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Sample records for deoxyribonucleic acid molecules

  1. Electrical Transport Properties of Au-Doped Deoxyribonucleic Acid Molecules

    NASA Astrophysics Data System (ADS)

    Hwang, Jong Seung; Hong, Su Heon; Kim, Hyung Kwon; Kwon, Young Whan; Jin, Jung Il; Hwang, Sung Woo; Ahn, Doyeol

    2005-04-01

    Deoxyribonucleic acid (DNA) molecules were doped with Au atoms and their electrical transport properties were measured. The Au doping was carried out by incubating a mixture of HAuCl4\\cdot3H2O and DNA solutions. The binding of Au atoms to DNA bases was identified using Fourier transform infrared spectroscopy and X-ray photoemission spectroscopy. The Au-doped DNA molecules were deposited on nanoelectrodes and the presence of the molecules between the electrodes was determined by both scanning electron microscopy and atomic force microscopy. Measurement of the current-voltage characteristics showed that the Au-doped DNA molecules exhibited a higher conductivity than undoped DNA molecules. Detailed analysis of the chemical composition shows that there is a strong possibility of reliably controlling the conductivity of DNA molecules using this method.

  2. Structure of Replicating Simian Virus 40 Deoxyribonucleic Acid Molecules 1

    PubMed Central

    Sebring, E. D.; Kelly, T. J.; Thoren, M. M.; Salzman, N. P.

    1971-01-01

    Properties of replicating simian virus 40 (SV40) deoxyribonucleic acid (DNA) have been examined by sedimentation analysis and by direct observation during a lytic cycle of infection of African green monkey kidney cells. Two types of replicating DNA molecules were observed in the electron microscope. One was an open structure containing two branch points, three branches, and no free ends whose length measurements were consistent with those expected for replicating SV40 DNA molecules. A second species had the same features as the open structure, but in addition it contained a superhelix in the unreplicated portion of the molecule. Eighty to ninety per cent of the replicative intermediates (RI) were in this latter configuration, and length measurements of these molecules also were consistent with replicating SV40 DNA. Replicating DNA molecules with this configuration have not been described previously. RI, when examined in ethidium bromide-cesium chloride (EB-CsCl) isopycnic gradients, banded in a heterogeneous manner. A fraction of the RI banded at the same density as circular SV40 DNA containing one or more single-strand nicks (component II). The remaining radioactive RI banded at densities higher than that of component II, and material was present at all densities between that of supercoiled double-stranded DNA (component I) and component II. When RI that banded at different densities in EB-CsCl were examined in alkaline gradients, cosedimentation of parental DNA and newly replicated DNA did not occur. All newly replicated DNA sedimented more slowly than did intact single-stranded SV40 DNA, a finding that is inconsistent with the rolling circle model of DNA replication. An inverse correlation exists between the extent of replication of the SV40 DNA and the banding density in EB-CsCl. Under alkaline conditions, the parental DNA strands that were contained in the RI sedimented as covalently closed structures. The sedimentation rates in alkali of the covalently closed

  3. Fabrication of nickel and gold nanowires by controlled electrodeposition on deoxyribonucleic acid molecules

    NASA Astrophysics Data System (ADS)

    Gu, Qun; Jin, Helena; Dai, Kun

    2009-01-01

    Magnetic and electrical nanowires are two important materials in the development of futuristic nanoelectronics, data storage media and nanosensors. Ni and Au nanowires with a diameter of a few tens of nanometres have been fabricated using deoxyribonucleic acid (DNA) molecules as a template through nanoparticle-controlled electroless deposition (ELD). Nanowire precursors, 1-3 nm Pt(0)-DNA and 1.4 nm Au(0)-DNA, were assembled using two different methods. Chemical reduction was used to deposit Pt(0) particles on DNA which catalyzed Ni nanowire growth. Positively charged Au nanoparticles were directly assembled on phosphate groups of DNA which were stretched and anchored between micrometre-spaced electrodes. Electrical measurement has shown that Au nanowires, catalyzed by Au(0)-DNA in a subsequent ELD, are highly conductive and show linear I-V characteristics. The major factors for the resistivity of nanowires were discussed in detail. This work involves important aspects in the field of DNA-based self-assembly, such as DNA and surface interaction, DNA nanoparticle assembly and electrical property of fabricated nanowires.

  4. Does the deoxyribonucleic acid shape dictate its conductivity?

    NASA Astrophysics Data System (ADS)

    Romano, P.; Polcari, A.; Granata, V.; Sabatino, L.; Colantuoni, V.

    2009-05-01

    We present the evolution of current-voltage characteristics measured on linear fragments of deoxyribonucleic acid (DNA) molecules as a function of their length. The nonlinear behavior systematically observed at room temperature and also reported on circular plasmids suggests that the more molecules are involved in the conduction process, the higher are the current values measured. At the same time, a characteristic steplike feature superimposed to an overall increasing background appears more pronounced. We interpret this behavior in terms of simultaneous coherent and incoherent transport processes, the former taking place inside the DNA molecule, the latter through the network of molecules. Following our previous analysis on circular molecules, a phenomenological model is developed, in which a tunneling current with an energy dependent transmission coefficient is superimposed to a hopping current. The model provides a semiquantitative evidence that the steplike feature represents the signature of charge transmission inside the molecule. Our results are consistent with many of the conductivity data present in the literature.

  5. Specific Initiation Site for Simian Virus 40 Deoxyribonucleic Acid Replication

    PubMed Central

    Thoren, Marilyn M.; Sebring, Edwin D.; Salzman, Norman P.

    1972-01-01

    Replicating simian virus 40 (SV40) deoxyribonucleic acid (DNA) molecules have been isolated under conditions in which the newly synthesized DNA is uniformly labeled with 3H-thymidine. These newly synthesized strands are released from the replicative intermediate molecules by alkaline treatment, and it has been possible to isolate single-stranded SV40 DNA which varies in size from 157,000 daltons (from molecules that are 10% replicated) to 1,360,000 daltons (85% replicated). The rates of duplex formation of newly synthesized DNA have been used to relate their genetic complexity to the extent of DNA replication. As DNA replication proceeds, the time required to effect 50% renaturation of the newly synthesized DNA increases at a proportional rate. The data establish that DNA replication is not initiated at random, but rather that there is a single specific initiation site for DNA replication. PMID:4342054

  6. Origin and Direction of Simian Virus 40 Deoxyribonucleic Acid Replication

    PubMed Central

    Fareed, George C.; Garon, Claude F.; Salzman, Norman P.

    1972-01-01

    Double-branched, circular, replicating deoxyribonucleic acid (DNA) molecules of simian virus 40 (SV40) have been cleaved by the R1 restriction endonuclease from Escherichia coli. This enzyme introduces one double-strand break in SV40 DNA, at a specific site. The site of cleavage in the replicating molecules was used in this study to position the origin and the two branch points. Radioactively labeled molecules fractionated according to their extent of replication were evaluated after cleavage by sedimentation analysis and electron microscopy. The results demonstrate that the R1 cleavage site is 33% of the genome length from the origin of replication and that both branch points are growing points. These data indicate that SV40 DNA replication is bidirectional and confirm other reports which have shown a unique origin of replication. Images PMID:4342055

  7. Photoelectrochemical deoxyribonucleic acid sensing on a nanostructured TiO2 electrode

    NASA Astrophysics Data System (ADS)

    Tokudome, Hiromasa; Yamada, Yoko; Sonezaki, Shuji; Ishikawa, Hiroshi; Bekki, Makoto; Kanehira, Koki; Miyauchi, Masahiro

    2005-11-01

    A nanostructured TiO2 electrode chemisorbed with probe deoxyribonucleic acid (DNA) can photoelectrochemically detect a dye-labeled target DNA molecule. After the hybridization between the probe and target DNA molecules, light irradiation generates electrons in the dye molecules, and these electrons are injected into the TiO2 electrode. The resulting photocurrent can be measured and corresponds to the concentration of target DNA. This sensor can quantitatively detect target DNA at lower than nanomolar concentrations. In addition, by utilizing two different dyes, different DNA sequences can be detected on the TiO2 electrode.

  8. Induction of cellular deoxyribonucleic acid synthesis in butyrate-treated cells by simian virus 40 deoxyribonucleic acid

    SciTech Connect

    Kawasaki, S.; Diamond, L.; Baserga, R.

