crystalline) photograph while the other showed good nematic alignment which could be enhanced slightly by annealing. A series of Siamese-twin diester model compounds also examined at their respective nematic temperatures in a magnetic field of compounds also were examined at their crystalline phase at room temperature. All displayed well-aligned nematic monodomains above the crystallization point.

  17. Spatial Arrangment of Organic Compounds on a Model Mineral Surface: Implications for Soil Organic Matter Stabilization

    SciTech Connect

    Petridis, Loukas; Ambaye, Haile Arena; Jagadamma, Sindhu; Kilbey, S. Michael; Lokitz, Bradley S; Lauter, Valeria; Mayes, Melanie

    2014-01-01

    The complexity of the mineral organic carbon interface may influence the extent of stabilization of organic carbon compounds in soils, which is important for global climate futures. The nanoscale structure of a model interface was examined here by depositing films of organic carbon compounds of contrasting chemical character, hydrophilic glucose and amphiphilic stearic acid, onto a soil mineral analogue (Al2O3). Neutron reflectometry, a technique which provides depth-sensitive insight into the organization of the thin films, indicates that glucose molecules reside in a layer between Al2O3 and stearic acid, a result that was verified by water contact angle measurements. Molecular dynamics simulations reveal the thermodynamic driving force behind glucose partitioning on the mineral interface: The entropic penalty of confining the less mobile glucose on the mineral surface is lower than for stearic acid. The fundamental information obtained here helps rationalize how complex arrangements of organic carbon on soil mineral surfaces may arise

  18. 1,4-Dihydropyridine Derivatives: Dihydronicotinamide Analogues—Model Compounds Targeting Oxidative Stress

    PubMed Central

    Velena, Astrida; Zarkovic, Neven; Gall Troselj, Koraljka; Bisenieks, Egils; Krauze, Aivars; Poikans, Janis; Duburs, Gunars

    2016-01-01

    Many 1,4-dihydropyridines (DHPs) possess redox properties. In this review DHPs are surveyed as protectors against oxidative stress (OS) and related disorders, considering the DHPs as specific group of potential antioxidants with bioprotective capacities. They have several peculiarities related to antioxidant activity (AOA). Several commercially available calcium antagonist, 1,4-DHP drugs, their metabolites, and calcium agonists were shown to express AOA. Synthesis, hydrogen donor properties, AOA, and methods and approaches used to reveal biological activities of various groups of 1,4-DHPs are presented. Examples of DHPs antioxidant activities and protective effects of DHPs against OS induced damage in low density lipoproteins (LDL), mitochondria, microsomes, isolated cells, and cell cultures are highlighted. Comparison of the AOA of different DHPs and other antioxidants is also given. According to the data presented, the DHPs might be considered as bellwether among synthetic compounds targeting OS and potential pharmacological model compounds targeting oxidative stress important for medicinal chemistry. PMID:26881016

  19. 1,4-Dihydropyridine Derivatives: Dihydronicotinamide Analogues-Model Compounds Targeting Oxidative Stress.

    PubMed

    Velena, Astrida; Zarkovic, Neven; Gall Troselj, Koraljka; Bisenieks, Egils; Krauze, Aivars; Poikans, Janis; Duburs, Gunars

    2016-01-01

    Many 1,4-dihydropyridines (DHPs) possess redox properties. In this review DHPs are surveyed as protectors against oxidative stress (OS) and related disorders, considering the DHPs as specific group of potential antioxidants with bioprotective capacities. They have several peculiarities related to antioxidant activity (AOA). Several commercially available calcium antagonist, 1,4-DHP drugs, their metabolites, and calcium agonists were shown to express AOA. Synthesis, hydrogen donor properties, AOA, and methods and approaches used to reveal biological activities of various groups of 1,4-DHPs are presented. Examples of DHPs antioxidant activities and protective effects of DHPs against OS induced damage in low density lipoproteins (LDL), mitochondria, microsomes, isolated cells, and cell cultures are highlighted. Comparison of the AOA of different DHPs and other antioxidants is also given. According to the data presented, the DHPs might be considered as bellwether among synthetic compounds targeting OS and potential pharmacological model compounds targeting oxidative stress important for medicinal chemistry.

  20. Understanding Karma Police: The Perceived Plausibility of Noun Compounds as Predicted by Distributional Models of Semantic Representation

    PubMed Central

    Günther, Fritz; Marelli, Marco

    2016-01-01

    Noun compounds, consisting of two nouns (the head and the modifier) that are combined into a single concept, differ in terms of their plausibility: school bus is a more plausible compound than saddle olive. The present study investigates which factors influence the plausibility of attested and novel noun compounds. Distributional Semantic Models (DSMs) are used to obtain formal (vector) representations of word meanings, and compositional methods in DSMs are employed to obtain such representations for noun compounds. From these representations, different plausibility measures are computed. Three of those measures contribute in predicting the plausibility of noun compounds: The relatedness between the meaning of the head noun and the compound (Head Proximity), the relatedness between the meaning of modifier noun and the compound (Modifier Proximity), and the similarity between the head noun and the modifier noun (Constituent Similarity). We find non-linear interactions between Head Proximity and Modifier Proximity, as well as between Modifier Proximity and Constituent Similarity. Furthermore, Constituent Similarity interacts non-linearly with the familiarity with the compound. These results suggest that a compound is perceived as more plausible if it can be categorized as an instance of the category denoted by the head noun, if the contribution of the modifier to the compound meaning is clear but not redundant, and if the constituents are sufficiently similar in cases where this contribution is not clear. Furthermore, compounds are perceived to be more plausible if they are more familiar, but mostly for cases where the relation between the constituents is less clear. PMID:27732599

  1. The elastic rod model for DNA and its application to the tertiary structure of DNA minicircles in mononucleosomes.

    PubMed Central

    Swigon, D; Coleman, B D; Tobias, I

    1998-01-01

    Explicit solutions to the equations of equilibrium in the theory of the elastic rod model for DNA are employed to develop a procedure for finding the configuration that minimizes the elastic energy of a minicircle in a mononucleosome with specified values of the minicircle size N in base pairs, the extent w of wrapping of DNA about the histone core particle, the helical repeat h(0)b of the bound DNA, and the linking number Lk of the minicircle. The procedure permits a determination of the set Y(N, w, h(0)b) of integral values of Lk for which the minimum energy configuration does not involve self-contact, and graphs of writhe versus w are presented for such values of Lk. For the range of N of interest here, 330 < N < 370, the set Y(N, w, h(0)b) is of primary importance: when Lk is not in Y(N, w, h(0)b), the configurations compatible with Lk have elastic energies high enough to preclude the occurrence of an observable concentration of topoisomer Lk in an equilibrium distribution of topoisomers. Equilibrium distributions of Lk, calculated by setting differences in the free energy of the extranucleosomal loop equal to differences in equilibrium elastic energy, are found to be very close to Gaussian when computed under the assumption that w is fixed, but far from Gaussian when it is assumed that w fluctuates between two values. The theoretical results given suggest a method by which one may calculate DNA-histone binding energies from measured equilibrium distributions of Lk. PMID:9591678

  2. New stutter ratio distribution for DNA mixture interpretation based on a continuous model.

    PubMed

    Manabe, Sho; Hamano, Yuya; Morimoto, Chie; Kawai, Chihiro; Fujimoto, Shuntaro; Tamaki, Keiji

    2016-03-01

    In forensic science, DNA mixture interpretation is traditionally based on a binary model, which does not account for peak-height information in DNA profiles. In recent years, some countries have adopted a continuous model in which peak heights are used and stochastic effects are considered to enable rigorous calculation of likelihood ratios. However, this model requires certain biological parameters which affect the expected allelic and stutter peak heights. In this paper, we focused on estimating the distribution of the stutter ratio (SR) in 15 short tandem repeat loci in relation to the allele repeat number. We estimated the SR values of 234 single-source DNA samples by using a commercially available kit. In all loci except for D8S1179, D21S11, and D2S1338, a simple log-normal distribution model was fitted to the variability of SR. For D21S11, we developed a new distribution model in which distinct log-normal distributions between complete and incomplete repeat units are used (a separate log-normal distribution model). For D8S1179 and D2S1338, we developed another new distribution model that mixes two log-normal distributions to explain two types of repeat structures appearing within the same number of allele repeats. These two models were fitted to the observed SR values more accurately than the simple log-normal distribution model. We expected these new SR models to be applied to DNA mixture interpretation based on a continuous model.

  3. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray.

    PubMed

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Wong, Hau-San

    2016-01-01

    Transcription factor binding sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, protein binding microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k = 8∼10). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build TFBS (also known as DNA motif) models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement if choosing di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

  4. Thermal Decomposition Mechanisms of Lignin Model Compounds: From Phenol to Vanillin

    NASA Astrophysics Data System (ADS)

    Scheer, Adam Michael

    Lignin is a complex, aromatic polymer abundant in cellulosic biomass (trees, switchgrass etc.). Thermochemical breakdown of lignin for liquid fuel production results in undesirable polycyclic aromatic hydrocarbons that lead to tar and soot byproducts. The fundamental chemistry governing these processes is not well understood. We have studied the unimolecular thermal decomposition mechanisms of aromatic lignin model compounds using a miniature SiC tubular reactor. Products are detected and characterized using time-of-flight mass spectrometry with both single photon (118.2 nm; 10.487 eV) and 1 + 1 resonance-enhanced multiphoton ionization (REMPI) as well as matrix isolation infrared spectroscopy. Gas exiting the heated reactor (300 K--1600 K) is subject to a free expansion after a residence time of approximately 100 micros. The expansion into vacuum rapidly cools the gas mixture and allows the detection of radicals and other highly reactive intermediates. By understanding the unimolecular fragmentation patterns of phenol (C6H5OH), anisole (C6H 5OCH3) and benzaldehyde (C6H5CHO), the more complicated thermocracking processes of the catechols (HO-C 6H4-OH), methoxyphenols (HO-C6H4-OCH 3) and hydroxybenzaldehydes (HO-C6H4-CHO) can be interpreted. These studies have resulted in a predictive model that allows the interpretation of vanillin, a complex phenolic ether containing methoxy, hydroxy and aldehyde functional groups. This model will serve as a guide for the pyrolyses of larger systems including lignin monomers such as coniferyl alcohol. The pyrolysis mechanisms of the dimethoxybenzenes (H3C-C 6H4-OCH3) and syringol, a hydroxydimethoxybenzene have also been studied. These results will aid in the understanding of the thermal fragmentation of sinapyl alcohol, the most complex lignin monomer. In addition to the model compound work, pyrolyisis of biomass has been studied via the pulsed laser ablation of poplar wood. With the REMPI scheme, aromatic lignin decomposition

  5. Modeling the bandstructures of B-DNA base stacks

    NASA Astrophysics Data System (ADS)

    Rengifo, E.; Murillo, G.; Arce, J. C.

    2013-05-01

    A pseudohelical approximation for the calculation of the bandstructures of DNA base homostacks in B conformation is introduced. It consists of choosing a unit cell of only two nucleobases with relative parallel displacement and twist that locally mimic the helical conformation. It is tested employing the extended Hückel method with a unique Wolfsberg-Helmholtz parameter. The resulting bandgaps and ionization potential trend agree well with the ones reported in the literature employing the full screw-axis symmetry and higher levels of theory. The electron and hole effective masses extracted from the bandstructures follow the same trends as the experimentally reported mobilities.

  6. Oxidative DNA damage background estimated by a system model of base excision repair

    SciTech Connect

    Sokhansanj, B A; Wilson, III, D M

    2004-05-13

    Human DNA can be damaged by natural metabolism through free radical production. It has been suggested that the equilibrium between innate damage and cellular DNA repair results in an oxidative DNA damage background that potentially contributes to disease and aging. Efforts to quantitatively characterize the human oxidative DNA damage background level based on measuring 8-oxoguanine lesions as a biomarker have led to estimates varying over 3-4 orders of magnitude, depending on the method of measurement. We applied a previously developed and validated quantitative pathway model of human DNA base excision repair, integrating experimentally determined endogenous damage rates and model parameters from multiple sources. Our estimates of at most 100 8-oxoguanine lesions per cell are consistent with the low end of data from biochemical and cell biology experiments, a result robust to model limitations and parameter variation. Our results show the power of quantitative system modeling to interpret composite experimental data and make biologically and physiologically relevant predictions for complex human DNA repair pathway mechanisms and capacity.

  7. A United Atom Model for Simulation of DNA from Angstroms to Microns in Length

    NASA Astrophysics Data System (ADS)

    Knotts, Thomas, IV; Rathore, Nitin; de Pablo, Juan

    2006-03-01

    For several years, single molecule pulling experiments have given insights into the stability of DNA. Many descriptions of DNA, from atomistic to continuum, have proven successful at reproducing observed behavior. We have found, however, that there is no suitable model for several problems of interest, including viral packaging of DNA and microarray interactions, where the size of the molecules prohibits atomistic representations, but continuum and linear bead-spring models do not contain the required molecular level of detail. Emerging technologies require that mesoscopic models of DNA be developed, capable of describing length scales in the 5 to 500 nm range. One of the main challenges is to preserve a coupling between the phenomena seen at longer length scales (e. g. a persistence length of 50 nm) while incorporating the features needed for smaller scales (e. g. charge effects, geometry, and base specificity). We have developed a coarse grain description of DNA which reduces the complexity of a nucleotide to three interaction sites. The model is capable of describing sequence information, bubble formation, and salt effects in simulations of DNA up to a few microns in length. The predictions are in remarkable, quantitative agreement with experiment, and shed light into the coupling of multiple length scales and interactions to yield unique behaviors and functions.

  8. Oxidative DNA damage background estimated by a system model of base excision repair.

    PubMed

    Sokhansanj, Bahrad A; Wilson, David M

    2004-08-01

    Human DNA can be damaged by natural metabolism through free radical production. It has been suggested that the equilibrium between innate damage and cellular DNA repair results in an oxidative DNA damage background that potentially contributes to disease and aging. Efforts to quantitatively characterize the human oxidative DNA damage background level, based on measuring 8-oxoguanine lesions as a biomarker, have led to estimates that vary over three to four orders of magnitude, depending on the method of measurement. We applied a previously developed and validated quantitative pathway model of human DNA base excision repair, integrating experimentally determined endogenous damage rates and model parameters from multiple sources. Our estimates of at most 100 8-oxoguanine lesions per cell are consistent with the low end of data from biochemical and cell biology experiments, a result robust to model limitations and parameter variation. Our findings show the power of quantitative system modeling to interpret composite experimental data and make biologically and physiologically relevant predictions for complex human DNA repair pathway mechanisms and capacity.

  9. Application of the S=1 underscreened Anderson lattice model to Kondo uranium and neptunium compounds

    NASA Astrophysics Data System (ADS)

    Thomas, Christopher; da Rosa Simões, Acirete S.; Iglesias, J. R.; Lacroix, C.; Perkins, N. B.; Coqblin, B.

    2011-01-01

    Magnetic properties of uranium and neptunium compounds showing the coexistence of the Kondo screening effect and ferromagnetic order are investigated within the Anderson lattice Hamiltonian with a two-fold degenerate f level in each site, corresponding to 5f2 electronic configuration with S=1 spins. A derivation of the Schrieffer-Wolff transformation is presented and the resulting Hamiltonian has an effective f-band term, in addition to the regular exchange Kondo interaction between the S=1 f spins and the s=1/2 spins of the conduction electrons. The resulting effective Kondo lattice model can describe both the Kondo regime and a weak delocalization of the 5f electrons. Within this model we compute the Kondo and Curie temperatures as a function of model parameters, namely the Kondo exchange interaction constant JK, the magnetic intersite exchange interaction JH, and the effective f bandwidth. We deduce, therefore, a phase diagram of the model which yields the coexistence of the Kondo effect and ferromagnetic ordering and also accounts for the pressure dependence of the Curie temperature of uranium compounds such as UTe.