    1981-11-01

    Sodium butyrate (3mM) inhibited the entry into the S phase of quiescent 3T3 cells stimulated by serum, but had no effect on the accumulation of cellular ribonucleic acid. Simian virus 40 infection or manual microinjection of cloned fragments from the simian virus 40 A gene caused quiescent 3T3 cells to enter the S phase even in the presence of butyrate. NGI cells, a line of 3T3 cells transformed by simian virus 40, grew vigorously in 3 mM butyrate. Homokaryons were formed between G/sub 1/ and S-phase 3T3 cells. Butyrate inhibited the induction of deoxyribonucleic acid synthesis that usually occurs in G/sub 1/ nuclei when G/sub 1/ cells are fused with S-phase cells. However, when G/sub 1/ 3T3 cells were fused with exponentially growing NGI cells, the 3T3 nuclei were induced to enter deoxyribonucleic acid synthesis. In tsAF8 cells, a ribonucleic acid polymerase II mutant that stops in the G/sub 1/ phase of the cell cycle, no temporal sequence was demonstrated between the butyrate block and the temperature-sensitive block. These results confirm previous reports that certain virally coded proteins can induce cell deoxyribonucleic acid synthesis in the absence of cellular functions that are required by serum-stimulated cells. The author's interpretation of these data is that butyrate inhibited cell growth by inhibiting the expression of genes required for the G/sub o/ ..-->.. G/sub 1/ ..-->.. S transition and that the product of the simian virus 40 A gene overrode this inhibition by providing all of the necessary functions for the entry into the S phase.

  9. Polyamines in the Synthesis of Bacteriophage Deoxyribonucleic Acid. I. Lack of Dependence of Polyamine Synthesis on Bacteriophage Deoxyribonucleic Acid Synthesis

    PubMed Central

    Dion, Arnold S.; Cohen, Seymour S.

    1972-01-01

    To determine whether polyamine synthesis is dependent on deoxyribonucleic acid (DNA) synthesis, polyamine levels were estimated after infection of bacterial cells with ultraviolet-irradiated T4 or T4 am N 122, a DNA-negative mutant. Although phage DNA accumulation was restricted to various degrees in comparison to cells infected with T4D, nearly commensurate levels of putrescine and spermidine synthesis were observed after infection, regardless of the rate of phage DNA synthesis. We conclude from these data that polyamine synthesis after infection is independent of phage DNA synthesis. PMID:4552549

  10. Incorporation of Deoxyribonucleic Acid Precursors by T4 Deoxyribonucleic Acid-Protein Complexes Retained on Glass Fiber Filters

    PubMed Central

    Miller, Robert C.; Kozinski, Andrzej W.

    1970-01-01

    Bacteriophage T4 deoxyribonucleic acid (DNA)-protein complexes were retained preferentially on glass fiber filters. DNA polymerase activity in the complex was detected through the incorporation of 3H-labeled DNA precursors. The primer-product DNA hybridized with both phage and Escherichia coli DNA. Density labeling experiments showed that about 30% of incorporated 3H-deoxyadenosine triphosphate was found in DNA which hybridized with phage DNA; this DNA was found to be covalently attached to the primer DNA. PMID:5497903

  11. DEOXYRIBONUCLEIC ACID BASE COMPOSITION OF PROTEUS AND PROVIDENCE ORGANISMS

    PubMed Central

    Falkow, Stanley; Ryman, I. R.; Washington, O.

    1962-01-01

    Falkow, Stanley (Walter Reed Army Institute of Research, Washington D.C.), I. R. Ryman, and O. Washington. Deoxyribonucleic acid base composition of Proteus and Providence organisms. J. Bacteriol. 83:1318–1321. 1962.—Deoxyribonucleic acids (DNA) from various species of Proteus and of Providence bacteria have been examined for their guanine + cytosine (GC) content. P. vulgaris, P. mirabilis, and P. rettgeri possess essentially identical mean GC contents of 39%, and Providence DNA has a GC content of 41.5%. In marked contrast, P. morganii DNA was found to contain 50% GC. The base composition of P. morganii is only slightly lower than those observed for representatives of the Escherichia, Shigella, and Salmonella groups. Aerobacter and Serratia differ significantly from the other members of the family by their relatively high GC content. Since a minimal requirement for genetic compatibility among different species appears to be similarity of their DNA base composition, it is suggested that P. morganii is distinct genetically from the other species of Proteus as well as Providence strains. The determination of the DNA base composition of microorganisms is important for its predictive information. This information should prove of considerable value in investigating genetic and taxonomic relationships among bacteria. PMID:13891463

  12. Adansonian Analysis and Deoxyribonucleic Acid Base Composition of Serratia marcescens

    PubMed Central

    Colwell, R. R.; Mandel, M.

    1965-01-01

    Colwell, R. R. (Georgetown University, Washington, D.C.), and M. Mandel. Adansonian analysis and deoxyribonucleic acid base composition of Serratia marcescens. J. Bacteriol. 89:454–461. 1965.—A total of 33 strains of Serratia marcescens were subjected to Adansonian analysis for which more than 200 coded features for each of the organisms were included. In addition, the base composition [expressed as moles per cent guanine + cytosine (G + C)] of the deoxyribonucleic acid (DNA) prepared from each of the strains was determined. Except for four strains which were intermediate between Serratia and the Hafnia and Aerobacter group C of Edwards and Ewing, the S. marcescens species group proved to be extremely homogeneous, and the different strains showed high affinities for each other (mean similarity, ¯S = 77%). The G + C ratio of the DNA from the Serratia strains ranged from 56.2 to 58.4% G + C. Many species names have been listed for the genus, but only a single clustering of the strains was obtained at the species level, for which the species name S. marcescens was retained. S. kiliensis, S. indica, S. plymuthica, and S. marinorubra could not be distinguished from S. marcescens; it was concluded, therefore, that there is only a single species in the genus. The variety designation kiliensis does not appear to be valid, since no subspecies clustering of strains with negative Voges-Proskauer reactions could be detected. The characteristics of the species are listed, and a description of S. marcescens is presented. PMID:14255714

  13. Endonuclease from Micrococcus luteus which has activity toward ultraviolet-irradiated deoxyribonucleic acid: its action on transforming deoxyribonucleic acid.

    PubMed

    Setlow, R B; Setlow, J K; Carrier, W L

    1970-04-01

    An endonuclease purified from Micrococcus luteus makes single-strand breaks in ultraviolet (UV)-irradiated, native deoxyribonucleic acid (DNA). The purified endonuclease is able to reactivate UV-inactivated transforming DNA of Haemophilus influenzae, especially when the DNA is assayed on a UV-sensitive mutant of H. influenzae. After extensive endonuclease action, there is a loss of transforming DNA when assayed on both UV-sensitive and -resistant cells. The endonuclease does not affect unirradiated DNA. The results indicate that the endonuclease function is involved in the repair of biological damage resulting from UV irradiation and that the UV-sensitive mutant is deficient in this step. We interpret the data as indicating that the various steps in the repair of DNA must be well coordinated if repair is to be effective. PMID:4314478

  14. Optoelectronic studies on heterocyclic bases of deoxyribonucleic acid for DNA photonics.

    PubMed

    El-Diasty, Fouad; Abdel-Wahab, Fathy

    2015-10-01

    The optoelectronics study of large molecules, particularly π-stacking molecules, such as DNA is really an extremely difficult task. We perform first electronic structure calculations on the heterocyclic bases of 2'-deoxyribonucleic acid based on Lorentz-Fresnel dispersion theory. In the UV-VIS range of spectrum, many of the optoelectronic parameters for DNA four bases namely adenine, guanine, cytosine and thymine are calculated and discussed. The results demonstrate that adenine has the highest hyperpolarizability, whereas thymine has the lowest hyperpolarizability. Cytosine has the lower average oscillator energy and the higher lattice energy. Thymine infers the most stable nucleic base with the lower phonon energy. Thymine also has the highest average oscillator energy and the lower lattice energy. Moreover, the four nucleic acid bases have large band gap energies less than 5 eV with a semiconducting behavior. Guanine shows the smallest band gap and the highest Fermi level energy, whereas adenine elucidates the highest band gap energy.

  15. Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers.

    PubMed

    Sérandour, Aurélien A; Avner, Stéphane; Oger, Frédérik; Bizot, Maud; Percevault, Frédéric; Lucchetti-Miganeh, Céline; Palierne, Gaëlle; Gheeraert, Céline; Barloy-Hubler, Frédérique; Péron, Christine Le; Madigou, Thierry; Durand, Emmanuelle; Froguel, Philippe; Staels, Bart; Lefebvre, Philippe; Métivier, Raphaël; Eeckhoute, Jérôme; Salbert, Gilles

    2012-09-01

    Enhancers are developmentally controlled transcriptional regulatory regions whose activities are modulated through histone modifications or histone variant deposition. In this study, we show by genome-wide mapping that the newly discovered deoxyribonucleic acid (DNA) modification 5-hydroxymethylcytosine (5hmC) is dynamically associated with transcription factor binding to distal regulatory sites during neural differentiation of mouse P19 cells and during adipocyte differentiation of mouse 3T3-L1 cells. Functional annotation reveals that regions gaining 5hmC are associated with genes expressed either in neural tissues when P19 cells undergo neural differentiation or in adipose tissue when 3T3-L1 cells undergo adipocyte differentiation. Furthermore, distal regions gaining 5hmC together with H3K4me2 and H3K27ac in P19 cells behave as differentiation-dependent transcriptional enhancers. Identified regions are enriched in motifs for transcription factors regulating specific cell fates such as Meis1 in P19 cells and PPARγ in 3T3-L1 cells. Accordingly, a fraction of hydroxymethylated Meis1 sites were associated with a dynamic engagement of the 5-methylcytosine hydroxylase Tet1. In addition, kinetic studies of cytosine hydroxymethylation of selected enhancers indicated that DNA hydroxymethylation is an early event of enhancer activation. Hence, acquisition of 5hmC in cell-specific distal regulatory regions may represent a major event of enhancer progression toward an active state and participate in selective activation of tissue-specific genes.

  16. Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers

    PubMed Central

    Sérandour, Aurélien A.; Avner, Stéphane; Oger, Frédérik; Bizot, Maud; Percevault, Frédéric; Lucchetti-Miganeh, Céline; Palierne, Gaëlle; Gheeraert, Céline; Barloy-Hubler, Frédérique; Péron, Christine Le; Madigou, Thierry; Durand, Emmanuelle; Froguel, Philippe; Staels, Bart; Lefebvre, Philippe; Métivier, Raphaël; Eeckhoute, Jérôme; Salbert, Gilles

    2012-01-01

    Enhancers are developmentally controlled transcriptional regulatory regions whose activities are modulated through histone modifications or histone variant deposition. In this study, we show by genome-wide mapping that the newly discovered deoxyribonucleic acid (DNA) modification 5-hydroxymethylcytosine (5hmC) is dynamically associated with transcription factor binding to distal regulatory sites during neural differentiation of mouse P19 cells and during adipocyte differentiation of mouse 3T3-L1 cells. Functional annotation reveals that regions gaining 5hmC are associated with genes expressed either in neural tissues when P19 cells undergo neural differentiation or in adipose tissue when 3T3-L1 cells undergo adipocyte differentiation. Furthermore, distal regions gaining 5hmC together with H3K4me2 and H3K27ac in P19 cells behave as differentiation-dependent transcriptional enhancers. Identified regions are enriched in motifs for transcription factors regulating specific cell fates such as Meis1 in P19 cells and PPARγ in 3T3-L1 cells. Accordingly, a fraction of hydroxymethylated Meis1 sites were associated with a dynamic engagement of the 5-methylcytosine hydroxylase Tet1. In addition, kinetic studies of cytosine hydroxymethylation of selected enhancers indicated that DNA hydroxymethylation is an early event of enhancer activation. Hence, acquisition of 5hmC in cell-specific distal regulatory regions may represent a major event of enhancer progression toward an active state and participate in selective activation of tissue-specific genes. PMID:22730288

  17. Escherichia coli Mutants Thermosensitive for Deoxyribonucleic Acid Gyrase Subunit A: Effects on Deoxyribonucleic Acid Replication, Transcription, and Bacteriophage Growth

    PubMed Central

    Kreuzer, Kenneth N.; Cozzarelli, Nicholas R.

    1979-01-01

    Temperature-sensitive nalA mutants of Escherichia coli have been used to investigate the structure and functions of deoxyribonucleic acid (DNA) gyrase. Extracts of one such mutant (nalA43) had thermosensitive DNA gyrase subunit A activity but normal gyrase subunit B activity, proving definitively that nalA is the structural gene for subunit A. Extracts of a second nalA (Ts) mutant (nalA45) had a 50-fold deficiency of gyrase subunit A activity. The residual DNA supertwisting was catalyzed by the mutant DNA gyrase rather than by a novel supertwisting enzyme. The nalA45(Ts) extract was also deficient in the nalidixic acid target, which is defined as the protein necessary to confer drug sensitivity to in vitro DNA replication directed by a nalidixic acid-resistant mutant extract. Thus, gyrase subunit A and the nalidixic acid target are one and the same protein, the nalA gene product. Shift of the nalA43(Ts) mutant to a nonpermissive temperature resulted in a precipitous decline in the rate of [3H]thymidine incorporation, demonstrating an obligatory role of the nalA gene product in DNA replication. The rates of incorporation of [3H]uridine pulses and continuously administered [3H]uracil were quickly reduced approximately twofold upon temperature shift of the nalA43(Ts) mutant, and therefore some but not all transcription requires the nalA gene product. The thermosensitive growth of bacteriophages φX174 and T4 in the nalA43(Ts) host shows that these phages depend on the host nalA gene product. In contrast, the growth of phage T7 was strongly inhibited by nalidixic acid but essentially unaffected by the nalA43(Ts) mutation. The inhibition of T7 growth by nalidixic acid was, however, eliminated by temperature inactivation of the nal43 gene product. Therefore, nalidixic acid may block T7 growth by a corruption rather than a simple elimination of the nalidixic acid target. Possible mechanisms for such a corruption are considered, and their relevance to the puzzling

  18. Escherichia coli mutants thermosensitive for deoxyribonucleic acid gyrase subunit A: effects on deoxyribonucleic acid replication, transcription, and bacteriophage growth.

    PubMed

    Kreuzer, K N; Cozzarelli, N R

    1979-11-01

    Temperature-sensitive nalA mutants of Escherichia coli have been used to investigate the structure and functions of deoxyribonucleic acid (DNA) gyrase. Extracts of one such mutant (nalA43) had thermosensitive DNA gyrase subunit A activity but normal gyrase subunit B activity, proving definitively that nalA is the structural gene for subunit A. Extracts of a second nalA (Ts) mutant (nalA45) had a 50-fold deficiency of gyrase subunit A activity. The residual DNA supertwisting was catalyzed by the mutant DNA gyrase rather than by a novel supertwisting enzyme. The nalA45(Ts) extract was also deficient in the nalidixic acid target, which is defined as the protein necessary to confer drug sensitivity to in vitro DNA replication directed by a nalidixic acid-resistant mutant extract. Thus, gyrase subunit A and the nalidixic acid target are one and the same protein, the nalA gene product. Shift of the nalA43(Ts) mutant to a nonpermissive temperature resulted in a precipitous decline in the rate of [(3)H]thymidine incorporation, demonstrating an obligatory role of the nalA gene product in DNA replication. The rates of incorporation of [(3)H]uridine pulses and continuously administered [(3)H]uracil were quickly reduced approximately twofold upon temperature shift of the nalA43(Ts) mutant, and therefore some but not all transcription requires the nalA gene product. The thermosensitive growth of bacteriophages phiX174 and T4 in the nalA43(Ts) host shows that these phages depend on the host nalA gene product. In contrast, the growth of phage T7 was strongly inhibited by nalidixic acid but essentially unaffected by the nalA43(Ts) mutation. The inhibition of T7 growth by nalidixic acid was, however, eliminated by temperature inactivation of the nal43 gene product. Therefore, nalidixic acid may block T7 growth by a corruption rather than a simple elimination of the nalidixic acid target. Possible mechanisms for such a corruption are considered, and their relevance to the puzzling

  19. Simian Virus 40 Deoxyribonucleic Acid Transcription In Vitro: Binding and Transcription Patterns with a Mammalian Ribonucleic Acid Polymerase 1

    PubMed Central

    Herzberg, Max; Winocour, Ernest

    1970-01-01

    The in vitro transcription pattern of simian virus 40 (SV40) deoxyribonucleic acid (DNA) by a mammalian ribonucleic acid (RNA) polymerase, was studied by electron microscopy and velocity sedimentation techniques. It was found that (i) the majority of supercoiled SV40 DNA molecules displayed a single binding site for the enzyme, (ii) the supercoiled structure of SV40 DNA was frequently retained during transcription, and (iii) the majority of RNA molecules synthesized from the supercoiled SV40 DNA template showed no self-complementarity and sedimented relatively homogeneously in the 15S to 16S region of a sucrose gradient (in contrast, the RNA product synthesized from the nicked-circular SV40 DNA template showed self-complementarity and sedimented heterogeneously). RNA polymerase preparations isolated from SV40-infected monkey cells were more active than those isolated from uninfected monkey cells. Images PMID:4320700

  20. Estimation of minimum electron dose necessary to resolve molecular structure of deoxyribonucleic acid by phase transmission electron microscopy

    SciTech Connect

    Nomaguchi, Tsunenori; Kimura, Yoshihide; Takai, Yoshizo

    2006-12-04

    The minimum electron dose that is necessary to resolve the molecular structure of deoxyribonucleic acid (DNA) was estimated based on experimental measurements of information limits and simulated DNA images, considering conditions of a low electron dose. From these results, a dose of {approx}400 e/A{sup 2} was found to be necessary to achieve observation of DNA on a molecular scale under the present experimental setup. A DNA molecule was observed by a phase reconstruction method using through-focus images under the limited electron dose. In the reconstructed images, the helical structure and the intervals of the base pairs of DNA were partially resolved.