  10. A cometabolic biotransformation model for halogenated aliphatic compounds exhibiting product toxicity

    SciTech Connect

    Alvarez-Cohen, L. ); McCarty, P.L. )

    1991-08-01

    A model is proposed to describe the rate and extent of cometabolic transformation of halogenated aliphatic compounds by resting microbial cells. The finite transformation capacity ({Tc}) of resting cells, which appears to be associated with cometabolic oxidation of many halogenated aliphatic compounds, is used to incorporate the effects of product toxicity and reductant supply into a modified expression of Monod kinetics. Applicability of the model of trichloroethylene transformation by resting cells from a mixed methanotrophic culture is evaluated by comparison with experimental data from batch transformation studies conducted over a range of conditions. A visually good and statistically reasonable fit was obtained between the experimental data and model predictions both with cells alone and with formate added as an exogenous reductant source. A comparison of parameter estimates (k and K{sub s}) derived by use of the cometabolic transformation model and those derived by use of conventional linearized Monod techniques (Lineweaver-Burk and concentration-normalized equations) indicates that, for reactions involving a finite transformation capacity, the linearized Monod equations yield artificially elevated parameters estimates.

  11. The relationship between UV-irradiance, photoprotective compounds and DNA damage in two intertidal invertebrates with contrasting mobility characteristics.

    PubMed

    Cubillos, Victor Mauricio; Burritt, David J; Lamare, Miles D; Peake, Barrie M

    2015-08-01

    The photoprotective role of mycosporine-like amino acids (MAA) against the generation of DNA cyclobutane pyrimidine dimers (CPD) was studied in the sessile intertidal anemone Actinia tenebrosa and the mobile intertidal gastropod Diloma aethiops through 27months at a mid-latitude New Zealand location. MAA were sequestered by A. tenebrosa and D. aethiops from their diet, although maximum total MAA levels in both species were not correlated with seasonal variation in maximum ambient UV-B levels recorded at the collection site. Temporal changes in total MAA in A. tenebrosa showed a six months lag-time in their concentration regarding to the environmental UV-B levels. This lag period corresponded to an observed increase in CPD production from spring to summer; suggesting that MAA do not completely protect the anemone from UV-B during summer. For D. aethiops, total MAA concentrations did not change significantly during the study, although qualitative changes in MAA were apparent. A month lag-time in MAA concentration in D. aethiops and possibly the physical barrier that the shell confers to the animal, can explain reduced CPD levels in comparative terms with A. tenebrosa. Although MAA are used by invertebrates for photoprotection, contrasting mobility characteristics and the presence of physical adaptations can confer them important protection levels during temporal changes of UV-B at mid-latitude places of the Southern Hemisphere.

  12. Highlighting the DNA damage response with ultrashort laser pulses in the near infrared and kinetic modeling

    PubMed Central

    Ferrando-May, Elisa; Tomas, Martin; Blumhardt, Philipp; Stöckl, Martin; Fuchs, Matthias; Leitenstorfer, Alfred

    2013-01-01

    Our understanding of the mechanisms governing the response to DNA damage in higher eucaryotes crucially depends on our ability to dissect the temporal and spatial organization of the cellular machinery responsible for maintaining genomic integrity. To achieve this goal, we need experimental tools to inflict DNA lesions with high spatial precision at pre-defined locations, and to visualize the ensuing reactions with adequate temporal resolution. Near-infrared femtosecond laser pulses focused through high-aperture objective lenses of advanced scanning microscopes offer the advantage of inducing DNA damage in a 3D-confined volume of subnuclear dimensions. This high spatial resolution results from the highly non-linear nature of the excitation process. Here we review recent progress based on the increasing availability of widely tunable and user-friendly technology of ultrafast lasers in the near infrared. We present a critical evaluation of this approach for DNA microdamage as compared to the currently prevalent use of UV or VIS laser irradiation, the latter in combination with photosensitizers. Current and future applications in the field of DNA repair and DNA-damage dependent chromatin dynamics are outlined. Finally, we discuss the requirement for proper simulation and quantitative modeling. We focus in particular on approaches to measure the effect of DNA damage on the mobility of nuclear proteins and consider the pros and cons of frequently used analysis models for FRAP and photoactivation and their applicability to non-linear photoperturbation experiments. PMID:23882280

  13. Binding properties of palmatine to DNA: spectroscopic and molecular modeling investigations.

    PubMed

    Mi, Ran; Tu, Bao; Bai, Xiao-Ting; Chen, Jun; Ouyang, Yu; Hu, Yan-Jun

    2015-12-01

    Palmatine, an isoquinoline alkaloid, is an important medicinal herbal extract with diverse pharmacological and biological properties. In this work, spectroscopic and molecular modeling approaches were employed to reveal the interaction between palmatine and DNA isolated from herring sperm. The absorption spectra and iodide quenching results indicated that groove binding was the main binding mode of palmatine to DNA. Fluorescence studies indicated that the binding constant (K) of palmatine and DNA was ~ 10(4)L·mol(-1). The associated thermodynamic parameters, ΔG, ΔH, and ΔS, indicated that hydrogen bonds and van der Waals forces played major roles in the interaction. The effects of chemical denaturant, thermal denaturation and pH on the interaction were investigated and provided further support for the groove binding mode. In addition to experimental approaches, molecular modeling was conducted to verify binding pattern of palmatine-DNA.

  14. Computational Model for DNA Organization Mediated by Protein Interaction in Prokaryotes

    NASA Astrophysics Data System (ADS)

    Garimella, Karthik; Kharel, Savan

    2016-03-01

    In Escherichia Coli, there are several mechanisms that drive chromosomal organization. We know through experiments that the E. Coli chromosome is condensed into highly structured regions known as macrodomains (MDs). One of the regions known as the Terminus undergoes DNA-bridging condensation that form loops between distant DNA sites and it is known to be mediated by a Terminus specific protein, which binds to specific markers within the Terminus region. In the absence of Terminus specific protein, however, the Terminus region is known to not condense nearly as much, which will likely impede several biological processes including DNA replication. In order to understand the molecular basis of protein mediation in vivo several models of Terminus specific segregation have been constructed in silico which model DNA as polymer chains.

  15. Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy

    PubMed Central

    Dębski, Konrad J.; Pitkanen, Asla; Puhakka, Noora; Bot, Anna M.; Khurana, Ishant; Harikrishnan, KN; Ziemann, Mark; Kaspi, Antony; El-Osta, Assam; Lukasiuk, Katarzyna; Kobow, Katja

    2016-01-01

    This study tested the hypothesis that acquired epileptogenesis is accompanied by DNA methylation changes independent of etiology. We investigated DNA methylation and gene expression in the hippocampal CA3/dentate gyrus fields at 3 months following epileptogenic injury in three experimental models of epilepsy: focal amygdala stimulation, systemic pilocarpine injection, or lateral fluid-percussion induced traumatic brain injury (TBI) in rats. In the models studies, DNA methylation and gene expression profiles distinguished controls from injured animals. We observed consistent increased methylation in gene bodies and hypomethylation at non-genic regions. We did not find a common methylation signature in all three different models and few regions common to any two models. Our data provide evidence that genome-wide alteration of DNA methylation signatures is a general pathomechanism associated with epileptogenesis and epilepsy in experimental animal models, but the broad pathophysiological differences between models (i.e. pilocarpine, amygdala stimulation, and post-TBI) are reflected in distinct etiology-dependent DNA methylation patterns. PMID:27157830

  16. Debaryomyces hansenii strains differ in their production of flavor compounds in a cheese-surface model

    PubMed Central

    Gori, Klaus; Sørensen, Louise Marie; Petersen, Mikael Agerlin; Jespersen, Lene; Arneborg, Nils

    2012-01-01

    Flavor production among 12 strains of Debaryomyces hansenii when grown on a simple cheese model mimicking a cheese surface was investigated by dynamic headspace sampling followed by gas chromatography-mass spectrometry. The present study confirmed that D. hansenii possess the ability to produce important cheese flavor compounds, primarily branched-chain aldehydes and alcohols, and thus important for the final cheese flavor. Quantification of representative aldehydes (2-Methylpropanal, 3-Methylbutanal) and alcohols (2-Methyl-1-propanol, 3-Methyl-1-butanol, and 3-Methyl-3-buten-1-ol) showed that the investigated D. hansenii strains varied significantly with respect to production of these flavor compounds. Contrary to the alcohols (2-Methyl-1-propanol, 3-Methyl-1-butanol, and 3-Methyl-3-buten-1-ol), the aldehydes (2-Methylpropanal, 3-Methylbutanal) were produced by the D. hansenii strains in concentrations higher than their sensory threshold values, and thus seemed more important than alcohols for cheese flavor. These results show that D. hansenii strains may have potential to be applied as cultures for increasing the nutty/malty flavor of cheese due to their production of aldehydes. However, due to large strain variations, production of flavor compounds has to be taken into consideration for selection of D. hansenii strains as starter cultures for cheese production. PMID:22950022

  17. 3D Models of the NCI60 Cell Lines for Screening Oncology Compounds.

    PubMed

    Selby, Mike; Delosh, Rene; Laudeman, Julie; Ogle, Chad; Reinhart, Russell; Silvers, Thomas; Lawrence, Scott; Kinders, Robert; Parchment, Ralph; Teicher, Beverly A; Evans, David M

    2017-03-01

    The NCI60 cell line panel screen includes 60 human tumor cell lines derived from nine tumor types that has been used over the past 20+ years to screen small molecules, biologics, and natural products for activity. Cells in monolayer culture in 96-well plates are exposed to compounds for 48 h, and Sulforhodamine B is used to determine cell viability. Data analysis tools such as COMPARE allow classification of compounds based on the pattern of cell line response. However, many compounds highly active in monolayer cell culture fail to show efficacy in vivo. Therefore, we explored 3D culture of the NCI60 panel as a strategy to improve the predictive accuracy of the screen. 3D cultures more closely resemble tumors than monolayer cultures with tighter cell-cell contact and nutrient and oxygen gradients between the periphery and the center. We optimized the NCI60 cell line panel for generating 3D spheroids of a prespecified diameter (300-500 µm) in ultra-low attachment (ULA) plates. Spheroids were classified into four categories based on imaging, and concentration response of select agents in 2D and 3D models is presented.

  18. Phase partitioning modeling of ethanol, isopropanol, and methanol with BTEX compounds in water.

    PubMed

    Lee, Kenneth Y

    2008-07-01

    This study investigates the equilibrium phase partitioning behavior of ethanol, isopropanol, and methanol in a two-phase liquid-liquid system consisting of water and an individual BTEX (Benzene, Toluene, Ethylbenzene, and Xylenes) compound. A previously developed computer program is enhanced to generate ternary phase diagrams for analysis of each three-component cosolvent-nonaqueous phase liquid (NAPL)-water mixture combination. The required activity coefficients are estimated using the UNIFAC (Universal Quasichemical Functional group Activity Coefficient) model. The UNIFAC-derived ternary phase diagrams generally show good agreement against published experimental data, and similar phase partitioning behavior is observed for every BTEX compound in the presence of the same cosolvent. Furthermore, a set of laboratory experiments is conducted to determine the maximum single-phase water content for every mixture combination considered in this study where the volume composition of the cosolvent and the NAPL components is a blend of 85% alcohol and 15% BTEX compound. Comparison of experimentally-derived maximum single-phase water contents against UNIFAC-derived results shows good agreement for mixtures containing ethanol and methanol, but relatively poor agreement for mixtures containing isopropanol.

  19. Graph theoretical analysis, insilico modeling, design, and synthesis of compounds containing benzimidazole skeleton as antidepressant agents.

    PubMed

    Theivendren, Panneerselvam; Subramanian, Arumugam; Murugan, Indhumathy; Joshi, Shrinivas D; More, Uttam A

    2016-10-31

    In this study, drug target was identified using KEGG database and network analysis through Cytoscape software. Designed series of novel benzimidazoles were taken along with reference standard Flibanserin for insilico modeling. The novel 4-(1H-benzo[d]imidazol-2-yl)-N-(substituted phenyl)-4-oxobutanamide (3a-j) analogs were synthesized and evaluated for their antidepressant activity. Reaction of 4-(1H-benzo[d]imidazol-2-yl)-4-oxobutanoic acid (1) with 4-(1H-benzo [d] imidazol-2-yl)-4-oxobutanoyl chloride (2) furnished novel 4-(1H-benzo [d] imidazol-2-yl)-N-(substituted phenyl)-4-oxobutanamide (3a-j). All the newly synthesized compounds were characterized by IR, (1) H-NMR, and mass spectral analysis. The antidepressant activities of synthesized derivatives were compared with standard drug clomipramine at a dose level of 20 mg/kg. Among the derivatives tested, most of the compounds were found to have potent activity against depression. The high level of activity was shown by the compounds 3d, 3e, 3i, and it significantly reduced the duration of immobility time at the dose level of 50 mg/kg.

  20. Priming of plant resistance by natural compounds. Hexanoic acid as a model

    PubMed Central

    Aranega-Bou, Paz; de la O Leyva, Maria; Finiti, Ivan; García-Agustín, Pilar; González-Bosch, Carmen

    2014-01-01

    Some alternative control strategies of currently emerging plant diseases are based on the use of resistance inducers. This review highlights the recent advances made in the characterization of natural compounds that induce resistance by a priming mechanism. These include vitamins, chitosans, oligogalacturonides, volatile organic compounds, azelaic and pipecolic acid, among others. Overall, other than providing novel disease control strategies that meet environmental regulations, natural priming agents are valuable tools to help unravel the complex mechanisms underlying the induced resistance (IR) phenomenon. The data presented in this review reflect the novel contributions made from studying these natural plant inducers, with special emphasis placed on hexanoic acid (Hx), proposed herein as a model tool for this research field. Hx is a potent natural priming agent of proven efficiency in a wide range of host plants and pathogens. It can early activate broad-spectrum defenses by inducing callose deposition and the salicylic acid (SA) and jasmonic acid (JA) pathways. Later it can prime pathogen-specific responses according to the pathogen’s lifestyle. Interestingly, Hx primes redox-related genes to produce an anti-oxidant protective effect, which might be critical for limiting the infection of necrotrophs. Our Hx-IR findings also strongly suggest that it is an attractive tool for the molecular characterization of the plant alarmed state, with the added advantage of it being a natural compound. PMID:25324848

  1. Laboratory testing and modeling to evaluate perfluorocarbon compounds as tracers in geothermal systems

    SciTech Connect

    Reimus, Paul W

    2011-01-21

    The thermal stability and adsorption characteristics of three perfluorinated hydrocarbon compounds were evaluated under geothermal conditions to determine the potential to use these compounds as conservative or thermally-degrading tracers in Engineered (or Enhanced) Geothermal Systems (EGS). The three compounds tested were perfluorodimethyl-cyclobutane (PDCB), perfluoromethylcyclohexane (PMCH), and perfluorotrimethylcyclohexane (PTCH), which are collectively referred to as perfluorinated tracers, or PFTs. Two sets of duplicate tests were conducted in batch mode in gold-bag reactors, with one pair of reactors charged with a synthetic geothermal brine containing the PFTs and a second pair was charged with the brine-PFT mixture plus a mineral assemblage chosen to be representative of activated fractures in an EGS reservoir. A fifth reactor was charged with deionized water containing the three PFTs. The experiments were conducted at {approx}100 bar, with temperatures ranging from 230 C to 300 C. Semi-analytical and numerical modeling was also conducted to show how the PFTs could be used in conjunction with other tracers to interrogate surface area to volume ratios and temperature profiles in EGS reservoirs. Both single-well and cross-hole tracer tests are simulated to illustrate how different suites of tracers could be used to accomplish these objectives. The single-well tests are especially attractive for EGS applications because they allow the effectiveness of a stimulation to be evaluated without drilling a second well.

  2. Photoproduction of hydrogen peroxide in aqueous solution from model compounds for chromophoric dissolved organic matter (CDOM).

    PubMed

    Clark, Catherine D; de Bruyn, Warren; Jones, Joshua G

    2014-02-15

    To explore whether quinone moieties are important in chromophoric dissolved organic matter (CDOM) photochemistry in natural waters, hydrogen peroxide (H2O2) production and associated optical property changes were measured in aqueous solutions irradiated with a Xenon lamp for CDOM model compounds (dihydroquinone, benzoquinone, anthraquinone, napthoquinone, ubiquinone, humic acid HA, fulvic acid FA). All compounds produced H2O2 with concentrations ranging from 15 to 500 μM. Production rates were higher for HA vs. FA (1.32 vs. 0.176 mM h(-1)); values ranged from 6.99 to 0.137 mM h(-1) for quinones. Apparent quantum yields (Θ app; measure of photochemical production efficiency) were higher for HA vs. FA (0.113 vs. 0.016) and ranged from 0.0018 to 0.083 for quinones. Dihydroquinone, the reduced form of benzoquinone, had a higher production rate and efficiency than its oxidized form. Post-irradiation, quinone compounds had absorption spectra similar to HA and FA and 3D-excitation-emission matrix fluorescence spectra (EEMs) with fluorescent peaks in regions associated with CDOM.

  3. Characterization of the nitrogen compounds released during yeast autolysis in a model wine system.

    PubMed

    Martínez-Rodríguez, A J; Polo, M C

    2000-04-01

    The nitrogen composition of wines aged with yeast for a long period of time, as in the case of sparkling wines, depends on the composition of the base wine and on the compounds released by the yeast. In this paper, the release of the different classes of nitrogen compounds during autolysis of one of the strains of yeast used in the manufacture of sparkling wines has been studied. The yeast, Saccharomyces bayanus, was suspended in a model wine buffer, pH 3.0 and 10% ethanol, and incubated at 30 degrees C. Samples of the autolysate were taken after 4, 24, 48, 72, 168, and 360 h of autolysis. An electrophoretic and chromatographic study was conducted of the proteins, peptides with molecular weights higher and lower than 700 Da, and amino acids released during the autolysis. Using SDS-PAGE, it was observed that it was predominantly polypeptides with molecular weights lower than 10 000 that were released. Through HPLC of the fraction lower than 10 000 Da, it was observed that it is polypeptides with molecular weights of between 10 000 and 700 Da that are released first and that these later break up to give rise to peptides with molecular weights lower than 700 Da, which in turn break down into amino acids. This indicates that the nature of the nitrogen compounds present in wines aged with yeast depends on the aging time, being less polymerized as the aging time increases.

  4. A physiologically based biodynamic (PBBD) model for estragole DNA binding in rat liver based on in vitro kinetic data and estragole DNA adduct formation in primary hepatocytes

    SciTech Connect

    Paini, Alicia; Punt, Ans; Viton, Florian; Scholz, Gabriele; Delatour, Thierry; Marin-Kuan, Maricel; Schilter, Benoit; Bladeren, Peter J. van; Rietjens, Ivonne M.C.M.

    2010-05-15

    Estragole has been shown to be hepatocarcinogenic in rodent species at high-dose levels. Translation of these results into the likelihood of formation of DNA adducts, mutation, and ultimately cancer upon more realistic low-dose exposures remains a challenge. Recently we have developed physiologically based biokinetic (PBBK) models for rat and human predicting bioactivation of estragole. These PBBK models, however, predict only kinetic characteristics. The present study describes the extension of the PBBK model to a so-called physiologically based biodynamic (PBBD) model predicting in vivo DNA adduct formation of estragole in rat liver. This PBBD model was developed using in vitro data on DNA adduct formation in rat primary hepatocytes exposed to 1'-hydroxyestragole. The model was extended by linking the area under the curve for 1'-hydroxyestragole formation predicted by the PBBK model to the area under the curve for 1'-hydroxyestragole in the in vitro experiments. The outcome of the PBBD model revealed a linear increase in DNA adduct formation with increasing estragole doses up to 100 mg/kg bw. Although DNA adduct formation of genotoxic carcinogens is generally seen as a biomarker of exposure rather than a biomarker of response, the PBBD model now developed is one step closer to the ultimate toxic effect of estragole than the PBBK model described previously. Comparison of the PBBD model outcome to available data showed that the model adequately predicts the dose-dependent level of DNA adduct formation. The PBBD model predicts DNA adduct formation at low levels of exposure up to a dose level showing to cause cancer in rodent bioassays, providing a proof of principle for modeling a toxicodynamic in vivo endpoint on the basis of solely in vitro experimental data.

  5. Reactions of aqueous chlorine and chlorine dioxide with model food compounds.

    PubMed Central

    Fukayama, M Y; Tan, H; Wheeler, W B; Wei, C I

    1986-01-01

    Chlorine and chlorine dioxide (ClO2), common disinfecting and bleaching chemicals used in the food industry, are potent oxidizing and chlorinating agents. Unfortunately, little is known about the nature of the reactions of chlorine with organic food constituents. This presentation reviews published information concerning the reactions of chlorine gas (Cl2[g]), aqueous chlorine, and ClO2 with model food compounds, the fate of chlorine during the chlorination of specific food products, and the potential toxicity of the reaction products. Fatty acids and their methyl esters react with chlorine with the degree of incorporation corresponding to their degree of unsaturation. Aqueous chlorine oxidizes and chlorinates lipids and amino acids much more readily than ClO2. Several amino acids are highly susceptible to oxidation and chlorination by chlorine compounds. Reactions of chlorine and ClO2 with several food products, including flour and shrimp, have also been characterized. In one model system, 99% of Cl2(g) either reacted with components of flour or was consumed by oxidation/chlorination reactions. The lipids extracted from the chlorinated flour contained significant amounts of chlorine. Exposure of shrimp to hypochlorous acid (HOCl) solution resulted in significant incorporation of chlorine into the edible portion. Although significant quantities of chlorine can be incorporated into specific model compounds and food products, the health risks associated with exposure to chlorinated organic products are unknown. Preliminary studies using the Ames Salmonella/microsome mutagenicity assay indicate that the reaction products from mixtures of aqueous chlorine and various lipids or tryptophan are nonmutagenic. Nevertheless, additional studies are warranted, so that the toxicological significance of these reaction products can be understood more fully. PMID:3545804

  6. Recent advances in hydrotreating of pyrolysis bio-oil and its oxygen-containing model compounds

    SciTech Connect

    Wang, Huamin; Male, Jonathan L.; Wang, Yong

    2013-05-01

    There is considerable world-wide interest in discovering renewable sources of energy that can substitute for fossil fuels. Lignocellulosic biomass, which is the most abundant and inexpensive renewable feedstock on the planet, has a great potential for sustainable production of fuels, chemicals, and carbon-based materials. Fast pyrolysis integrated with hydrotreating is one of the simplest, most cost-effective and most efficient processes to convert lignocellulosic biomass to liquid hydrocarbon fuels for transportation, which has attracted significant attention in recent decades. However, effective hydrotreating of pyrolysis bio-oil presents a daunting challenge to the commercialization of biomass conversion via pyrolysis-hydrotreating. Specifically, development of active, selective, and stable hydrotreating catalysts is the bottleneck due to the poor quality of pyrolysis bio-oil feedstock (high oxygen content, molecular complexity, coking propensity, and corrosiveness). Significant research has been conducted to address the practical issues and provide the fundamental understanding of the hydrotreating/hydrodeoxygenation (HDO) of bio-oils and their oxygen-containing model compounds, including phenolics, furans, and carboxylic acids. A wide range of catalysts have been studied, including conventional Mo-based sulfide catalysts and noble metal catalysts, with the latter being the primary focus of the recent research because of their excellent catalytic performances and no requirement of environmentally unfriendly sulfur. The reaction mechanisms of HDO of model compounds on noble metal catalysts as well as their efficacy for hydrotreating or stabilization of bio-oil have been recently reported. This review provides a survey of the relevant literatures of recent 10 years about the advances in the understanding of the HDO chemistry of bio-oils and their model compounds mainly on noble metal catalysts.

  7. Pathways in coal thermolysis: a theoretical and experimental study with model compounds

    SciTech Connect

    Ekpenyong, I.A.; Virk, P.S.

    1982-01-01

    Fundamental aspects of coal thermolysis were investigated, including how the chemical structures of aromatics, hydroaromatics, and alcohols affect their reactivities as hydrogen donors and acceptors in coal processing. The susceptibilities of substructural entities in coals to fragmentation via a number of thermal pericyclic and free radical mechanisms were probed, as were the factors governing relative reactivities within series of such coal model compounds. The theoretical part of the work applied perturbation molecular orbital (PMO) and frontier orbital theories, in conjunction with ..pi..- and pseudo-..pi.. MO's, to the study of model compound reactivity. This enabled prediction of reactivity patterns of H-donors, H-acceptors and coal-like structures as functions of their ..pi..- and sigma-bond configurations, including heteroatomic effects. Experimentally, the liquid phase reactions of the coal model compound PhOCH/sub 2/Ph (Benzyl phenyl ether, BPE) were detailed for the first time in each of four hydronaphthalene H-donor solvents in the temperature range 220/sup 0/ to 300/sup 0/C. The thermolysis of BPE exhibited a pronounced dependence on solvent structure, both with respect to product selectivities and reaction kinetics. BPE thermolysis pathways were delineated as involving (a) rearrangement, leading to isomerization, (b) hydrogenations, leading ultimately to PhOH and PhCH/sub 3/ products, and (c) addition reactions, engendering heavy products. Pathways (b) and (c) are competitive and, in each, self-reactions of BPE-derivatives vie against reactions between these and the donor solvent. Of the detailed free radical and pericyclic reaction mechanisms postulated, the latter rationalized many more facets of the BPE results than the former. The theoretical and experimental results were appraised against previous coal thermolysis literature.

  8. An Integrated Modeling Approach for Describing Fate and Transport of Perfluorinated Compounds (PFCs) in Estuarine Reservoir

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Nguyen Viet, T.; Wang, X.; Chen, H.; Gin, K. Y. H.

    2014-12-01

    The fate and transport processes of emerging contaminants in aquatic ecosystems are complex, which are not only determined by their own properties but also influenced by the environmental setting, physical, chemical and biological processes. A 3D-emerging contaminant model has been developed based on Delft3D water quality model and coupled with a hydrodynamic model and a catchment-scale 1D- hydrological and hydraulic model to study the possible fate and transport mechanisms of perfluorinated compounds (PFCs) in Marina Reservoir in Singapore. The main processes in the contaminant model include partitioning (among detritus, dissolved organic matter and phytoplankton), settling, resuspension and degradation. We used the integrated model to quantify the distribution of the total PFCs and two major components, namely perfluorooctanoate (PFOA) and perfluorooctane sulfonate (PFOS) in the water, sediments and organisms in the reservoir. The model yielded good agreement with the field measurements when evaluated based on the datasets in 2009 and 2010 as well as recent observations in 2013 and 2014. Our results elucidate that the model can be a useful tool to characterize the occurrence, sources, sinks and trends of PFCs both in the water column and in the sediments in the reservoir. Thisapproach provides a better understanding of mechanisms that influence the fate and transport of emerging contaminants and lays down a framework for future experiments to further explore how the dominant environmental factors change towards mitigation of emerging contaminants in the reservoirs.

  9. Theoretical modeling of masking DNA application in aptamer-facilitated biomarker discovery.

    PubMed

    Cherney, Leonid T; Obrecht, Natalia M; Krylov, Sergey N

    2013-04-16

    In aptamer-facilitated biomarker discovery (AptaBiD), aptamers are selected from a library of random DNA (or RNA) sequences for their ability to specifically bind cell-surface biomarkers. The library is incubated with intact cells, and cell-bound DNA molecules are separated from those unbound and amplified by the polymerase chain reaction (PCR). The partitioning/amplification cycle is repeated multiple times while alternating target cells and control cells. Efficient aptamer selection in AptaBiD relies on the inclusion of masking DNA within the cell and library mixture. Masking DNA lacks primer regions for PCR amplification and is typically taken in excess to the library. The role of masking DNA within the selection mixture is to outcompete any nonspecific binding sequences within the initial library, thus allowing specific DNA sequences (i.e., aptamers) to be selected more efficiently. Efficient AptaBiD requires an optimum ratio of masking DNA to library DNA, at which aptamers still bind specific binding sites but nonaptamers within the library do not bind nonspecific binding sites. Here, we have developed a mathematical model that describes the binding processes taking place within the equilibrium mixture of masking DNA, library DNA, and target cells. An obtained mathematical solution allows one to estimate the concentration of masking DNA that is required to outcompete the library DNA at a desirable ratio of bound masking DNA to bound library DNA. The required concentration depends on concentrations of the library and cells as well as on unknown cell characteristics. These characteristics include the concentration of total binding sites on the cell surface, N, and equilibrium dissociation constants, K(nsL) and K(nsM), for nonspecific binding of the library DNA and masking DNA, respectively. We developed a theory that allows the determination of N, K(nsL), and K(nsM) based on measurements of EC50 values for cells mixed separately with the library and masking DNA

  10. Modeling the performance limits of novel microcantilever heaters for volatile organic compound detection

    NASA Astrophysics Data System (ADS)

    Jahangir, Ifat; Koley, Goutam

    2017-01-01

    We present a theoretical model estimating the performance limits of novel AlGaN/GaN heterostructure based microcantilever heater sensors to perform advanced volatile organic compound (VOC) detection and mixture analysis. Operating without any specific surface functionalization or treatment; these devices utilize the strong surface polarization of AlGaN as well as the unique device geometries, to perform selective detection of analytes based on their latent heat of evaporation and molecular dipole moment over a wide concentration range. The presented model incorporates heat transfer, Joule heating, thermal expansion and evaporative heat loss mechanisms, to predict device behaviors such as temperature profiles and sensing performance limits under various steady-state and transient test conditions. In addition, the versatility of the proposed model enables us to successfully predict the capability of the device to perform mixture analysis, and provides guidelines to further optimize the device properties to achieve a limit of detection in sub-ppm concentration.