  1. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 6 2013-04-01 2013-04-01 false Bc6 recombinant deoxyribonucleic acid construct. 528.1070 Section 528.1070 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS NEW ANIMAL DRUGS IN GENETICALLY ENGINEERED ANIMALS § 528.1070 Bc6...

  2. Study on the interaction of morphine chloride with deoxyribonucleic acid by fluorescence method

    NASA Astrophysics Data System (ADS)

    Li, J. F.; Dong, C.

    2009-01-01

    The mode and mechanism of the interaction of morphine chloride, an important alkaloid compound to calf thymus deoxyribonucleic acid (ct DNA) was investigated from absorption and fluorescence titration techniques. Hypochromic effect was founded in the absorption spectra of morphine when concentration of DNA increased. The decreased fluorescence study revealed non-cooperative binding of the morphine to DNA with an affinity of 3.94 × 10 3 M -1, and the stoichiometry of binding was characterized to be about one morphine molecule per nucleotide. Stern-Volmer plots at different temperatures proved that the quenching mechanism was static. Ferrocyanide quenching study showed that the magnitude of KSV of the bound morphine was lower than that of the free one. In addition, it was found that ionic strength could affect the binding of morphine and DNA. Fluorescence polarization and denatured DNA studies also applied strong evidences that morphine molecule was partially intercalated between every alternate base pairs of ct DNA. As observed from above experiments, intercalation was well supported as the binding mode of morphine and ct DNA.

  3. Plasmid-Controlled Variation in the Content of Methylated Bases in Bacteriophage Lambda Deoxyribonucleic Acid

    PubMed Central

    Hattman, Stanley

    1972-01-01

    The N6-methyladenine (MeAde) and 5-methylcytosine (MeC) contents in deoxyribonucleic acid (DNA) of bacteriophage lambda has been analyzed as a function of host specificity. The following facts have emerged: (i) lambda grown on strains harboring the P1 prophage contain ca. 70 more MeAde residues/DNA molecule than lambda grown either in the P1-sensitive parent, or in a P1 immune-defective lysogen which does not confer P1 modification; (ii) lambda grown on strains harboring the N-3 drug-resistance factor contain ca. 60 more MeC residues/DNA molecule than lambda grown on the parental strain lacking the factor; (iii) lambda grown in Escherichia coli B strains is devoid of MeC, whereas lambda grown in a B (N-3) host contains a high level of MeC; (iv) the MeAde content in lambda DNA is not affected by the N-3 factor. These results suggest that P1 controls an adenine-specific DNA methylase, and that the N-3 plasmid controls a cytosine-specific DNA methylase. The N-3 factor has been observed previously to direct cytosine-specific methylation of phage P22 DNA and E. coli B DNA in vivo; in vitro studies presented here demonstrate this activity. PMID:4561202

  4. Auxotroph Accumulation in Deoxyribonucleic Acid Polymeraseless Strains of Escherichia coli K-121

    PubMed Central

    Berg, Claire M.

    1971-01-01

    Spontaneous auxotrophs are found with high frequency in several strains of Escherichia coli K-12 deficient in Kornberg deoxyribonucleic acid polymerase. These include amino acid-, vitamin-, purine-, and pyrimidine-requiring strains. Although this was suggestive evidence that these strains might be mutators, reconstruction experiments demonstrate that auxotrophs possess a selective advantage over prototrophs in the same culture. Thus, despite the high frequency of auxotrophs in polymerase-deficient strains, it is not yet clear whether they have elevated mutation rates. PMID:4934065

  5. Transformation of Streptococcus sanguis Challis by plasmid deoxyribonucleic acid from Streptococcus faecalis.

    PubMed Central

    LeBlanc, D J; Hassell, F P

    1976-01-01

    Plasmid deoxyribonucleic acid (DNA) from Streptococcus faecalis, strain DS5, was transferred to the Challis strain of Streptococcus sanguis by transformation. Two antibiotic resistance markers carried by the beta plasmid from strain DS5, erythromycin and lincomycin, were transferred to S. sanguis at a maximum frequency of 1.8 x 10-5/colony-forming unit. Approximately 70% of the covalently closed circular DNA isolated from transformant cultures by dye buoyant density gradients was shown to be hybridizable to beta plasmid DNA. Two major differences were observed between the beta plasmid from S. faecalis and the plasmid isolated from transformed S. sanguis: (i) the beta plasmid from strain DS5 sedimented in velocity gradients at 43S, whereas the covalently closed circular DNA from transformed Challis sedimented at 41S, suggesting a 1.5-Mdal deletion from the beta plasmid occurred; (ii) although the 43S beta plasmid remained in the supercoiled configuration for several weeks after isolation, the 41S plasmid was rapidly converted to a linear double-stranded molecule. Attempts to transform S. sanguis with the alpha plasmid from S. faecalis, strain DS5, were unsuccessful. PMID:824275

  6. An optical deoxyribonucleic acid-based half-subtractor.

    PubMed

    Yang, Chia-Ning; Chen, Yi-Li; Lin, Hung-Yin; Hsu, Chun-Yu

    2013-10-01

    This study introduces an optical DNA-based logic circuit that mimics a half-subtractor. The system contains an Au-surface immobilized molecular-beacon molecule that serves as a dual-gate molecule and outputs two series of fluorescence signals following Boolean INH and XOR patterns after interacting with one or two single-stranded DNA molecules as input. To the best of our knowledge, the system reported herein is rather concise compared to other molecular logic gate systems.

  7. Excision of pyrimidine dimers from nuclear deoxyribonucleic acid in ultraviolet-irradiated Dictyostelium discoideum

    SciTech Connect

    Clark, J.M.; Deering, R.A.

    1987-02-01

    A sensitive endonuclease assay was used to study the fate of pyrimidine dimers introduced by ultraviolet irradiation into the nuclear deoxyribonucleic acid of the cellular slime mold Dictyostellium discoideum. Analysis of the frequency of T4 endonuclease V-induced single-strand breaks by alkaline sucrose gradient sedimentation showed that strain NC4 (rad/sup +/) removed >98% of the dimers induced by irradiation at 40 J/m/sup 2/ (254 nm) within 215 min after irradiation. HPS104 (radC44), a mutant sensitive to ultraviolet irradiation, removed 91% under these conditions, although at a significantly slower rate than NC4: only 8% were removed during the 10- to 15- min period immediately after irradiation, whereas NC4 excised 64% during this interval. HPS104 thus appears to be deficient in the activity(ies) responsible for rapidly incising ultraviolet-irradiated nuclear deoxyribonucleic acid at the sites of pyrimidine dimers.

  8. Deoxyribonucleic Acid Relatedness Among Species of Erwinia and Between Erwinia Species and Other Enterobacteria

    PubMed Central

    Brenner, Don J.; Fanning, G. R.; Steigerwalt, A. G.

    1972-01-01

    Relatedness in species of Erwinia was assessed by determining the extent of reassociation in heterologous deoxyribonucleic acid preparations. Thermal elution chromatography on hydroxyapatite was used to separate reassociated nucleotide sequences from nonreassociated sequences and to determine the thermal stability of related nucleotide sequences. An apparent 15% core of relatedness is present between fire blight, soft-rot, and “atypical” Erwinia species. All Erwinia species showed low to moderate reaction with representative enteric bacteria. PMID:5018020

  9. Interpretation of sucrose gradient sedimentation pattern of deoxyribonucleic acid fragments resulting from random breaks.

    PubMed

    Litwin, S; Shahn, E; Kozinski, A W

    1969-07-01

    Mass distribution in a sucrose gradient of deoxyribonucleic acid (DNA) fragments arising as a result of random breaks is predicted by analytical means from which computer evaluations are plotted. The analytical results are compared with the results of verifying experiments: (i) a Monte Carlo computer experiment in which simulated molecules of DNA were individuals of unit length subjected to random "breaks" applied by a random number generator, and (ii) an in vitro experiment in which molecules of T4 DNA, highly labeled with (32)P, were stored in liquid nitrogen for variable periods of time during which a precisely known number of (32)P atoms decayed, causing single-stranded breaks. The distribution of sizes of the resulting fragments was measured in an alkaline sucrose gradient. The profiles obtained in this fashion were compared with the mathematical predictions. Both experiments agree with the analytical approach and thus permit the use of the graphs obtained from the latter as a means of determining the average number of random breaks in DNA from distributions obtained experimentally in a sucrose gradient. An example of the application of this procedure to a previously unresolved problem is provided in the case of DNA from ultraviolet-irradiated phage which undergoes a dose-dependent intracellular breakdown. The relationship between the number of lethal hits and the number of single-stranded breaks was not previously established. A comparison of the calculated number of nicks per strand of DNA with the known dose in phage-lethal hits reveals a relationship closely approximating one lethal hit to one single-stranded break. PMID:5804949

  10. Molecular beacon mediated circular strand displacement strategy for constructing a ratiometric electrochemical deoxyribonucleic acid sensor.