  11. Two-dimensional modeling of volatile organic compounds adsorption onto beaded activated carbon.

    PubMed

    Tefera, Dereje Tamiru; Jahandar Lashaki, Masoud; Fayaz, Mohammadreza; Hashisho, Zaher; Philips, John H; Anderson, James E; Nichols, Mark

    2013-10-15

    A two-dimensional heterogeneous computational fluid dynamics model was developed and validated to study the mass, heat, and momentum transport in a fixed-bed cylindrical adsorber during the adsorption of volatile organic compounds (VOCs) from a gas stream onto a fixed bed of beaded activated carbon (BAC). Experimental validation tests revealed that the model predicted the breakthrough curves for the studied VOCs (acetone, benzene, toluene, and 1,2,4-trimethylbenzene) as well as the pressure drop and temperature during benzene adsorption with a mean relative absolute error of 2.6, 11.8, and 0.8%, respectively. Effects of varying adsorption process variables such as carrier gas temperature, superficial velocity, VOC loading, particle size, and channelling were investigated. The results obtained from this study are encouraging because they show that the model was able to accurately simulate the transport processes in an adsorber and can potentially be used for enhancing absorber design and operation.

  12. A general mathematical model for chemical-enhanced flushing of soil contaminated by organic compounds

    NASA Astrophysics Data System (ADS)

    Ji, Wei; Brusseau, Mark L.

    The use of chemical agents to enhance the in situ removal of hydrophobic organic compounds (HOCs) from porous media is an emerging remediation technology. Whereas surfactants and cosolvents are the primary agents examined to date, others, such as natural organic matter and complexing agents, have also been examined for their ability to enhance the solubilization of HOCs. While the mode of action of each type of enhanced-solubilization agent may be different, they all induce similar responses. In this paper, a general mathematical model is developed to simulate the enhanced-solubilization process for various chemical agents, including cosolvents, surfactants, natural organic matter, and complexing agents. This model is developed using a master-equation approach that incorporates the solubilization mechanisms associated with each type of agent. A limited evaluation of the model is conducted by comparing simulations to the results of two laboratory experiments. A sensitivity analysis is performed to illustrate the influence of various factors on contaminant removal.

  13. Model System for DNA Replication of a Plasmid DNA Containing the Autonomously Replicating Sequence from Saccharomyces cerevisiae

    NASA Astrophysics Data System (ADS)

    Ishimi, Yukio; Matsumoto, Ken

    1993-06-01

    A negatively supercoiled plasmid DNA containing autonomously replicating sequence (ARS) 1 from Saccharomyces cerevisiae was replicated with the proteins required for simian virus 40 DNA replication. The proteins included simian virus 40 large tumor antigen as a DNA helicase, DNA polymerase α^\\cdotprimase, and the multisubunit human single-stranded DNA-binding protein from HeLa cells; DNA gyrase from Escherichia coli, which relaxes positive but not negative supercoils, was included as a "swivelase." DNA replication started from the ARS region, proceeded bidirectionally with the synthesis of leading and lagging strands, and resulted in the synthesis of up to 10% of the input DNA in 1 h. The addition of HeLa DNA topoisomerase I, which relaxes both positive and negative supercoils, to this system inhibited DNA replication, suggesting that negative supercoiling of the template DNA is required for initiation. These results suggest that DNA replication starts from the ARS region where the DNA duplex is unwound by torsional stress; this unwound region can be recognized by a DNA helicase with the assistance of the multisubunit human single-stranded DNA-binding protein.

  14. Modelling Robust Feedback Control Mechanisms That Ensure Reliable Coordination of Histone Gene Expression with DNA Replication

    PubMed Central

    Corrigall, Holly; Ebenhöh, Oliver; Müller, Berndt

    2016-01-01

    Histone proteins are key elements in the packing of eukaryotic DNA into chromosomes. A little understood control system ensures that histone gene expression is balanced with DNA replication so that histone proteins are produced in appropriate amounts. Disturbing or disrupting this system affects genome stability and gene expression, and has detrimental consequences for human development and health. It has been proposed that feedback control involving histone proteins contributes to this regulation and there is evidence implicating cell cycle checkpoint molecules activated when DNA synthesis is impaired in this control. We have developed mathematical models that incorporate these control modes in the form of inhibitory feedback of histone gene expression from free histone proteins, and alternatively a direct link that couples histone RNA synthesis to DNA synthesis. Using our experimental evidence and related published data we provide a simplified description of histone protein synthesis during S phase. Both models reproduce the coordination of histone gene expression with DNA replication during S phase and the down-regulation of histone RNA when DNA synthesis is interrupted, but only the model incorporating histone protein feedback control was able to effectively simulate the coordinate expression of a simplified histone gene family. Our combined theoretical and experimental approach supports the hypothesis that the regulation of histone gene expression involves feedback control. PMID:27798685

  15. Animal Models That Best Reproduce the Clinical Manifestations of Human Intoxication with Organophosphorus Compounds

    PubMed Central

    Pereira, Edna F. R.; Aracava, Yasco; DeTolla, Louis J.; Beecham, E. Jeffrey; Basinger, G. William; Wakayama, Edgar J.

    2014-01-01

    The translational capacity of data generated in preclinical toxicological studies is contingent upon several factors, including the appropriateness of the animal model. The primary objectives of this article are: 1) to analyze the natural history of acute and delayed signs and symptoms that develop following an acute exposure of humans to organophosphorus (OP) compounds, with an emphasis on nerve agents; 2) to identify animal models of the clinical manifestations of human exposure to OPs; and 3) to review the mechanisms that contribute to the immediate and delayed OP neurotoxicity. As discussed in this study, clinical manifestations of an acute exposure of humans to OP compounds can be faithfully reproduced in rodents and nonhuman primates. These manifestations include an acute cholinergic crisis in addition to signs of neurotoxicity that develop long after the OP exposure, particularly chronic neurologic deficits consisting of anxiety-related behavior and cognitive deficits, structural brain damage, and increased slow electroencephalographic frequencies. Because guinea pigs and nonhuman primates, like humans, have low levels of circulating carboxylesterases—the enzymes that metabolize and inactivate OP compounds—they stand out as appropriate animal models for studies of OP intoxication. These are critical points for the development of safe and effective therapeutic interventions against OP poisoning because approval of such therapies by the Food and Drug Administration is likely to rely on the Animal Efficacy Rule, which allows exclusive use of animal data as evidence of the effectiveness of a drug against pathologic conditions that cannot be ethically or feasibly tested in humans. PMID:24907067

  16. A developmental model for branching morphogenesis of lake cress compound leaf.

    PubMed

    Nakamasu, Akiko; Nakayama, Hokuto; Nakayama, Naomi; Suematsu, Nobuhiko J; Kimura, Seisuke

    2014-01-01

    Lake cress, Rorippa aquatica (Brassicaceae), is a semi-aquatic plant that exhibits a variety of leaf shapes, from simple leaves to highly branched compound leaves, depending on the environment. Leaf shape can vary within a single plant, suggesting that the variation can be explained by a simple model. In order to simulate the branched structure in the compound leaves of R. aquatica, we implemented reaction-diffusion (RD) patterning onto a theoretical framework that had been developed for serration distribution in the leaves of Arabidopsis thaliana, with the modification of the one-dimensional reaction-diffusion domain being deformed with the spatial periodicity of the RD pattern while expanding. This simple method using an iterative pattern could create regular and nested branching patterns. Subsequently, we verified the plausibility of our theoretical model by comparing it with the experimentally observed branching patterns. The results suggested that our model successfully predicted both the qualitative and quantitative aspects of the timing and positioning of branching in growing R. aquatica leaves.

  17. A Developmental Model for Branching Morphogenesis of Lake Cress Compound Leaf

    PubMed Central

    Nakamasu, Akiko; Nakayama, Hokuto; Nakayama, Naomi; Suematsu, Nobuhiko J.; Kimura, Seisuke

    2014-01-01

    Lake cress, Rorippa aquatica (Brassicaceae), is a semi-aquatic plant that exhibits a variety of leaf shapes, from simple leaves to highly branched compound leaves, depending on the environment. Leaf shape can vary within a single plant, suggesting that the variation can be explained by a simple model. In order to simulate the branched structure in the compound leaves of R. aquatica, we implemented reaction-diffusion (RD) patterning onto a theoretical framework that had been developed for serration distribution in the leaves of Arabidopsis thaliana, with the modification of the one-dimensional reaction-diffusion domain being deformed with the spatial periodicity of the RD pattern while expanding. This simple method using an iterative pattern could create regular and nested branching patterns. Subsequently, we verified the plausibility of our theoretical model by comparing it with the experimentally observed branching patterns. The results suggested that our model successfully predicted both the qualitative and quantitative aspects of the timing and positioning of branching in growing R. aquatica leaves. PMID:25375102

  18. Drosophila melanogaster as a model to characterize fungal volatile organic compounds.

    PubMed

    Inamdar, Arati A; Zaman, Taslim; Morath, Shannon U; Pu, David C; Bennett, Joan W

    2014-05-01

    Fungi are implicated in poor indoor air quality and may pose a potential risk factor for building/mold related illnesses. Fungi emit numerous volatile organic compounds (VOCs) as alcohols, esters, ethers, ketones, aldehydes, terpenoids, thiols, and their derivatives. The toxicity profile of these VOCs has never been explored in a model organism, which could enable the performance of high throughput toxicological assays and lead to a better understanding of the mechanism of toxicity. We have established a reductionist Drosophila melanogaster model to evaluate the toxicity of fungal VOCs. In this report, we assessed the toxicity of fungal VOCs emitted from living cultures of species in the genera, Trichoderma, Aspergillus, and Penicillium and observed a detrimental effect on larval survival. We then used chemical standards of selected fungal VOCs to assess their toxicity on larval and adult Drosophila. We compared the survival of adult flies exposed to these fungal VOCs with known industrial toxic chemicals (formaldehyde [37%], xylene, benzene, and toluene). Among the tested fungal VOC standards, the compounds with eight carbons (C8) caused greater truncation of fly lifespan than tested non-C8 fungal VOCs and industrial toxins. Our data validate the use of Drosophila melanogaster as a model with the potential to elucidate the mechanistic attributes of different toxic VOCs emitted by fungi and also to explore the potential link between reported human illnesses/symptoms and exposure to water damaged and mold contaminated buildings.

  19. Analytic model of energy-absorption response functions in compound X-ray detector materials.

    PubMed

    Yun, Seungman; Kim, Ho Kyung; Youn, Hanbean; Tanguay, Jesse; Cunningham, Ian A

    2013-10-01

    The absorbed energy distribution (AED) in X-ray imaging detectors is an important factor that affects both energy resolution and image quality through the Swank factor and detective quantum efficiency. In the diagnostic energy range (20-140 keV), escape of characteristic photons following photoelectric absorption and Compton scatter photons are primary sources of absorbed-energy dispersion in X-ray detectors. In this paper, we describe the development of an analytic model of the AED in compound X-ray detector materials, based on the cascaded-systems approach, that includes the effects of escape and reabsorption of characteristic and Compton-scatter photons. We derive analytic expressions for both semi-infinite slab and pixel geometries and validate our approach by Monte Carlo simulations. The analytic model provides the energy-dependent X-ray response function of arbitrary compound materials without time-consuming Monte Carlo simulations. We believe this model will be useful for correcting spectral distortion artifacts commonly observed in photon-counting applications and optimal design and development of novel X-ray detectors.

  20. A model for the implementation of symmetry breaking from B-to-Z-DNA configurations

    NASA Astrophysics Data System (ADS)

    Reséndiz-Antonio, M.; Godina-Nava, J. J.

    2012-02-01

    Supported in the helicoidal model performed by M. Barbi et al, we propose a extended Morse potential version to study the symmetry breaking in a simple non-linear DNA model based in two plane base rotors. The intention is study the development of the intermediate states appearing in the junction B-to-Z DNA, useful for understanding its biological function, once is characterized the phase transition involved. With this model, we make a comparison between the non-linear dynamics of a handedness homogeneous base-pair winding in a right-handed sense and a left handed sense. Numerical results determine that the right-handed sense is the preferential direction of winding of our spring's model that can emulate the common DNA behavior.

  1. Infrared spectra and normal coordinate analysis of a model compound for superoxide dismutase

    NASA Astrophysics Data System (ADS)

    Yin, Jun; Li, Chongde; Chen, Xianyang; Luo, Qinhui

    1997-10-01

    Infrared spectra have been measured and vibrational assignment are given for a new model compound of superoxide dismutase (SOD): [(tren)CuimZn(tren)](ClO 4) 3·CH 3OH (where tren = tris(2-aminoethyl)amine, im = imidazolate). In order to check the empirical assignment, we have performed a detailed normal coordinate analysis (NCA) based on a Urey-Bradley force field. Due to introducing an appropriate set of internal coordinates and force constants in the course of calculation, the agreement between the experimental and calculated frequencies is satisfactory.

  2. Flash Vacuum Pyrolysis of Lignin Model Compounds: Reaction Pathways of Aromatic Methoxy Groups

    SciTech Connect

    Britt, P.F.; Buchanan, A.C., III; Martineau, D.R.

    1999-03-21

    Currently, there is interest in utilizing lignin, a major constituent of biomass, as a renewable source of chemicals and fuels. High yields of liquid products can be obtained from the flash or fast pyrolysis of biomass, but the reaction pathways that lead to product formation are not understood. To provide insight into the primary reaction pathways under process relevant conditions, we are investigating the flash vacuum pyrolysis (FVP) of lignin model compounds at 500 C. This presentation will focus on the FVP of {beta}-ether linkages containing aromatic methoxy groups and the reaction pathways of methoxy-substituted phenoxy radicals.

  3. Numerical synthesis of ionograms in horizontally inhomogeneous ionosphere on the basis of compound parabolic layer model

    NASA Astrophysics Data System (ADS)

    Laryunin, Oleg

    2016-09-01

    Characteristic U-shaped traces cusps on ionograms have been identified as off-angle echoes from sloping electron density contours caused by the presence of traveling ionospheric disturbances (TIDs). Dynamics of the cusps is associated with horizontal drift of the disturbances. A potential for reducing calculation time in numerical synthesis of vertical ionograms is under discussion. Since numerical ray tracing is expensive in terms of computer time, we have developed simplified formulation for this study. The suggested model of compound parabolic layer allows us to analytically calculate ray paths. Changes in the shape of the ionogram cusp caused by varying TID characteristics are examined.

  4. Cleavage pattern of DNA caused by endonuclease: Theoretical modeling and experimental verification

    NASA Astrophysics Data System (ADS)

    Inagaki, Shio; Liu, Li; Takinoue, Masahiro; Yoshikawa, Kenichi

    2010-02-01

    In apoptotic cells, genomic DNA molecules are fragmented into multiple fragments with lengths that are integer multiples of approximately 180-200 base pairs (bp), i.e., the size of a single nucleosome. Here we propose a simple mathematical model for interpreting this cleavage pattern of DNA. Under the condition of a purely stochastic cleavage process, we derive a time evolution of the probability distribution of the fragment length by a Poisson distribution. We examine the applicability of our model by analyzing experimental results with apoptotic cells. Our model enables us to satisfactorily interpret the experimental trends. Interestingly, this theoretical fitting of the experimental data provides kinetic information for the cleavage reaction.

  5. Biokinetic models for the behaviour of carbon-14 from labelled compounds in the human body: can a single generic model be justified?

    PubMed

    Taylor, David M

    2004-01-01

    The published data on the biokinetic behaviour of 27 14C-labelled compounds in humans or animals have been reviewed. Effective doses have been calculated for those compounds for which this information had not been published and doses have been compared to that calculated with the International Commission on Radiological Protection (ICRP) default model for carbon compounds of unknown composition. The compound-specific effective doses for a few natural human biochemical substrates are quite close to the ICRP default dose coefficient, but for the remainder of the compounds considered the doses are smaller by factors ranging from about 5 to 200. Comparison of the dosimetric data suggests that although the ICRP default model will overestimate the dose for very many compounds it could remain useful as a guide for general prospective radiological protection purposes. However, a comparison of the biokinetic information indicates that the ICRP default model would not be reliable for the interpretation of bioassay data.

  6. Combinatorial modeling of chromatin features quantitatively predicts DNA replication timing in Drosophila.

    PubMed

    Comoglio, Federico; Paro, Renato

    2014-01-01

    In metazoans, each cell type follows a characteristic, spatio-temporally regulated DNA replication program. Histone modifications (HMs) and chromatin binding proteins (CBPs) are fundamental for a faithful progression and completion of this process. However, no individual HM is strictly indispensable for origin function, suggesting that HMs may act combinatorially in analogy to the histone code hypothesis for transcriptional regulation. In contrast to gene expression however, the relationship between combinations of chromatin features and DNA replication timing has not yet been demonstrated. Here, by exploiting a comprehensive data collection consisting of 95 CBPs and HMs we investigated their combinatorial potential for the prediction of DNA replication timing in Drosophila using quantitative statistical models. We found that while combinations of CBPs exhibit moderate predictive power for replication timing, pairwise interactions between HMs lead to accurate predictions genome-wide that can be locally further improved by CBPs. Independent feature importance and model analyses led us to derive a simplified, biologically interpretable model of the relationship between chromatin landscape and replication timing reaching 80% of the full model accuracy using six model terms. Finally, we show that pairwise combinations of HMs are able to predict differential DNA replication timing across different cell types. All in all, our work provides support to the existence of combinatorial HM patterns for DNA replication and reveal cell-type independent key elements thereof, whose experimental investigation might contribute to elucidate the regulatory mode of this fundamental cellular process.

  7. [Combined hopping-superexchange mechanism of charge transfer in DNA; a model with nearest interactions].

    PubMed

    Lakhno, V D; Sultanov, V B

    2007-01-01

    In the framework of the earlier developed combined hopping-superexchange mechanism of charge transfer in DNA, a model with all nearest interactions between nucleobases is proposed. It is shown that the transfer rates for various types of nucleotide sequences calculated within this model are in a good agreement with experimental data.

  8. Study on kinetic model of microwave thermocatalytic treatment of biomass tar model compound.

    PubMed

    Anis, Samsudin; Zainal, Z A

    2014-01-01

    Kinetic model parameters for toluene conversion under microwave thermocatalytic treatment were evaluated. The kinetic rate constants were determined using integral method based on experimental data and coupled with Arrhenius equation for obtaining the activation energies and pre-exponential factors. The model provides a good agreement with the experimental data. The kinetic model was also validated with standard error of 3% on average. The extrapolation of the model showed a reasonable trend to predict toluene conversion and product yield both in thermal and catalytic treatments. Under microwave irradiation, activation energy of toluene conversion was lower in the range of 3-27 kJ mol(-1) compared to those of conventional heating reported in the literatures. The overall reaction rate was six times higher compared to conventional heating. As a whole, the kinetic model works better for tar model removal in the absence of gas reforming within a level of reliability demonstrated in this study.

  9. Correction: Cucurbit[7]uril inclusion complexation as a supramolecular strategy for color stabilization of anthocyanin model compounds.

    PubMed

    Held, Barbara; Tang, Hao; Natarajan, Palani; Silva, Cassio Pacheco da; Silva, Volnir de Oliveira; Bohne, Cornelia; Quina, Frank H

    2016-06-08

    Correction for 'Cucurbit[7]uril inclusion complexation as a supramolecular strategy for color stabilization of anthocyanin model compounds' by Barbara Held, et al., Photochem. Photobiol. Sci., 2016, DOI: 10.1039/c6pp00060f.

  10. Predicting Age-appropriate Pharmacokinetics of Six Volatile Organic Compounds in the Rat Utilizing Physiologically-based Pharmacokinetic Modeling (T)

    EPA Science Inventory

    The capability of physiologically-based pharmacokinetic (PBPK) models to incorporate ageappropriate physiological and chemical-specific parameters was utilized in this study to predict changes in internal dosimetry for six volatile organic compounds (VOCs) across different ages o...

  11. PREDICTING AGE-DEPENDENT PHARMACOKINETICS OF SIX VOLATILE ORGANIC COMPOUNDS UTILIZING PHYSIOLOGICALLY BASED PHARMACOKINETIC MODELING OF RAT

    EPA Science Inventory

    In this study, age-appropriate physiological and chemical-specific parameters were incorporated into a physiologically based pharmacokinetic (PBPK) model to predict changes in internal dosimetry for six volatile organic compounds (VOCs) across different lifestages of the rat and ...

  12. Predicting Age-Appropriate Pharmacokinetics of Six Volatile Organic Compounds in the Rat Utilizing Physiologically Based Pharmacokinetic Modeling

    EPA Science Inventory

    The capability of physiologically based pharmacokinetic models to incorporate age-appropriate physiological and chemical-specific parameters was utilized to predict changes in internal dosimetry for six volatile organic compounds (VOCs) across different ages of rats.

  13. The elastic rod provides a model for DNA and its functions

    SciTech Connect

    Hearst, J.E.; Shi, Yaoming

    1996-12-31

    The processes of transcription and replication are catalyzed by processive enzyme complexes which move translationally along the DNA helix, unwinding the DNA helix ahead of the complex and reforming a duplex helix behind the complex. These processes are known to torsionally stress DNA. The biological implications of the torsional tension associated with transcription are potentially significant, and a fundamental question is the extent to which transcription determines the level of DNA supercoiling in vivo. Transcription can induce supercoiling of the template by virtue of the topological relationship between DNA and elongating RNA polymerase. Some models of transcription elongation require that polymerase follow the helical screw of the DNA such that there is one 360{degrees} rotation between the enzyme and DNA for each 10.5 bp transcribed. Since RNA polymerase elongates at the rate of about 40 nucleotides per sec, an efficiently anchored transcription complex should introduce approximately four negative superturns upstream and four positive superturns downstream from an actively expressed gene each second. This would suggest extraordinarily fast rates of localized supercoiling after the onset of transcription. 54 refs., 1 tab.

  14. Segregation of Naturally Occurring Mitochondrial DNA Variants in a Mini-Pig Model.

    PubMed

    Cagnone, Gael; Tsai, Te-Sha; Srirattana, Kanokwan; Rossello, Fernando; Powell, David R; Rohrer, Gary; Cree, Lynsey; Trounce, Ian A; St John, Justin C

    2016-03-01

    The maternally inherited mitochondrial genome (mtDNA) is present in multimeric form within cells and harbors sequence variants (heteroplasmy). While a single mtDNA variant at high load can cause disease, naturally occurring variants likely persist at low levels across generations of healthy populations. To determine how naturally occurring variants are segregated and transmitted, we generated a mini-pig model, which originates from the same maternal ancestor. Following next-generation sequencing, we identified a series of low-level mtDNA variants in blood samples from the female founder and her daughters. Four variants, ranging from 3% to 20%, were selected for validation by high-resolution melting analysis in 12 tissues from 31 animals across three generations. All four variants were maintained in the offspring, but variant load fluctuated significantly across the generations in several tissues, with sex-specific differences in heart and liver. Moreover, variant load was persistently reduced in high-respiratory organs (heart, brain, diaphragm, and muscle), which correlated significantly with higher mtDNA copy number. However, oocytes showed increased heterogeneity in variant load, which correlated with increased mtDNA copy number during in vitro maturation. Altogether, these outcomes show that naturally occurring mtDNA variants segregate and are maintained in a tissue-specific manner across generations. This segregation likely involves the maintenance of selective mtDNA variants during organogenesis, which can be differentially regulated in oocytes and preimplantation embryos during maturation.

  15. Synthesis of model compounds for coal liquefaction research. Final report, April 15, 1990--April 14, 1991

    SciTech Connect

    Not Available

    1991-11-01

    Coal liquefaction investigations required the availability of model compounds for mechanistic investigations. Towards this end, IITRI was funded to develop an approach for the synthesis of one of the target compound. This study was carried out in several phases as outlined here. Initial synthetic investigations on obtaining 2-tetrolol was carried out using high pressure and temperature reduction with Raney nickel catalyst. The next step consisted in incorporation of a hydroxymethyelene group at the C-3 position. This was successfully carried out utilizing 2-tetrolol, formaldehyde, and calcium oxide. An alternate improved method was developed using 3-carboxyl-2-naphthol. This required less time, gave a cheer product in higher yield. Efforts at the introduction of a chloromethylene group only yielded polymeric material or starting material in spite of protection the phenolic group by various groups. They synthesis of 3, 5-dimethyl-6- bromobenzyl chloride was successfully carried out by performing the Blank reaction of 2, 4-dimethyl bromobenzene. The product was characterized by GC/MS. Purification was not possible, as it was a complex mixture. Efforts at converting it to the acetate followed by separation to was not feasible. Unlike in the case of 2- hydroxyteralol, hydroxymetylation by established procedure yielded only the starting materials. Commercially available 4-methoxy-1- maphthaldehyde was protected as the ethylene acetal. The Wittig reagent 3-chlorobenzyl phosphonium bromide was prepared and condensed with 4-methoxy-1-napthaldehyde successfully and proved that the overall synthetic approach was proceeding in the desired direction. All the necessary intermediates have been synthesized,and we have demonstrated using model compounds, that the synthetic objective can be attained.

  16. The Synthesis and Evaluation of Third-Order Optical Nonlinearities of Model Compounds Containing Benzothiazole, Benzimidazole and Benzoxazole Moieties.

    DTIC Science & Technology

    1991-02-01

    AD-A235 622 WL-TR-91-4015 THE SYNTHESIS AND EVALUATION OF THIRD-ORDER OPTICAL NONLINEARITIES OF MODEL COMPOUNDS CONTAINING BENZOTHIAZOLE ...Nonlinearities of Model Compounds Containing Benzothiazole , Benzimidazole, and Benzoxazole Moieties 12 PERSONAL AUTHOR(S) Bruce A. Reinhardt, Marilyn R...necessary and identify by block number) FIELD GROUP SUB-GROUP nonlinear optical properties benzothiazole u/ 03 degenerate four-wave mixing benzimidazole 21

  17. The usual suspects-influence of physicochemical properties on lag time, skin deposition, and percutaneous penetration of nine model compounds.

    PubMed

    Bo Nielsen, Jesper; Ahm Sørensen, Jens; Nielsen, Flemming

    2009-01-01

    The influence of physicochemical properties of nine model compounds on lag time, skin deposition, and percutaneous penetration was evaluated. Static diffusion cells mounted with human skin were used as the experimental model, and experiments were carried out in accordance with Organization for Economic Cooperation and Development (OECD) guidelines. The model compounds were chosen to cover a wide spectrum of solubilities and molecular weights. The pesticides included were glyphosate, dimethoate, pirimicarb, malathion, paclobutrazol, methiocarb, prochloraz, and benzoic acid, with the ninth model compound being caffeine. The fastest dermal penetration was observed for compounds with log Pow values between 1.5 and 4. Malathion did not fit into this generalization. No clear relationship was observed between molecular weight and Kp values. The shortest lag time was observed for the most hydrophilic model compounds. With increasing molecular weight, the lag time rose. Thus, the lag time for the smallest model compound was close to 1.5 h, while the lag time exceeded 20 h for a model compound with a molecular weight of 377 g. A difference in lag time of this magnitude inevitably produces differences in the amounts of a chemical able to penetrate the skin within a limited period of time. The relative deposition in the skin was highest for the lipophilic model compounds. For log Pow values between -1 and 2, a linear relationship was observed between log Pow and log Kp. Comparisons between theoretical Kp values based on the Potts-Guy equation and experimental Kp values demonstrated good agreement. Experimental Kp values based on experiments using full-thickness human skin generally underestimated the calculated Kp values by 25%. The observations are relevant to industrial hygienists and regulatory agencies using experimental data for assessing systemic toxicity following dermal exposures as for development of structure activity relationships for dermal absorption of chemicals.

  18. Exclusion of small terminase mediated DNA threading models for genome packaging in bacteriophage T4

    PubMed Central

    Gao, Song; Zhang, Liang; Rao, Venigalla B.

    2016-01-01

    Tailed bacteriophages and herpes viruses use powerful molecular machines to package their genomes. The packaging machine consists of three components: portal, motor (large terminase; TerL) and regulator (small terminase; TerS). Portal, a dodecamer, and motor, a pentamer, form two concentric rings at the special five-fold vertex of the icosahedral capsid. Powered by ATPase, the motor ratchets DNA into the capsid through the portal channel. TerS is essential for packaging, particularly for genome recognition, but its mechanism is unknown and controversial. Structures of gear-shaped TerS rings inspired models that invoke DNA threading through the central channel. Here, we report that mutations of basic residues that line phage T4 TerS (gp16) channel do not disrupt DNA binding. Even deletion of the entire channel helix retained DNA binding and produced progeny phage in vivo. On the other hand, large oligomers of TerS (11-mers/12-mers), but not small oligomers (trimers to hexamers), bind DNA. These results suggest that TerS oligomerization creates a large outer surface, which, but not the interior of the channel, is critical for function, probably to wrap viral genome around the ring during packaging initiation. Hence, models involving TerS-mediated DNA threading may be excluded as an essential mechanism for viral genome packaging. PMID:26984529

  19. Multi-Orbital Molecular Compound (TTM-TTP)I3: Effective Model and Fragment Decomposition

    NASA Astrophysics Data System (ADS)

    Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent; Ishibashi, Shoji; Seo, Hitoshi

    2011-01-01

    The electronic structure of the molecular compound (TTM-TTP)I3, which exhibits a peculiar intra-molecular charge ordering, has been studied using multi-configuration ab initio calculations. First we derive an effective Hubbard-type model based on the molecular orbitals (MOs) of TTM-TTP; we set up a two-orbital Hamiltonian for the two MOs near the Fermi energy and determine its full parameters: the transfer integrals, the Coulomb and exchange interactions. The tight-binding band structure obtained from these transfer integrals is consistent with the result of the direct band calculation based on density functional theory. Then, by decomposing the frontier MOs into two parts, i.e., fragments, we find that the stacked TTM-TTP molecules can be described by a two-leg ladder model, while the inter-fragment Coulomb energies are scaled to the inverse of their distances. This result indicates that the fragment picture that we proposed earlier [M.-L. Bonnet et al.: J. Chem. Phys. 132 (2010) 214705] successfully describes the low-energy properties of this compound.

  20. Retrograde reactions in coal processing: The behavior of ether and sulfide model compounds

    SciTech Connect

    Buchanan, A.C. III; Britt, P.F.; Skeen, J.T.

    1997-04-01

    Retrograde reactions that produce more refractory molecular structures are undesirable in coal liquefaction. The authors previously found that restricted mass transport, induced by immobilization on a silica support, promotes retrograde reactions for 1,2-diphenylethane (C{sub 6}H{sub 5}CH{sub 2}CH{sub 2}C{sub 6}H{sub 5}) by both skeletal rearrangement and ring growth (cyclization-dehydrogenation) pathways involving free-radical intermediates. They are now examining the influence of heteroatoms on the retrograde pathways for the corresponding surface-immobilized ether (C{sub 6}H{sub 5}OCH{sub 2}C{sub 6}H{sub 5}) and sulfide (C{sub 6}H{sub 5}SCH{sub 2}C{sub 6}H{sub 5}) model compounds at 275--350 C. Cyclization-dehydrogenation pathways are not detected for either model compound. However, retrograde skeletal rearrangements involving 1,2-phenyl shifts in C{sub 6}H{sub 5}XCH{center_dot}C{sub 6}H{sub 5} (X = O,S) are found to be significant under restricted diffusion, and for X = O, radical coupling at ring carbons to form benzylphenols is also observed as a major pathway. For surface-immobilized benzyl phenyl ether, the two retrograde processes account for ca. 50% of the thermolysis products, and also generate reactive hydroxyl and keto functionalities that can be involved in additional retrograde reactions.