    PubMed

    Gao, Fenglei; Du, Lili; Zhang, Yu; Tang, Daoquan; Du, Yan

    2015-07-01

    A novel ratiometric electrochemical sensor for sensitive and selective determination of deoxyribonucleic acid (DNA) had been developed based on signal-on and signal-off strategy. The target DNA hybridized with the loop portion of ferrocene (Fc) labeled hairpin probe immobilized on the gold electrode (GE), the Fc away from the surface of GE and the methylene blue (MB) was attached to an electrode surface by hybridization between hairpin probe and MB labeled primer. Such conformational changes resulted in the oxidation peak current of Fc decreased and that of MB increased, and the changes of dual signals are linear with the concentration of DNA. Furthermore, with the help of strand-displacement polymerization, polymerase catalyzed the extension of the primer and the sequential displacement of the target DNA, which led to the release of target and another polymerization cycle. Thus the circular strand displacement produced the multiplication of the MB confined near the GE surface and Fc got away from the GE surface. Therefore, the recognition of target DNA resulted in both the "signal-off" of Fc and the "signal-on" of MB for dual-signal electrochemical ratiometric readout. The dual signal strategy offered a dramatic enhancement of the stripping response. The dynamic range of the target DNA detection was from 10(-13) to 10(-8) mol L(-1) with a detection limit down to 28 fM level. Compared with the single signaling electrochemical sensor, the dual-signaling electrochemical sensing strategy developed in this paper was more selective. It would have important applications in the sensitive and selective electrochemical determination of other small molecules and proteins.

  11. Amplified spontaneous emission of Rhodamine 6G embedded in pure deoxyribonucleic acid

    NASA Astrophysics Data System (ADS)

    Rau, Ileana; Szukalski, Adam; Sznitko, Lech; Miniewicz, Andrzej; Bartkiewicz, Stanislaw; Kajzar, Francois; Sahraoui, Bouchta; Mysliwiec, Jaroslaw

    2012-10-01

    Deoxyribonucleic acid (DNA) is commonly viewed as a genetic information carrier. However, now it is recognized as a nanomaterial, rather than as a biological material, in the research field of nanotechnology. Here, we show that using pure DNA, doped with rhodamine 6G, we are able to observe amplified spontaneous emission (ASE) phenomenon. Moderate ASE threshold, photodegradation, and reasonable gain coefficient observed in this natural host gives some perspectives for practical applications of this system in biophotonics. Obtained results open the way and will be leading to construction of truly bio-lasers using nature made luminophores, such as anthocyanins.

  12. A novel chaotic based image encryption using a hybrid model of deoxyribonucleic acid and cellular automata

    NASA Astrophysics Data System (ADS)

    Enayatifar, Rasul; Sadaei, Hossein Javedani; Abdullah, Abdul Hanan; Lee, Malrey; Isnin, Ismail Fauzi

    2015-08-01

    Currently, there are many studies have conducted on developing security of the digital image in order to protect such data while they are sending on the internet. This work aims to propose a new approach based on a hybrid model of the Tinkerbell chaotic map, deoxyribonucleic acid (DNA) and cellular automata (CA). DNA rules, DNA sequence XOR operator and CA rules are used simultaneously to encrypt the plain-image pixels. To determine rule number in DNA sequence and also CA, a 2-dimension Tinkerbell chaotic map is employed. Experimental results and computer simulations, both confirm that the proposed scheme not only demonstrates outstanding encryption, but also resists various typical attacks.

  13. Loss of activity of transforming deoxyribonucleic acid after uptake by Haemophilus influenzae.

    PubMed

    Voll, M J; Goodgal, S H

    1965-10-01

    Voll, Mary Jane (University of Pennsylvania, Philadelphia), and Sol H. Goodgal. Loss of activity of transforming deoxyribonucleic acid after uptake by Haemophilus influenzae. J. Bacteriol. 90:873-883. 1965.-Transforming deoxyribonucleic acid (DNA) which has been irreversibly removed from solution by competent cells undergoes a progressive loss in marker activity when tested by lysis of the cells and exposure to new recipient cells. The loss of activity is limited and marker-specific, with greater inactivation of those markers with lower efficiencies of transformation. Recipient factors or donor factors which have undergone recombination, as measured by the appearance of linked markers, do not undergo inactivation. The efficiency of transformation can be correlated with the sensitivity of a marker to inactivation after DNA uptake. A mutation which affects the efficiency of transformation is found to increase sensitivity to postuptake inactivation. The rate of inactivation is temperature-dependent. At temperatures of 20 and 45 C, marker inactivation can occur without concomitant recombination. During the uptake process, DNA is retained in an acid-insoluble form, indicating that the fate of Haemophilus influenzae DNA differs from the fate of transforming DNA in pneumococcus.

  14. BASE COMPOSITION OF THE DEOXYRIBONUCLEIC ACID OF SULFATE-REDUCING BACTERIA

    PubMed Central

    Sigal, Nicole; Senez, Jacques C.; Le Gall, Jean; Sebald, Madeleine

    1963-01-01

    Sigal, Nicole (Laboratoire de Chimie Bactérienne du CNRS, Marseille, France), Jacques C. Senez, Jean Le Gall, and Madeleine Sebald. Base composition of the deoxyribonucleic acid of sulfate-reducing bacteria. J. Bacteriol. 85:1315–1318. 1963—The deoxyribonucleic acid constitution of several strains of sulfate-reducing bacteria has been analytically determined. The results of these studies show that this group of microorganisms includes at least four subgroups characterized by significantly different values of the adenine plus thymine to guanine plus cytosine ratio. The nonsporulated forms with polar flagellation, containing both cytochrome c3 and desulfoviridin, are divided into two subgroups. One includes the fresh-water, nonhalophilic strains with base ratio from 0.54 to 0.59, and the other includes the halophilic or halotolerant strains with base ratio from 0.74 to 0.77. The sporulated, peritrichous strains without cytochrome and desulfoviridin (“nigrificans” and “orientis”) are distinct from the above two types and differ from each other, having base ratios of 1.20 and 1.43, respectively. PMID:14047223

  15. ADANSONIAN ANALYSIS AND DEOXYRIBONUCLEIC ACID BASE COMPOSITION OF SOME GRAM-NEGATIVE BACTERIA

    PubMed Central

    Colwell, R. R.; Mandel, M.

    1964-01-01

    Colwell, R. R. (Georgetown University, Washington, D.C.), and M. Mandel. Adansonian analysis and deoxyribonucleic acid base composition of some gram-negative bacteria. J. Bacteriol. 87:1412–1422. 1964.—The deoxyribonucleic acid (DNA) base compositions and S values for a minimum of 134 coded properties were determined for representative cultures of the genera Pseudomonas, Xanthomonas, Aeromonas, Vibrio, Aerobacter, Escherichia, Alcaligenes, and Flavobacterium. Those cultures having a high degree of similarity by the criterion of numerical taxonomy were found to have similar DNA base compositions. The relative affinities of clusters of cultures suggest taxonomic relations. Eleven species of Xanthomonas might be a single species, and V. metschnikovii was shown to be more closely related to enteric bacteria than to other vibrios which, in turn, were found to be like pseudomonads. Aeromonas was found to be intermediate in similarity to enterics and pseudomonads and divisible into at least two, but possibly three, species. F. aquatile was unlike any of the other organisms studied, and its DNA also differed greatly in composition from other representatives of the genus. PMID:14188722

  16. Separation and partial characterization of two deoxyribonucleic acid polymerases from Spiroplasma citri.

    PubMed Central

    Charron, A; Bebear, C; Brun, G; Yot, P; Latrille, J; Bove, J M

    1979-01-01

    The separation and partial characterization of two deoxyribonucleic acid polymerases from Spiroplasma citri have been achieved. The two enzymes had different elution properties on diethylaminoethyl (DEAE) cellulose and differed in their sensitivity to N-ethylmaleimide (NEM), preference for different template-primers, and sedimentation velocity in linear glycerol gradients. The first enzyme activity, ScA, was retained on DEAE-cellulose and was not inhibited by NEM. Activated deoxyribonucleic acid and poly(dA)-oligo(dT12) were the preferred template-primers. Arabinosyl-cytidine triphosphate had no effect. The sedimentation coefficient of ScA was 6.3s. The second activity, ScB, was not retained on DEAE-cellulose and was inhibited by NEM. Poly(dA)-oligo(dT12) was the preferred template-primer, whereas activated DNA was only poorly utilized. ScB was not affected by arabinosyl-cytidine triphosphate, and its sedimentation coefficient was 4.4s. The polymerization activities of the two enzymes were maximum at 37 to 40 degrees C. PMID:42638

  17. Studies of Nondefective Adenovirus 2-Simian Virus 40 Hybrid Viruses II. Relationship of Adenovirus 2 Deoxyribonucleic Acid and Simian Virus 40 Deoxyribonucleic Acid in the Ad2+ND1 Genome

    PubMed Central

    Levin, Myron J.; Crumpacker, Clyde S.; Lewis, Andrew M.; Oxman, Michael N.; Henry, Patrick H.; Rowe, Wallace P.