  1. Saturation magnetization of Ni(II) in metalloproteins and model compounds

    SciTech Connect

    Sendova, M.; Day, E.P.; Kiick, K.; Johnson, M.; Ma, L.; Scott, B.; Hausinger, R.; Todd, M.; Peterson, J. Univ. of Georgia, Athens Michigan State Univ., East Lansing Univ. of Alabama, Tuscaloosa )

    1992-01-01

    The Ni(II) sites of urease (from Klebsiella aerogenes and jack bean), coenzyme F[sub 430] (from Methanobacterium thermoautotrophicum), and several model compounds having octahedral symmetry have been studied using the saturation megnetization technique. Data were collected at four fixed fields over the temperature range from 2 - 200K. Theoretical curves calculated from the spin Hamiltonian were used to fit the experimentally obtained magnetization curves. The following parameters were determined: the spine state (S), the amount of the sample in this spin state ([S]), the gyromagnetic ratio (g), and the zero field splitting parameters (D, E/D). The amount of S=1 paramagnetism of the Ni(II) sites was found to depend on the pH of the buffer and on the concentration of the protein in D[sub 2]O (for coenzyme F[sub 430]). The relationship of the strength of the ligand field to the zero field splitting parameter was studied for the model compounds. There was no evidence for exchange coupling between the two Ni(II) ions at the active sites of either plant or bacterial urease.

  2. Compounds from Silicones Alter Enzyme Activity in Curing Barnacle Glue and Model Enzymes

    PubMed Central

    Rittschof, Daniel; Orihuela, Beatriz; Harder, Tilmann; Stafslien, Shane; Chisholm, Bret; Dickinson, Gary H.

    2011-01-01

    Background Attachment strength of fouling organisms on silicone coatings is low. We hypothesized that low attachment strength on silicones is, in part, due to the interaction of surface available components with natural glues. Components could alter curing of glues through bulk changes or specifically through altered enzyme activity. Methodology/Principal Findings GC-MS analysis of silicone coatings showed surface-available siloxanes when the coatings were gently rubbed with a cotton swab for 15 seconds or given a 30 second rinse with methanol. Mixtures of compounds were found on 2 commercial and 8 model silicone coatings. The hypothesis that silicone components alter glue curing enzymes was tested with curing barnacle glue and with commercial enzymes. In our model, barnacle glue curing involves trypsin-like serine protease(s), which activate enzymes and structural proteins, and a transglutaminase which cross-links glue proteins. Transglutaminase activity was significantly altered upon exposure of curing glue from individual barnacles to silicone eluates. Activity of purified trypsin and, to a greater extent, transglutaminase was significantly altered by relevant concentrations of silicone polymer constituents. Conclusions/Significance Surface-associated silicone compounds can disrupt glue curing and alter enzyme properties. Altered curing of natural glues has potential in fouling management. PMID:21379573

  3. Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field

    PubMed Central

    2015-01-01

    The charge distribution of halogen atoms on organochlorine compounds can be highly anisotropic and even display a so-called σ-hole, which leads to strong halogen bonds with electron donors. In this paper, we have systematically investigated a series of chloromethanes with one to four chloro substituents using a polarizable multipole-based molecular mechanics model. The atomic multipoles accurately reproduced the ab initio electrostatic potential around chloromethanes, including CCl4, which has a prominent σ-hole on the Cl atom. The van der Waals parameters for Cl were fitted to the experimental density and heat of vaporization. The calculated hydration free energy, solvent reaction fields, and interaction energies of several homo- and heterodimer of chloromethanes are in good agreement with experimental and ab initio data. This study suggests that sophisticated electrostatic models, such as polarizable atomic multipoles, are needed for accurate description of electrostatics in organochlorine compounds and halogen bonds, although further improvement is necessary for better transferability. PMID:24484473

  4. Reaction pathways for the deoxygenation of vegetable oils and related model compounds.

    PubMed

    Gosselink, Robert W; Hollak, Stefan A W; Chang, Shu-Wei; van Haveren, Jacco; de Jong, Krijn P; Bitter, Johannes H; van Es, Daan S

    2013-09-01

    Vegetable oil-based feeds are regarded as an alternative source for the production of fuels and chemicals. Paraffins and olefins can be produced from these feeds through catalytic deoxygenation. The fundamentals of this process are mostly studied by using model compounds such as fatty acids, fatty acid esters, and specific triglycerides because of their structural similarity to vegetable oils. In this Review we discuss the impact of feedstock, reaction conditions, and nature of the catalyst on the reaction pathways of the deoxygenation of vegetable oils and its derivatives. As such, we conclude on the suitability of model compounds for this reaction. It is shown that the type of catalyst has a significant effect on the deoxygenation pathway, that is, group 10 metal catalysts are active in decarbonylation/decarboxylation whereas metal sulfide catalysts are more selective to hydrodeoxygenation. Deoxygenation studies performed under H2 showed similar pathways for fatty acids, fatty acid esters, triglycerides, and vegetable oils, as mostly deoxygenation occurs indirectly via the formation of fatty acids. Deoxygenation in the absence of H2 results in significant differences in reaction pathways and selectivities depending on the feedstock. Additionally, using unsaturated feedstocks under inert gas results in a high selectivity to undesired reactions such as cracking and the formation of heavies. Therefore, addition of H2 is proposed to be essential for the catalytic deoxygenation of vegetable oil feeds.

  5. An Experimental Model for the Rapid Screening of Compounds with Potential Use Against Mycobacteria.

    PubMed

    Costa, Sofia Santos; Lopes, Elizeth; Azzali, Elisa; Machado, Diana; Coelho, Tatiane; da Silva, Pedro Eduardo Almeida; Viveiros, Miguel; Pieroni, Marco; Couto, Isabel

    2016-11-01

    Infections caused by Mycobacterium tuberculosis and other mycobacteria are major challenges for global public health. Particularly worrisome are infections caused by multidrug-resistant bacteria, which are increasingly difficult to treat because of the loss of efficacy of the current antibacterial agents, a problem that continues to escalate worldwide. There has been a limited interest and investment on the development of new antibacterial agents in the past decades. This has led to the current situation, in which there is an urgent demand for innovative therapeutic alternatives to fight infections caused by multidrug-resistant pathogens, such as multidrug-resistant tuberculosis. The identification of compounds that can act as adjuvants in antimycobacterial therapeutic regimens is an appealing strategy to restore the efficacy lost by some of the antibiotics currently used and shorten the duration of the therapeutic regimen. In this work, by setting Mycobacterium smegmatis as a model organism, we have developed a methodological strategy to identify, in a fast and simple approach, compounds with antimycobacterial activity or with potential adjuvant properties, by either inhibition of efflux or other unrelated mechanisms. Such an approach may increase the rate of identification of promising molecules, to be further explored in pathogenic models for their potential use either as antimicrobials or as adjuvants, in combination with available therapeutic regimens for the treatment of mycobacterial infections. This method allowed us to identify a new molecule that shows promising activity as an efflux inhibitor in M. smegmatis.

  6. A novel model to predict gas-phase hydroxyl radical oxidation kinetics of polychlorinated compounds.

    PubMed

    Luo, Shuang; Wei, Zongsu; Spinney, Richard; Yang, Zhihui; Chai, Liyuan; Xiao, Ruiyang

    2017-04-01

    In this study, a novel model based on aromatic meta-substituent grouping was presented to predict the second-order rate constants (k) for OH oxidation of PCBs in gas-phase. Since the oxidation kinetics are dependent on the chlorination degree and position, we hypothesized that it may be more accurate for k value prediction if we group PCB congeners based on substitution positions (i.e., ortho (o), meta (m), and para (p)). To test this hypothesis, we examined the correlation of polarizability (α), a quantum chemical based descriptor for k values, with an empirical Hammett constant (σ(+)) on each substitution position. Our result shows that α is highly linearly correlated to ∑σo,m,p(+) based on aromatic meta-substituents leading to the grouping based predictive model. With the new model, the calculated k values exhibited an excellent agreement with experimental measurements, and greater predictive power than the quantum chemical based quantitative structure activity relationship (QSAR) model. Further, the relationship of α and ∑σo,m,p(+) for PCDDs congeners, together with highest occupied molecular orbital (HOMO) distribution, were used to validate the aromatic meta-substituent grouping method. This newly developed model features a combination of good predictability of quantum chemical based QSAR model and simplicity of Hammett relationship, showing a great potential for fast and computational tractable prediction of k values for gas-phase OH oxidation of polychlorinated compounds.

  7. LakeVOC; A Deterministic Model to Estimate Volatile Organic Compound Concentrations in Reservoirs and Lakes

    USGS Publications Warehouse

    Bender, David A.; Asher, William E.; Zogorski, John S.

    2003-01-01

    This report documents LakeVOC, a model to estimate volatile organic compound (VOC) concentrations in lakes and reservoirs. LakeVOC represents the lake or reservoir as a two-layer system and estimates VOC concentrations in both the epilimnion and hypolimnion. The air-water flux of a VOC is characterized in LakeVOC in terms of the two-film model of air-water exchange. LakeVOC solves the system of coupled differential equations for the VOC concentration in the epilimnion, the VOC concentration in the hypolimnion, the total mass of the VOC in the lake, the volume of the epilimnion, and the volume of the hypolimnion. A series of nine simulations were conducted to verify LakeVOC representation of mixing, dilution, and gas exchange characteristics in a hypothetical lake, and two additional estimates of lake volume and MTBE concentrations were done in an actual reservoir under environmental conditions. These 11 simulations showed that LakeVOC correctly handled mixing, dilution, and gas exchange. The model also adequately estimated VOC concentrations within the epilimnion in an actual reservoir with daily input parameters. As the parameter-input time scale increased (from daily to weekly to monthly, for example), the differences between the measured-averaged concentrations and the model-estimated concentrations generally increased, especially for the hypolimnion. This may be because as the time scale is increased from daily to weekly to monthly, the averaging of model inputs may cause a loss of detail in the model estimates.

  8. An Efficient Approach in Analysis of DNA Base Calling Using Neural Fuzzy Model

    PubMed Central

    2017-01-01

    This paper presented the issues of true representation and a reliable measure for analyzing the DNA base calling is provided. The method implemented dealt with the data set quality in analyzing DNA sequencing, it is investigating solution of the problem of using Neurofuzzy techniques for predicting the confidence value for each base in DNA base calling regarding collecting the data for each base in DNA, and the simulation model of designing the ANFIS contains three subsystems and main system; obtain the three features from the subsystems and in the main system and use the three features to predict the confidence value for each base. This is achieving effective results with high performance in employment. PMID:28261268

  9. Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model

    SciTech Connect

    Engh, G. van den; Trask, B.J. ); Sachs, R. )

    1992-09-04

    The folding of chromatin in interphase cell nuclei was studied by fluorescent in situ hybridization with pairs of unique DNA sequence probes. The sites of DNA sequences separated by 100 to 2000 kilobase pairs (kbp) are distributed in interphase chromatin according to a random walk model. This model provides the basis for calculating the spacing of sequences along the linear DNA molecule from interphase distance measurements. An interphase mapping strategy based on this model was tested with 13 probes from a 4-megabase pair (Mbp) region of chromosome 4 containing the Huntington disease locus. The results confirmed the locations of the probes and showed that the remaining gap in the published maps of this region is negligible in size. Interphase distance measurements should facilitate construction of chromosome maps with an average marker density of one per 100 kbp, approximately ten times greater than that achieved by hybridization to metaphase chromosomes.

  10. Estimating Genomic Distance from DNA Sequence Location in Cell Nuclei by a Random Walk Model

    NASA Astrophysics Data System (ADS)

    van den Engh, Ger; Sachs, Rainer; Trask, Barbara J.

    1992-09-01

    The folding of chromatin in interphase cell nuclei was studied by fluorescent in situ hybridization with pairs of unique DNA sequence probes. The sites of DNA sequences separated by 100 to 2000 kilobase pairs (kbp) are distributed in interphase chromatin according to a random walk model. This model provides the basis for calculating the spacing of sequences along the linear DNA molecule from interphase distance measurements. An interphase mapping strategy based on this model was tested with 13 probes from a 4-megabase pair (Mbp) region of chromosome 4 containing the Huntington disease locus. The results confirmed the locations of the probes and showed that the remaining gap in the published maps of this region is negligible in size. Interphase distance measurements should facilitate construction of chromosome maps with an average marker density of one per 100 kbp, approximately ten times greater than that achieved by hybridization to metaphase chromosomes.

  11. Approaching mathematical model of the immune network based DNA Strand Displacement system.

    PubMed

    Mardian, Rizki; Sekiyama, Kosuke; Fukuda, Toshio

    2013-12-01

    One biggest obstacle in molecular programming is that there is still no direct method to compile any existed mathematical model into biochemical reaction in order to solve a computational problem. In this paper, the implementation of DNA Strand Displacement system based on nature-inspired computation is observed. By using the Immune Network Theory and Chemical Reaction Network, the compilation of DNA-based operation is defined and the formulation of its mathematical model is derived. Furthermore, the implementation on this system is compared with the conventional implementation by using silicon-based programming. From the obtained results, we can see a positive correlation between both. One possible application from this DNA-based model is for a decision making scheme of intelligent computer or molecular robot.

  12. Femtosecond to microsecond photochemistry of a [FeFe]hydrogenase enzyme model compound.

    PubMed

    Kaziannis, Spyridon; Santabarbara, Stefano; Wright, Joseph A; Greetham, Gregory M; Towrie, Michael; Parker, Anthony W; Pickett, Christopher J; Hunt, Neil T

    2010-11-25

    The photochemistry and dynamics of a model compound of the active site of the [FeFe]hydrogenase enzyme system have been studied on a wide range of time scales using a unique combination of femtosecond time-resolved infrared spectroscopy, nanosecond time-resolved infrared spectroscopy, and steady-state UV-FTIR methods. Using three different solvents, heptane, acetonitrile, and cyanoheptane, we have observed the rapid formation of solvent adduct species from the first solvation shell of the solute following photolysis of a carbonyl ligand and global fitting techniques have been employed to provide new insights into the ultrafast dynamics of this process. In addition, the use of solvent mixtures has enabled the observation of competitive ligand substitution processes at the newly created coordination site on time scales of a few nanoseconds, shedding new light on the chemical behavior of these enzyme models.

  13. NMR structural study of the prototropic equilibrium in solution of Schiff bases as model compounds.

    PubMed

    Ortegón-Reyna, David; Garcías-Morales, Cesar; Padilla-Martínez, Itzia; García-Báez, Efren; Aríza-Castolo, Armando; Peraza-Campos, Ana; Martínez-Martínez, Francisco

    2013-12-31

    An NMR titration method has been used to simultaneously measure the acid dissociation constant (pKa) and the intramolecular NHO prototropic constant ΔKNHO on a set of Schiff bases. The model compounds were synthesized from benzylamine and substituted ortho-hydroxyaldehydes, appropriately substituted with electron-donating and electron-withdrawing groups to modulate the acidity of the intramolecular NHO hydrogen bond. The structure in solution was established by 1H-, 13C- and 15N-NMR spectroscopy. The physicochemical parameters of the intramolecular NHO hydrogen bond (pKa, ΔKNHO and ΔΔG°) were obtained from 1H-NMR titration data and pH measurements. The Henderson-Hasselbalch data analysis indicated that the systems are weakly acidic, and the predominant NHO equilibrium was established using Polster-Lachmann δ-diagram analysis and Perrin model data linearization.