    1971-01-01

    A nondefective adenovirus 2 (Ad2)-simian virus 40 (SV40) hybrid virus, Ad2+ND1, has been plaque-isolated from an Ad2-SV40 hybrid population. This virus, unlike the defective Ad-SV40 hybrid populations previously described, replicates without the aid of nonhybrid adenovirus helper. Consequently, the hybrid virus deoxyribonucleic acid (DNA) can be obtained free of nonhybrid adenovirus DNA. The DNA of the Ad2+ND1 virus was shown by ribonucleic acid (RNA)-DNA hybridization to consist of nucleotide sequences complementary to Ad2- and SV40-specific RNA. Techniques of equilibrium density and rate zonal centrifugation were employed to demonstrate that these Ad2 and SV40 nucleotide sequences were linked together in the same DNA molecules by alkali-resistant bonds. Calibration curves were established relating the amount of tritium-labeled SV40-specific RNA (prepared in vitro or in vivo) bound to given amounts of SV40 DNA in a hybridization reaction, and these curves were employed to determine the equivalent amount of SV40 DNA in the Ad2+ND1 molecule. From the results obtained, it was estimated that 1% of the Ad2+ND1 DNA consists of SV40 nucleotide sequences. PMID:4323709

  18. Assistant deoxyribonucleic acid recycling with Zn(2+) and molecular beacon for electrochemical detection of deoxyribonucleic acid via target-triggered assembly of mutated DNAzyme.

    PubMed

    Qian, Yong; Wang, Chunyan; Gao, Fenglei

    2014-10-01

    A novel enzyme-free amplification strategy was designed for sensitive electrochemical detection of deoxyribonucleic acid (DNA) based on Zn(2+) assistant DNA recycling via target-triggered assembly of mutated DNAzyme. A gold electrode was used to immobilize molecular beacon (MB) as the recognition probe and perform the amplification procedure. In the presence of target DNA, the hairpin probe 1 was opened, and the DNAzyme was liberated from the caged structure. The activated DNAzyme first hybridized and then cleaved the MB in the presence of cofactor Zn(2+). After cleavage, the MB was cleaved into two pieces and the ferrocene (Fc) labeled piece dissociated from the gold electrode, thus obviously decreasing the Fc signal and forming a free DNAzyme strand. Finally, each target-induced activated DNAzyme underwent many cycles to trigger the cleavage of many MB substrates. Therefore, the peak current of Fc dramatically decreased to approximately zero. The strategy showed a detection limit at 35 fM levels, which was about 2 orders of magnitude lower than that of the conventional hybridization without Zn(2+)-based amplification. The Zn(2+) assistant DNA recycling offers a versatile platform for DNA detection in a cost-effective manner, and has a promising application in clinical diagnosis.

  19. Comparisons of the Distribution of Nucleotides and Common Sequences in Deoxyribonucleic Acid from Selected Bacteriophages

    PubMed Central

    Skalka, A.; Hanson, P.

    1972-01-01

    Results from comparisons of deoxyribonucleic acid (DNA) from several classes of bacteriophages suggest that most phage chromosomes contain either a homogeneous distribution of nucleotides or are made up of a few, rather large segments of different quanine plus cytosine (G + C) contents which are internally homogeneous. Among those temperate phages tested, most contained segmented DNA. Comparisons of sequence similarities among segments from lambdoid phage DNA species revealed the following order in relatedness to λ: 82 (and 434) > 21 > 424 > φ80. Most common sequences are found in the highest G + C segments, which in λ contain head and tail genes. Hybridization tests with λ and 186 or P2 DNA species verified that the lambdoids and 186 and P2 belong to two distinct groups. There are fewer homologous sequences between the DNA species of coliphages λ and P2 or 186 than there are between the DNA species of coliphage λ and salmonella phage P22. PMID:4553679

  20. Application of Markov chain to the pattern of mitochondrial deoxyribonucleic acid mutations

    NASA Astrophysics Data System (ADS)

    Vantika, Sandy; Pasaribu, Udjianna S.

    2014-03-01

    This research explains how Markov chain used to model the pattern of deoxyribonucleic acid mutations in mitochondrial (mitochondrial DNA). First, sign test was used to see a pattern of nucleotide bases that will appear at one position after the position of mutated nucleotide base. Results obtained from the sign test showed that for most cases, there exist a pattern of mutation except in the mutation cases of adenine to cytosine, adenine to thymine, and cytosine to guanine. Markov chain analysis results on data of mutations that occur in mitochondrial DNA indicate that one and two positions after the position of mutated nucleotide bases tend to be occupied by particular nucleotide bases. From this analysis, it can be said that the adenine, cytosine, guanine and thymine will mutate if the nucelotide base at one and/or two positions after them is cytosine.

  1. Transcription of exogenous and endogenous deoxyribonucleic acid templates in cold-shocked Bacillus subtilis.

    PubMed Central

    Kuhl, S J; Brown, L R

    1980-01-01

    Ribonucleic acid (RNA) synthesis was examined in cold-shocked Bacillus subtilis cells. The cells were grown to mid-log stage, harvested, and cold shocked. RNA synthesis was monitored by the incorporation of [3H]uridine triphosphate or [alpha 32P]adenosine triphosphate into trichloroacetic acid-precipitable material in the presence of all four nucleoside triphosphates. The inhibition of RNA synthesis in cold-shocked cells by lipiarmycin, ethidium bromide, rifampin. or streptolydigin was analyzed using mutant or wild-type cells. Also examined were the effects of temperature, salt concentration, and the addition of polyamines or highly phosphorylated nucleotides. In ultraviolet-irradiated and cold-shocked cells, RNA wynthesis decreased to low levels. The addition of exogenous phi 29 or TSP-1 template to these cells caused a 13- to 20-fold increase in RNA synthesis, as monitored by trichloroacetic acid-precipitable counts. RNA synthesized in the presence of phi 29 deoxyribonucleic acid (DNA) hybridizes mainly to EcoRI fragments A and C of phi 29 DBA, These two fragments direct transcription by purified RNA polymerase in vitro and hybridize to early phi 29 DNA produced in vivo. Our results with TSP-1 DNA in this system indicated that the RNA produced hybridizes to the same fragments as early RNA produced in vivo. Plasmic pUB110 DNA was not transcribed in this system. Images PMID:6157674

  2. Spermidine-Deoxyribonucleic acid interaction in vitro and in Escherichia coli.

    PubMed Central

    Rubin, R L

    1977-01-01

    The binding of spermidine to deoxyribonucleic acid (DNA) was studied by equilibrium dialysis in a wide range of salt concentrations. The association constants ranged from 6 x 10(5) M-1 in 1 mM sodium cacodylate, pH 7.5, to 3 x 10(2) M-1 in 0.3 M NaCl. MgCl2 reduced spermidine-DNA interaction even more than NaCl so that in moderate-ionic-strength solutions (0.3 M NaCl, 0.002 M MgCl2) there was little detectable binding. Low-ionic-strength media were used to isolate DNA from Escherichia coli by a method shown to minimize loss of spermidine from the DNA. Considerable spermidine was associated with E. coli DNA, but control experiments indicated that complex formation had taken place during or after lysis of the cells. Exogenous DNA or ribonucleic acid added to spheroplasts at the time of their lysis caused most of the cellular spermidine to be scavenged by the extra nucleic acid. The data suggest that spermidine is relatively free in the cell and thereby capable of strong (high-affinity) associations with nucleic acids only after the ionic strength of the cell environment is lowered. PMID:320196

  3. Deoxyribonucleic Acid Base Sequence Homologies of Some Budding and Prosthecate Bacteria

    PubMed Central

    Moore, Richard L.; Hirsch, Peter

    1972-01-01

    The genetic relatedness of a number of budding and prosthecate bacteria was determined by deoxyribonucleic acid (DNA) homology experiments of the direct binding type. Strains of Hyphomicrobium sp. isolated from aquatic habitats were found to have relatedness values ranging from 9 to 70% with strain “EA-617,” a subculture of the Hyphomicrobium isolated by Mevius from river water. Strains obtained from soil enrichments had lower values with EA-617, ranging from 3 to 5%. Very little or no homology was detected between the amino acid-utilizing strain Hyphomicrobium neptunium and other Hyphomicrobium strains, although significant homology was observed with the two Hyphomonas strains examined. No homology could be detected between prosthecate bacteria of the genera Rhodomicrobium, Prosthecomicrobium, Ancalomicrobium, or Caulobacter, and Hyphomicrobium strain EA-617 or H. neptunium LE-670. The grouping of Hyphomicrobium strains by their relatedness values agrees well with a grouping according to the base composition of their DNA species. It is concluded that bacteria possessing cellular extensions represent a widely diverse group of organisms. PMID:5018022

  4. A fluorometric deoxyribonucleic acid assay for tridimensional lattice cultures of fibroblasts.

    PubMed

    Gillery, P; Bonnet, A; Borel, J P

    1993-05-01

    A fast and sensitive in situ assay of deoxyribonucleic acid in miniaturized lattice cultures of fibroblasts is described. Tridimensional collagen and fibrin lattices prepared in 24-well plates were seeded with 50,000 to 200,000 cells. Cultures were fixed with formaldehyde, rinced with isopropanol, and dried. DNA assay was performed directly in the wells by addition of 3,5-diaminobenzoic acid (DABA) reagent. A calibration curve was prepared with calf thymus DNA. Fluorescence of DNA-DABA was evaluated after 45 min incubation (excitation wavelength 420 nm, emission wavelength 490 nm). The method showed linear results from 0.5 to 10 micrograms DNA and proved sensitive for low cell numbers (50,000 per dish). DNA assay in monolayers and in different types of lattices showed that comparable results were obtained in the different models without interference of the extracellular matrix. This technique is regarded as a costless and efficient tool for evaluating the number of cells in lattices in basal conditions or under pharmacological stimulation. PMID:8512073

  5. Deoxyribonucleic acid base composition and biochemical properties of certain coagulase-negative enterotoxigenic cocci.

    PubMed

    Lotter, L P; Genigeorgis, C A

    1975-02-01

    Eight coagulase-negative, enterotoxigenic strains of cocci and one weakly coagulase-positive strain isolated from a number of different sources, including cases of food poisoning incidents, were evaluated for their relationship to Staphylococcus aureus on the basis of deoxyribonucleic acid (DNA) buoyant density and physiological studies. One strain of cocci produced enterotoxins A and C, two strains produced types B and C, four strains produced only type C, and one strain only type D. The enterotoxin produced by one strain of cocci was serologically untypable. None of the test organisms produced detectable amounts of enterotoxin in broth cultures. The test strains of cocci exhibited the following profile: all produced catalase; all grew anaerobically and fermented glucse; five were sensitive to lysostaphin; the percentage of guanine plus cytosine content of their DNA varied from 32.7 to 37.6; five produced acid from mannitol both aerobically and anaerobically; two formed delta-hemolysin; five produced phosphatase and acetoin; and all produced heat-stable nuclease. None of the organisms exhibited typical characteristics of S. aureus, S. epidermidis, or S. saprophyticus. On the basis of the present data and data reported elsewhere, these organisms should be considered as variants or mutants of S. aureus.

  6. pH-responsive deoxyribonucleic acid capture/release by polydopamine functionalized magnetic nanoparticles.

    PubMed

    Wang, Yu; Ma, Xiangdong; Ding, Chun; Jia, Li

    2015-03-01

    Polydopamine functionalized magnetic nanoparticles (PDA@Fe3O4) were prepared and characterized by transmission electron microscopy, scanning electron microscopy, zeta potential and vibrating sample magnetometry. They were found to enable highly efficient capture of genomic deoxyribonucleic acid (DNA). The adsorption capacity of PDA@Fe3O4 for genomic DNA can reach 161 mg g(-1). The extraction protocol used aqueous solutions for DNA binding to and releasing from the surface of the magnetic particles based on the pH inducing the charge switch of amino and phenolic hydroxyl groups on PDA@Fe3O4. The extracted DNA with high quality (A260/A280=1.80) can be directly used as templates for polymerase chain reaction (PCR) followed by capillary electrophoresis (CE) analysis. None of the toxic chemical reagents and PCR inhibitors was used throughout the whole procedure. PDA@Fe3O4 based magnetic solid phase extraction (MSPE) method was superior to those using commercial kit and traditional phenol-chloroform extraction methods in yield of DNA. The developed PDA@Fe3O4 based MSPE-PCR-CE method was applied for simultaneous and fast detection of Listeria monocytogenes and Escherichia coli O157:H7 in milk. PMID:25682426

  7. Particle acceleration for delivery deoxyribonucleic acid vaccine into skin in vivo

    NASA Astrophysics Data System (ADS)

    Xinglong, Yu; Xiwen, Zhang; Yuan, Wang; Junshi, Xie; Pengfei, Hao

    2001-08-01

    Skin represents an important immunogenic inductive site, 3%-4% epidermis cells are special antigen-presenting cells. Deoxyribonucleic acid (DNA) vaccine can elicit vigorous immune responses in epidermis cells. The means of delivering DNA vaccine into epidermis cells becomes an important step in DNA vaccine applications. This article presents a new type of gene gun based on the principle of two-stage injector acceleration. DNA coated particles are attached on an screen-type carrier located at the negative pressure inlet, the particles will be sucked into the accelerating channel by negative pressure and be accelerated at a great speed. FLUENT, a computation fluid dynamic application software is used to simulate the flow condition of the injector. Distribution of Mach number, total pressure on exit cross section, and negative pressure on negative pressure inlet are analyzed, by which the process of acceleration of particles is determined. We also measured these parameters in this study. The data show that the particle velocity can be up to 500 m/s and the particles distribute evenly over a circle of Φ 20 mm. The numerical simulation results coincide with experimental data well. Therefore, the results of numerical simulation can be served as guidance for an optimal design of the gene gun and for practical operations. When gene coated particles are distributed evenly, they can penetrate into or even through epidermis cells where the gene can be expressed and subsequently elicits host immune responses. This device may be evaluated in human objects in future.

  8. Deoxyribonucleic acid damage study in primary amenorrhea by comet assay and karyotyping

    PubMed Central

    Ramamurthy, Sarah; Chand, Parkash; Chaturvedula, Latha; Rao, K. Ramachandra

    2013-01-01

    AIM: This study aims at evaluating the chromosomal abnormalities and deoxyribonucleic acid (DNA) damage in cases with primary amenorrhea by karyotyping and comet assay. STUDY DESIGN: A total of 30 cases of primary amenorrhea were recruited. Secondary sexual characters were assessed by Tanner staging. Chromosomal analysis was performed by conventional phytohemagglutinin stimulated lymphocyte cell culture technique. Alkaline version of comet assay was used to evaluate DNA damage. RESULTS: The chromosomal pattern of 20 subjects (66.7%) was found to be normal (46,XX). Two subjects had 46,XY pattern and eight subjects had Turner syndrome (45,X or 45,X/46,XX). The comet parameters were found to be increased among subjects with 45,X monosomy, when compared to the rest of the study group and also in subjects with Tanner stage 1 when compared to stage 2. CONCLUSION: Comet assay revealed increased DNA damage in cases with 45,X monosomy, compared with subjects with 46,XX and 46,XY karyotype, which correlated with clinical features. PMID:24497702

  9. Target-driven self-assembly of stacking deoxyribonucleic acids for highly sensitive assay of proteins.

    PubMed

    Cao, Ya; Chen, Weiwei; Han, Peng; Wang, Zhuxin; Li, Genxi

    2015-08-26

    In this paper, we report a new signal amplification strategy for highly sensitive and enzyme-free method to assay proteins based on the target-driven self-assembly of stacking deoxyribonucleic acids (DNA) on an electrode surface. In the sensing procedure, binding of target protein with the aptamer probe is used as a starting point for a scheduled cycle of DNA hairpin assembly, which consists of hybridization, displacement and target regeneration. Following numbers of the assembly repeats, a great deal of DNA duplexes can accordingly be formed on the electrode surface, and then switch on a succeeding propagation of self-assembled DNA concatemers that provide further signal enhancement. In this way, each target binding event can bring out two cascaded DNA self-assembly processes, namely, stacking DNA self-assembly, and therefore can be converted into remarkably intensified electrochemical signals by associating with silver nanoparticle-based readout. Consequently, highly sensitive detection of target proteins can be achieved. Using interferon-gamma as a model, the assay method displays a linear range from 1 to 500 pM with a detection limit of 0.57 pM, which is comparable or even superior to other reported amplified assays. Moreover, the proposed method eliminates the involvement of any enzymes, thereby enhancing the feasibility in clinical diagnosis.