  14. Magnetic properties of RCo2 compounds in the exchange-striction model of ferrimagnets

    NASA Astrophysics Data System (ADS)

    Valiev, E. Z.; Teplykh, A. E.

    2017-01-01

    The original version of the exchange-striction model of a ferrimagnet has been employed for calculating a number of magnetic properties of RCo2 ferrimagnets, where R = Er, Ho, Dy, Tb, and Gd are rareearth ions. The following magnetic properties are calculated: pressure dependence of the Curie temperature ( T C), temperature dependences of magnetization in sublattices of cobalt and rare-earth atoms, and isotherms of magnetization of these lattices at T > T C. For an ErCo2 sample, the H-T phase diagram has been constructed and the magnetization in the magnetic fields H = 0-70 T has been calculated. The calculated and experimental results have been compared. Based on the exchange-striction model, the qualitative explanation of the difference in the type of the magnetic phase transformation in the intermetallic compounds with R = Tb and Gd and R = Er, Ho, and Dy is given.

  15. DNA Cleaving "Tandem-Array" Metallopeptides Activated With KHSO5: Towards the Development of Multi-Metallated Bioactive Conjugates and Compounds.

    PubMed

    Lewis, Mark A; Williams, Katie M; Fang, Ya-Yin; Schultz, Franklin A; Long, Eric C

    2014-01-01

    Amino terminal peptides of the general form Gly-Gly-His have been used to introduce single sites of metal binding and redox activity into a wide range of biomolecules to create bioactive compounds and conjugates capable of substrate oxidation. We report here that Gly-Gly-His-like peptides linked in a tandem fashion can also be generated leading to multi-metal binding arrays. While metal binding by the native Gly-Gly-His motif (typically to Cu(2+), Ni(2+), or Co(2+)) requires a terminal peptide amine ligand, previous work has demonstrated that an ornithine (Orn) residue can be substituted for the terminal Gly residue to allow solid-phase peptide synthesis to continue via the side chain N-δ. This strategy thus frees the Orn residue N-α for metal binding and permits placement of a Gly-Gly-His-like metal binding domain at any location within a linear, synthetic peptide chain. As we show here, this strategy also permits the assembly of tandem arrays of metal binding units in linear peptides of the form: NH2-Gly-Gly-His-[(δ)-Orn-Gly-His]n-(δ)-Orn-Gly-His-CONH2 (where n = 0, 1, and 2). Metal binding titrations of these tandem arrays monitored by UV-vis and ESI-MS indicated that they bind Cu(2+), Ni(2+), or Co(2+) at each available metal binding site. Further, it was found that these systems retained their ability to modify DNA oxidatively and to an extent greater than their parent M(II)•Gly-Gly-His. These findings suggest that the tandem array metallopeptides described here may function with increased efficiency as "next generation" appendages in the design of bioactive compounds and conjugates.

  16. Effects of natural organic matter model compounds on the transformation of carbon tetrachloride by chloride green rust.

    PubMed

    Liang, Xiaoming; Butler, Elizabeth C

    2010-04-01

    Interest has grown in the use of reactive minerals for natural and engineered transformation of ground water contaminants. This study investigated how the structural properties of 10 model compounds representing natural organic matter (NOM) influenced their adsorption to chloride green rust (GR-Cl), and how this adsorption affected rate constants for transformation of carbon tetrachloride (CT) by GR-Cl. The affinity of benzoic acid, phthalic acid, trimesic acid, pyromellitic acid, and mellitic acid for the GR-Cl surface generally increased in the order of increasing number of carboxylic acid functional groups, increasing acidity of these functional groups, and increasing charge density. For NOM model compounds that had phenolic functional groups (p-hydroxybenzoic acid, alpha-resorcylic acid, and caffeic acid), the affinity for the GR-Cl surface was greatest for caffeic acid, which had two adjacent phenolic functional groups. Some NOM model compounds had experimentally determined Langmuir maximum adsorption capacities (q(max-Langmuir)) greater than those calculated based on external surface area measurements and the size of the NOM model compound, suggesting adsorption to internal as well as external sites at the GR-Cl surface for these compounds. Rate constants for CT transformation by GR-Cl generally decreased as the affinity of the NOM model compounds (estimated by Langmuir K values) increased, but there was no statistically significant correlation between Langmuir parameters (i.e., K and q(max-Langmuir)) and rate constants, perhaps due to significant adsorption of some NOM model compounds to sites that were not accessible to CT, such as interlayer sites. Unlike the other NOM model compounds, caffeic acid, which adsorbed to a significant extent to the GR-Cl surface, increased the rate constant for CT transformation. The influence of NOM on rate constants for CT transformation by green rusts should be considered in ground water remediation planning.

  17. Application of a source apportionment model in consideration of volatile organic compounds in an urban stream

    USGS Publications Warehouse

    Asher, W.E.; Luo, W.; Campo, K.W.; Bender, D.A.; Robinson, K.W.; Zogorski, J.S.; Pankow, J.F.

    2007-01-01

    Position-dependent concentrations of trichloroethylene and methyl-tert-butyl ether are considered for a 2.81-km section of the Aberjona River in Massachusetts, USA. This river flows through Woburn and Winchester (Massachusetts, USA), an area that is highly urbanized, has a long history of industrial activities dating to the early 1800s, and has gained national attention because of contamination from chlorinated solvent compounds in Woburn wells G and H. The river study section is in Winchester and begins approximately five stream kilometers downstream from the Woburn wells superfund site. Approximately 300 toxic release sites are documented in the watershed upstream from the terminus of the study section. The inflow to the river study section is considered one source of contamination. Other sources are the atmosphere, a tributary flow, and groundwater flows entering the river; the latter are categorized according to stream zone (1, 2, 3, etc.). Loss processes considered include outflows to groundwater and water-to-atmosphere transfer of volatile compounds. For both trichloroethylene and methyl-rerf-butyl ether, degradation is neglected over the timescale of interest. Source apportionment fractions with assigned values ??inflow, ??1, ??2, ??3, etc. are tracked by a source apportionment model. The strengths of the groundwater and tributary sources serve as fitting parameters when minimizing a reduced least squares statistic between water concentrations measured during a synoptic study in July 2001 versus predictions from the model. The model fits provide strong evidence of substantial unknown groundwater sources of trichloroethylene and methyl-tert-butyl ether amounting to tens of grams per day of trichloroethylene and methyl-tert-butyl ether in the river along the study section. Modeling in a source apportionment manner can be useful to water quality managers allocating limited resources for remediation and source control. ?? 2007 SETAC.

  18. A parsimonious model for the release of volatile organic compounds (VOCs) encapsulated in products

    NASA Astrophysics Data System (ADS)

    Huang, Lei; Jolliet, Olivier

    2016-02-01

    Studies have demonstrated that near-field chemical intakes may exceed environmentally mediated exposures and are therefore essential to be considered when assessing chemical emissions across a product's life cycle. VOCs encapsulated in materials/products can be a major emission source in the use phase. Previous models describing such emissions require complex analytical or numerical solutions, which poses a great computational burden and lack transparency for use in high-throughput screening of chemicals. In the present study, we adapted a model which describes VOC emissions from building materials and subsequent removal by ventilation, and decoupled the material and air governing equations by assuming a pseudo-steady-state between emission and loss. Results of this decoupled model show good agreement with the original more complex model and the experimental data. The solution of this decoupled model for mass fraction emitted, which still consists of an infinite sum of exponential terms, is further reduced to a sum of only two exponentials with parameters which can be predicted from physiochemical properties using explicit equations. Results of this simple two-exponential model agree well with the original full model over a 15-year time period with R-square greater than 0.99 for a wide range of compounds and material thicknesses. Moreover, the chemical concentration at the material surface can be simply calculated from the derivative of this two-exponential model, which also agrees well with the surface concentration calculated using the original full model. The present parsimonious approach greatly reduces the computational burden, and can be easily implemented for high-throughput screening.

  19. VOLATILE ORGANIC COMPOUND EMISSIONS FROM LATEX PAINT-PART 2. TEST HOUSE STUDIES AND INDOOR AIR QUALITY (IAQ) MODELING

    EPA Science Inventory

    Emission models developed using small chamber data were combined with an Indoor Air Quality (IAQ) model to analyze the impact of volatile organic compound (VOC) emissions from latex paint on indoor environments. Test house experiments were conducted to verify the IAQ model's pred...

  20. Aqueous and Tissue Residue-Based Interspecies Correlation Estimation Models Provide Conservative Hazard Estimates for Aromatic Compounds

    EPA Science Inventory

    Interspecies correlation estimation (ICE) models were developed for 30 nonpolar aromatic compounds to allow comparison of prediction accuracy between 2 data compilation approaches. Type 1 models used data combined across studies, and type 2 models used data combined only within s...

  1. Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison

    SciTech Connect

    Dahlen, Oda Erp, Titus S. van

    2015-06-21

    Using rare event simulation techniques, we calculated DNA denaturation rate constants for a range of sequences and temperatures for the Peyrard-Bishop-Dauxois (PBD) model with two different parameter sets. We studied a larger variety of sequences compared to previous studies that only consider DNA homopolymers and DNA sequences containing an equal amount of weak AT- and strong GC-base pairs. Our results show that, contrary to previous findings, an even distribution of the strong GC-base pairs does not always result in the fastest possible denaturation. In addition, we applied an adaptation of the PBD model to study hairpin denaturation for which experimental data are available. This is the first quantitative study in which dynamical results from the mesoscopic PBD model have been compared with experiments. Our results show that present parameterized models, although giving good results regarding thermodynamic properties, overestimate denaturation rates by orders of magnitude. We believe that our dynamical approach is, therefore, an important tool for verifying DNA models and for developing next generation models that have higher predictive power than present ones.

  2. Modeling Human Exposure Levels to Airborne Volatile Organic Compounds by the Hebei Spirit Oil Spill

    PubMed Central

    Kim, Jong Ho; Kwak, Byoung Kyu; Ha, Mina; Cheong, Hae-Kwan

    2012-01-01

    Objectives The goal was to model and quantify the atmospheric concentrations of volatile organic compounds (VOCs) as the result of the Hebei Spirit oil spill, and to predict whether the exposure levels were abnormally high or not. Methods We developed a model for calculating the airborne concentration of VOCs that are produced in an oil spill accident. The model was applied to a practical situation, namely the Hebei Spirit oil spill. The accuracy of the model was verified by comparing the results with previous observation data. The concentrations were compared with the currently used air quality standards. Results Evaporation was found to be 10- to 1,000-fold higher than the emissions produced from a surrounding industrial complex. The modeled concentrations for benzene failed to meet current labor environmental standards, and the concentration of benzene, toluene, ortho- meta- para-xylene were higher than the values specified by air quality standards and guideline values on the ocean. The concentrations of total VOCs were much higher than indoor environmental criteria for the entire Taean area for a few days. Conclusions The extent of airborne exposure was clearly not the same as that for normal conditions. PMID:22468262

  3. Adsorption and degradation of model volatile organic compounds by a combined titania-montmorillonite-silica photocatalyst.

    PubMed

    Chen, Jiangyao; Li, Guiying; He, Zhigui; An, Taicheng

    2011-06-15

    A series of adsorptive photocatalysts, combined titania-montmorillonite-silica were synthesized. The resultant photocatalysts consisted of more and more spherically agglomerated TiO(2) particles with increasing of TiO(2) content, and anatase was the only crystalline phase with nano-scale TiO(2) particles. With increasing of the cation exchange capacity to TiO(2) molar ratio, specific surface area and pore volume increased very slightly. In a fluidized bed photocatalytic reactor by choosing toluene, ethyl acetate and ethanethiol as model pollutants, all catalysts had relatively high adsorption capacities and preferred to adsorb higher polarity pollutants. Langmuir isotherm model better described equilibrium data compared to Freundlich model. Competitive adsorptions were observed for the mixed pollutants on the catalysts, leading to decrease adsorption capacity for each pollutant. The combined titania-montmorillonite-silica photocatalyst exhibited excellent photocatalytic removal ability to model pollutants of various components. Almost 100% of degradation efficiency was achieved within 120 min for each pollutant with about 500 ppb initial concentration, though the efficiencies of multi-component compounds slightly decreased. All photocatalytic reactions followed the Langmuir-Hinshelwood model. Degradation rate constants of multi-component systems were lower than those for single systems, following the order of toluene

  4. Modeling the repair of DNA strand breaks caused by γ-radiation in a minichromosome

    NASA Astrophysics Data System (ADS)

    Łakomiec, K.; Kumala, S.; Hancock, R.; Rzeszowska-Wolny, J.; Fujarewicz, K.

    2014-08-01

    The objective of the studies described here was the development of a mathematical model which would fit experimental data for the repair of single and double strand breaks induced in DNA in living cells by exposure to ionizing radiation, and which would allow to better understand the processes of DNA repair. DNA breaks are believed to play the major role in radiation-induced lethality and formation of chromosome deletions, and are therefore crucial to the response of cells to radiotherapy. In an initial model which we reported on the basis of data for the repair of Epstein-Barr minichromosomes in irradiated Raji cells, we assumed that DNA breaks are induced only at the moment of irradiation and are later removed by repair systems. This work gives a development of that mathematical model which fits the experimental results more precisely and suggests strongly that DNA breaks are generated not only by direct irradiation but also later, probably by systems engaged in repair of oxidative damage.

  5. Aberrant DNA methylation occurs in colon neoplasms arising in the azoxymethane colon cancer model

    PubMed Central

    Borinstein, Scott C.; Conerly, Melissa; Dzieciatkowski, Slavomir; Biswas, Swati; Washington, M. Kay; Trobridge, Patty; Henikoff, Steve; Grady, William M.

    2010-01-01

    Mouse models of intestinal tumors have advanced our understanding of the role of gene mutations in colorectal malignancy. However, the utility of these systems for studying the role of epigenetic alterations in intestinal neoplasms remains to be defined. Consequently, we assessed the role of aberrant DNA methylation in the azoxymethane (AOM) rodent model of colon cancer. AOM induced tumors display global DNA hypomethylation, which is similar to human colorectal cancer. We next assessed the methylation status of a panel of candidate genes previously shown to be aberrantly methylated in human cancer or in mouse models of malignant neoplasms. This analysis revealed different patterns of DNA methylation that were gene specific. Zik1 and Gja9 demonstrated cancer-specific aberrant DNA methylation, whereas, Cdkn2a/p16, Igfbp3, Mgmt, Id4, and Cxcr4 were methylated in both the AOM tumors and normal colon mucosa. No aberrant methylation of Dapk1 or Mlt1 was detected in the neoplasms, but normal colon mucosa samples displayed methylation of these genes. Finally, p19Arf, Tslc1, Hltf, and Mlh1 were unmethylated in both the AOM tumors and normal colon mucosa. Thus, aberrant DNA methylation does occur in AOM tumors, although the frequency of aberrantly methylated genes appears to be less common than in human colorectal cancer. Additional studies are necessary to further characterize the patterns of aberrantly methylated genes in AOM tumors. PMID:19777566

  6. A DNA-based semantic fusion model for remote sensing data.

    PubMed

    Sun, Heng; Weng, Jian; Yu, Guangchuang; Massawe, Richard H

    2013-01-01

    Semantic technology plays a key role in various domains, from conversation understanding to algorithm analysis. As the most efficient semantic tool, ontology can represent, process and manage the widespread knowledge. Nowadays, many researchers use ontology to collect and organize data's semantic information in order to maximize research productivity. In this paper, we firstly describe our work on the development of a remote sensing data ontology, with a primary focus on semantic fusion-driven research for big data. Our ontology is made up of 1,264 concepts and 2,030 semantic relationships. However, the growth of big data is straining the capacities of current semantic fusion and reasoning practices. Considering the massive parallelism of DNA strands, we propose a novel DNA-based semantic fusion model. In this model, a parallel strategy is developed to encode the semantic information in DNA for a large volume of remote sensing data. The semantic information is read in a parallel and bit-wise manner and an individual bit is converted to a base. By doing so, a considerable amount of conversion time can be saved, i.e., the cluster-based multi-processes program can reduce the conversion time from 81,536 seconds to 4,937 seconds for 4.34 GB source data files. Moreover, the size of result file recording DNA sequences is 54.51 GB for parallel C program compared with 57.89 GB for sequential Perl. This shows that our parallel method can also reduce the DNA synthesis cost. In addition, data types are encoded in our model, which is a basis for building type system in our future DNA computer. Finally, we describe theoretically an algorithm for DNA-based semantic fusion. This algorithm enables the process of integration of the knowledge from disparate remote sensing data sources into a consistent, accurate, and complete representation. This process depends solely on ligation reaction and screening operations instead of the ontology.

  7. Phenolic mediators enhance the manganese peroxidase catalyzed oxidation of recalcitrant lignin model compounds and synthetic lignin.

    PubMed

    Nousiainen, Paula; Kontro, Jussi; Manner, Helmiina; Hatakka, Annele; Sipilä, Jussi

    2014-11-01

    Fungal oxidative enzymes, such as peroxidases and laccases, are the key catalysts in lignin biodegradation in vivo, and consequently provide an important source for industrial ligninolytic biocatalysts. Recently, it has been shown that some syringyl-type phenolics have potential as industrial co-oxidants or mediators, in laccase-catalyzed modification of lignocellulosic material. We have now studied the effect of such mediators with ligninolytic peroxidases on oxidation of the most recalcitrant lignin model compounds. We found that they are able to enhance the manganese peroxidase (MnP) catalyzed oxidation reactions of small non-phenolic compounds, veratryl alcohol and veratrylglycerol β-guaiacyl ether (adlerol), which are not usually oxidized by manganese peroxidases alone. In these experiments we compared two peroxidases from white-rot fungi, MnP from Phlebia sp. Nf b19 and versatile peroxidase (VP) from Bjerkandera adusta under two oxidation conditions: (i) the Mn(III) initiated mediated oxidation by syringyl compounds and (ii) the system involving MnP-dependent lipid peroxidation, both with production of (hydrogen) peroxides in situ to maintain the peroxidase catalytic cycle. It was found that both peroxidases produced α-carbonyl oxidation product of veratryl alcohol in clearly higher yields in reactions mediated by phenoxy radicals than in lipid-peroxyl radical system. The oxidation of adlerol, on the other hand, was more efficient in lipid-peroxidation-system. VP was more efficient than MnP in the oxidation of veratryl alcohol and showed its lignin peroxidase type activity in the reaction conditions indicated by some cleavage of Cα-Cβ-bond of adlerol. Finally, the mediator assisted oxidation conditions were applied in the oxidation of synthetic lignin (DHP) and the structural analysis of the oxidized polymers showed clear modifications in the polymer outcome, e.g. the oxidation resulted in reduced amount of aliphatic hydroxyls indicated by (31)P NMR.

  8. Inhibition of growth of Zymomonas mobilis by model compounds found in lignocellulosic hydrolysates

    PubMed Central

    2013-01-01

    Background During the pretreatment of biomass feedstocks and subsequent conditioning prior to saccharification, many toxic compounds are produced or introduced which inhibit microbial growth and in many cases, production of ethanol. An understanding of the toxic effects of compounds found in hydrolysate is critical to improving sugar utilization and ethanol yields in the fermentation process. In this study, we established a useful tool for surveying hydrolysate toxicity by measuring growth rates in the presence of toxic compounds, and examined the effects of selected model inhibitors of aldehydes, organic and inorganic acids (along with various cations), and alcohols on growth of Zymomonas mobilis 8b (a ZM4 derivative) using glucose or xylose as the carbon source. Results Toxicity strongly correlated to hydrophobicity in Z. mobilis, which has been observed in Escherichia coli and Saccharomyces cerevisiae for aldehydes and with some exceptions, organic acids. We observed Z. mobilis 8b to be more tolerant to organic acids than previously reported, although the carbon source and growth conditions play a role in tolerance. Growth in xylose was profoundly inhibited by monocarboxylic organic acids compared to growth in glucose, whereas dicarboxylic acids demonstrated little or no effects on growth rate in either substrate. Furthermore, cations can be ranked in order of their toxicity, Ca++ > > Na+ > NH4+ > K+. HMF (5-hydroxymethylfurfural), furfural and acetate, which were observed to contribute to inhibition of Z. mobilis growth in dilute acid pretreated corn stover hydrolysate, do not interact in a synergistic manner in combination. We provide further evidence that Z. mobilis 8b is capable of converting the aldehydes furfural, vanillin, 4-hydroxybenzaldehyde and to some extent syringaldehyde to their alcohol forms (furfuryl, vanillyl, 4-hydroxybenzyl and syringyl alcohol) during fermentation. Conclusions Several key findings in this report provide a

  9. Overlapping gene expression profiles of model compounds provide opportunities for immunotoxicity screening

    SciTech Connect

    Baken, Kirsten A. Pennings, Jeroen L.A.; Jonker, Martijs J.; Schaap, Mirjam M.; Vries, Annemieke de; Steeg, Harry van; Breit, Timo M.; Loveren, Henk van

    2008-01-01

    In order to investigate immunotoxic effects of a set of model compounds in mice, a toxicogenomics approach was combined with information on macroscopical and histopathological effects on spleens and on modulation of immune function. Bis(tri-n-butyltin)oxide (TBTO), cyclosporin A (CsA), and benzo[a]pyrene (B[a]P) were administered to C57BL/6 mice at immunosuppressive dose levels. Acetaminophen (APAP) was included in the study since indications of immunomodulating properties of this compound have appeared in the literature. TBTO exposure caused the most pronounced effect on gene expression and also resulted in the most severe reduction of body weight gain and induction of splenic irregularities. All compounds caused inhibition of cell division in the spleen as shown by microarray analysis as well as by suppression of lymphocyte proliferation after application of a contact sensitizer as demonstrated in an immune function assay that was adapted from the local lymph node assay. The immunotoxicogenomics approach applied in this study thus pointed to immunosuppression through cell cycle arrest as a common mechanism of action of immunotoxicants, including APAP. Genes related to cell division such as Ccna2, Brca1, Birc5, Incenp, and Cdkn1a (p21) were identified as candidate genes to indicate anti-proliferative effects of xenobiotics in immune cells for future screening assays. The results of our experiments also show the value of group wise pathway analysis for detection of more subtle transcriptional effects and the potency of evaluation of effects in the spleen to demonstrate immunotoxicity.

  10. Preliminary Investigation of Microdosimetric Track Structure Physics Models in Geant4-DNA and RITRACKS.

    PubMed

    Douglass, Michael; Penfold, Scott; Bezak, Eva

    2015-01-01

    The major differences between the physics models in Geant4-DNA and RITRACKS Monte Carlo packages are investigated. Proton and electron ionisation interactions and electron excitation interactions in water are investigated in the current work. While these packages use similar semiempirical physics models for inelastic cross-sections, the implementation of these models is demonstrated to be significantly different. This is demonstrated in a simple Monte Carlo simulation designed to identify differences in interaction cross-sections.

  11. Preliminary Investigation of Microdosimetric Track Structure Physics Models in Geant4-DNA and RITRACKS

    PubMed Central

    Bezak, Eva

    2015-01-01

    The major differences between the physics models in Geant4-DNA and RITRACKS Monte Carlo packages are investigated. Proton and electron ionisation interactions and electron excitation interactions in water are investigated in the current work. While these packages use similar semiempirical physics models for inelastic cross-sections, the implementation of these models is demonstrated to be significantly different. This is demonstrated in a simple Monte Carlo simulation designed to identify differences in interaction cross-sections. PMID:26124856

  12. Correction of the lack of commutability between plasmid DNA and genomic DNA for quantification of genetically modified organisms using pBSTopas as a model.

    PubMed

    Zhang, Li; Wu, Yuhua; Wu, Gang; Cao, Yinglong; Lu, Changming

    2014-10-01

    Plasmid calibrators are increasingly applied for polymerase chain reaction (PCR) analysis of genetically modified organisms (GMOs). To evaluate the commutability between plasmid DNA (pDNA) and genomic DNA (gDNA) as calibrators, a plasmid molecule, pBSTopas, was constructed, harboring a Topas 19/2 event-specific sequence and a partial sequence of the rapeseed reference gene CruA. Assays of the pDNA showed similar limits of detection (five copies for Topas 19/2 and CruA) and quantification (40 copies for Topas 19/2 and 20 for CruA) as those for the gDNA. Comparisons of plasmid and genomic standard curves indicated that the slopes, intercepts, and PCR efficiency for pBSTopas were significantly different from CRM Topas 19/2 gDNA for quantitative analysis of GMOs. Three correction methods were used to calibrate the quantitative analysis of control samples using pDNA as calibrators: model a, or coefficient value a (Cva); model b, or coefficient value b (Cvb); and the novel model c or coefficient formula (Cf). Cva and Cvb gave similar estimated values for the control samples, and the quantitative bias of the low concentration sample exceeded the acceptable range within ±25% in two of the four repeats. Using Cfs to normalize the Ct values of test samples, the estimated values were very close to the reference values (bias -13.27 to 13.05%). In the validation of control samples, model c was more appropriate than Cva or Cvb. The application of Cf allowed pBSTopas to substitute for Topas 19/2 gDNA as a calibrator to accurately quantify the GMO.

  13. The two isomers of HDTIC compounds from Astragali Radix slow down telomere shortening rate via attenuating oxidative stress and increasing DNA repair ability in human fetal lung diploid fibroblast cells.

    PubMed

    Wang, Peichang; Zhang, Zongyu; Sun, Ying; Liu, Xinwen; Tong, Tanjun

    2010-01-01

    4-Hydroxy-5-hydroxymethyl-[1,3]dioxolan-2,6'-spirane-5',6',7',8'-tetrahydro-indolizine-3'-carbaldehyde (HDTIC)-1 and HDTIC-2 are two isomers extracted from Astragalus membranaceus (Fisch) Bunge Var. mongholicus (Bge) Hsiao. Our previous study had demonstrated that they could extend the lifespan of human fetal lung diploid fibroblasts (2BS). To investigate the mechanisms of the HDTIC-induced delay of replicative senescence, in this study, we assessed the effects of these two compounds on telomere shortening rate and DNA repair ability in 2BS cells. The telomere shortening rates of the cells cultured with HDTIC-1 or HDTIC-2 were 31.5 and 41.1 bp with each division, respectively, which were much less than that of the control cells (71.1 bp/PD). We also found that 2BS cells pretreated with HDTIC-1 or HDTIC-2 had a significant reduction in DNA damage after exposure to 200 microM H(2)O(2) for 5 min. Moreover, the 100 microM H(2)O(2)-induced DNA damage was significantly repaired after the damaged cells were continually cultured with HDTIC for 1 h. These results suggest that HDTIC compounds slow down the telomere shortening rate of 2BS cells, which is mainly due to the biological properties of the compounds including the reduction of DNA damage and the improvement of DNA repair ability. In addition, the slow down of telomere shortening rate, the reduction of DNA damage, and the improvement of DNA repair ability induced by HDTIC may be responsible for their delay of replicative senescence.

  14. Application of inverse dispersion model for estimating volatile organic compounds emitted from the offshore industrial park

    NASA Astrophysics Data System (ADS)

    Tsai, M.; Lee, C.; Yu, H.

    2013-12-01

    In the last 20 years, the Yunlin offshore industrial park has significantly contributed to the economic development of Taiwan. Its annual production value has reached almost 12 % of Taiwan's GDP in 2012. The offshore industrial park also balanced development of urban and rural in areas. However, the offshore industrial park is considered the major source of air pollution to nearby counties, especially, the emission of Volatile Organic Compounds(VOCs). Studies have found that exposures to high level of some VOCs have caused adverse health effects on both human and ecosystem. Since both health and ecological effects of air pollution have been the subject of numerous studies in recent years, it is a critical issue in estimating VOCs emissions. Nowadays emission estimation techniques are usually used emissions factors in calculation. Because the methodology considered totality of equipment activities based on statistical assumptions, it would encounter great uncertainty between these coefficients. This study attempts to estimate VOCs emission of the Yunlin Offshore Industrial Park using an inverse atmospheric dispersion model. The inverse modeling approach will be applied to the combination of dispersion modeling result which input a given one-unit concentration and observations at air quality stations in Yunlin. The American Meteorological Society-Environmental Protection Agency Regulatory Model (AERMOD) is chosen as the tool for dispersion modeling in the study. Observed concentrations of VOCs are collected by the Taiwanese Environmental Protection Administration (TW EPA). In addition, the study also analyzes meteorological data including wind speed, wind direction, pressure and temperature etc. VOCs emission estimations from the inverse atmospheric dispersion model will be compared to the official statistics released by Yunlin Offshore Industrial Park. Comparison of estimated concentration from inverse dispersion modeling and official statistical concentrations will

  15. Development of a whole-organism model to screen new compounds for sun protection.

    PubMed

    Wang, Yun-Hsin; Wen, Chi-Chung; Yang, Zhi-Shiang; Cheng, Chien-Chung; Tsai, Jen-Ning; Ku, Chia-Chen; Wu, Hsin-Ju; Chen, Yau-Hung

    2009-01-01

    We used zebrafish as a whole-organism model to screen new compounds for sun protection activity. First of all, we designed a series of UVB exposure experiments and recorded the phenotypic changes of zebrafish embryos. Results showed that 100 mJ/cm(2) of UVB given six times separated by 30 min intervals is the best condition. Fin malformation (reduced and/or absent fin) phenotypes are the most evident consequences after exposure to UVB. Each fin was affected by UVB, including pelvic, ventral, caudal, and dorsal fin, but pelvic fin seemed to be the most sensitive target after UVB exposure. We furthermore carried out "prevention" and "treatment" experiments using green tea extract and/or (-)-epigallocatechin (EGCG) to test this whole-organism model by observing the morphological changes of all fins (especially pelvic fin) after UVB exposure. Effects of UVB, green tea extract and EGCG on fin development were assessed using the Kaplan-Meier analysis, log-rank test and Cox proportional hazards regression. Results showed that a zebrafish pelvic fin in the UVB + green tea (treatment) group is 5.51 (range from 2.39 to 14.90) times, one in the UVB + green tea (prevention) group is 7.04 (range from 3.11 to 18.92) times, and one in the 25 ppm of EGCG (prevention) group is 22.19 (range from 9.40 to 61.50) times more likely to return to normal fin than one in the UVB only group. On the basis of these observations, we believe this model is effective for screening the higher stability and lower toxicity of new compounds, such as small chemicals which are derivative from EGCG or othe