  10. Mechanism of Inactivation of Haemophilus influenzae Transforming Deoxyribonucleic Acid by Sonic Radiation1

    PubMed Central

    Randolph, M. L.; Setlow, Jane K.

    1972-01-01

    Transforming deoxyribonucleic acid (DNA) from Haemophilus influenzae was exposed to sonic radiation of various durations. Reductions in transforming ability of the DNA, cellular DNA uptake, and integration into the genome, and single- and double-stranded molecular weights of the transforming DNA were measured and compared. We conclude that (i) sonic radiation causes DNA strand breaks (almost always double-strand breaks with relatively few alkaline-labile bonds), the number increasing with exposure until the double-stranded molecular weight is reduced to less than 106 daltons; and (ii) since transformation is reduced about as much as integration and much more than uptake, inactivation of transforming DNA by sonic radiation appears to be caused mostly by failure of Haemophilus cells to integrate the transforming DNA that is taken into the cells. These results are similar to those for inactivation by X radiation but differ from those for ultraviolet radiation. A strand break caused by sonic radiation, however, does not necessarily inactivate the transforming DNA, whereas in the case of ionizing radiation it may. The results may be fit by the model proposed by Cato and Guild. From our data and the equation of Lacks, the minimum active site of DNA necessary for transformation and the frequency of exchanges between donor and recipient strands upon integration of transforming DNA were estimated as 0.35 × 106 to 0.7 × 106 daltons and 0.15 to 0.4 switches per 106 daltons, respectively. PMID:4544285

  11. Nuclear and mitochondrial deoxyribonucleic acid replication during mitosis in Saccharomyces cerevisiae.

    PubMed

    Sena, E P; Welch, J W; Halvorson, H O; Fogel, S

    1975-08-01

    To study nuclear and mitochondrial deoxyribonucleic acid (DNA) synthesis during the cell cycle, a 15N-labeled log-phase population of Saccharomyces cervisiae was shifted to 14N medium. After one-half generation, the cells were centrifuged on a sorbitol gradient in a zonal rotor to fractionate the population according to cell size and age into fractions representing the yeast cell cycle. DNA samples isolated from the zonal rotor cell samples were centrifuged to equilibrium in CsC1 in an analytical ultracentrifuge to separate the nuclear and mitochondrial DNA components. The amount of 14N incorporated into each 15N-labeled DNA species was measured. The extent of nuclear DNA replication per sample was obtained by measuring the amount of hybrid DNA. The percentage of hybrid nuclear DNA increased from 6 to 68% and then decreased to 44% during the cell cycle. Upon ultracentrifugation, mitochondrial DNA banded as a unimodal peak in all zonal rotor samples. Mitochondrial DNA replication could be ascertained only by the 14N level in each mitochondrial peak and not, as with nuclear DNA, by hybrid DNA level. In contrast to the nuclear incorporation pattern, the 14N percentage in mitochondrial DNA remained effectively constant during the cell cycle. Comparison of the data to theoretical distributions showed that nuclear DNA was replicated discontinuously during the cell cycle, whereas mitochondrial DNA was replicated continuously throughout the entire mitotic cycle. PMID:1097413

  12. RAD6/sup +/ gene of Saccharomyces cerevisiae codes for two mutationally separable deoxyribonucleic acid repair functions

    SciTech Connect

    Tuite, M.F.; Cox, B.S.

    1981-02-01

    The response of two mutant alleles of the RAD6/sup +/ gene of Saccharomyces cerevisiae to the ochre translational suppressor SUQ5 was determined. Both the ultraviolet sensitivity phenotype and the deficiency in ultraviolet-induced mutagenesis phenotype of the rad6-1 allelle were suppressed in a (psi/sup +/) background. For the rad6-3 allelle, only the ultraviolet-sensitivity phenotype was suppressible in a (psi/sup +/) background. An SUQ5 rad6-3 (psi/sup +/) strain that was examined showed the normal rad6-3 deficiency in ultraviolet-induced mutagenesis. The authors propose that the RAD6/sup +/ gene is divided into two cistrons, RAD6A and RAD6B. RAD6A codes for an activity responsible for the error-prone repair of ultraviolet-induced lesions in deoxyribonucleic acid but is not involved in a cell's resistance to the lethal effects of ultraviolet light. RAD6B codes for an activity essential for error-free repair of potentially lethal mutagenic damage.

  13. Comparison of three phenotypic and deoxyribonucleic acid extraction methods for isolation and Identification of Nocardia spp

    PubMed Central

    Faghri, Jamshid; Bourbour, Samane; Moghim, Sharare; Meidani, Mohsen; Safaei, Hajiye Ghasemian; Hosseini, Nafise; Esfahani, Bahram Nasr; Fazeli, Hussein; Sedighi, Mansour

    2014-01-01

    Background: The aerobic Actinomycetes are a large group of soil-indwelling bacteria that are distributed in world-wide. These Gram-positive bacteria are most commonly associated with opportunistic infections in both immunocompromised and immunocompetent hosts. Materials and Methods: In this study, three phenotypic and deoxyribonucleic acid (DNA) extraction methods for isolation and identification of Nocardia genus were compared. Samples were taken in five different locations of Isfahan's suburb from hospitals area, parks, agricultural lands, gardens, arid lands with different soil temperature and pH. Results: In this study, showed that slip-buried-method was better than two other phenotypic methods; 14 out of 70 soil samples (20%) were positive for Nocardia spp. DNA of positive samples were extracted with three techniques and DNA extraction by microwave technique was better than others. This technique was confirmed with observation of DNA bands on 1% agarose gel. Conclusions: These bacteria are important in immune deficient patients such as cancer patients, transplant recipients, tuberculosis; acquired immunodeficiency syndrome etc., Their affluence is unsteady in different zones of the world. In this study, among the three phenotypic methods for the isolation of Nocardia slip-buried method was better than other methods. Among DNA extraction techniques, DNA extraction by microwave method would be selective method for DNA extraction of Nocardia spp. compared with others techniques. PMID:25221754

  14. Ribosomes, Polyribosomes, and Deoxyribonucleic Acid from Thermophilic, Mesophilic, and Psychrophilic Clostridia

    PubMed Central

    Irwin, Carol C.; Akagi, James M.; Himes, Richard H.

    1973-01-01

    Analysis of deoxyribonucleic acid (DNA) from four species of Clostridium, including two thermophiles, a mesophile, and a psychrophile, revealed no obvious relationship between growth temperature and DNA base composition. The melting temperatures (Tm) of the DNA from the four species varied no more among the thermophilic, mesophilic, and psychrophilic species than among many related mesophilic species. Characterization of ribosomes from the clostridia by means of optical rotatory dispersion yielded similar spectra in common with other unrelated organisms. Only small differences were noted in the base composition of ribosomal ribonucleic acid (RNA) and in the amino acid composition of ribosomal proteins, including half-cystine content, as determined by cysteic acid analysis, and accessible sulfhydryl groups, as determined by titration with dithiobis (2-nitrobenzoic acid). Except for the two thermophiles, the ribosomal protein electrophoretic patterns were dissimilar. No unusual thermal stability was manifested in the Tm values of thermophile ribosomal RNA. However, thermophile ribosome Tm values (69 C) were higher than were mesophile and psychrophile Tm values (64 C). Ribosomes from the four clostridial species were also examined in regard to the effect of heat on their functional integrity, measured by their activity in poly U-directed 14C-phenylaline incorporation, and their gross physical integrity, measured by sucrose gradient analysis. The Td, 5 values (temperature which produces 50% inactivation after 5 min) was found to be 70 and 72 C for the two thermophiles C. tartarivorum and C. thermosaccharolyticum, respectively; 57 C for a mesophile, C. pasteurianum; and 53 C for a psychrophile, Clostridium sp. strain 69. At 55 C, little effect was seen on the thermophile ribosomes, but the mesophile ribosomes lost 90% of their activity in 1 hr, and psychrophile ribosomes lost 100% of their activity within 10 min. According to sucrose gradient profiles, heating at 55 C

  15. Fabrication of a deoxyribonucleic acid polymer ridge waveguide electro-optic modulator by nanoimprint lithography

    NASA Astrophysics Data System (ADS)

    Fehrman Cory, Emily Marie

    The purpose of this dissertation is to develop the nanoimprint lithography (NIL) technique for direct patterning of the deoxyribonucleic acid biopolymer DNA-CTMA. The Mach Zehnder modulator was chosen as the test device to demonstrate the NIL patterning technique for DNA-CTMA as well as the unique optical and electrical properties of the DNA-CTMA as a cladding material for poled electro-optic polymers. Towards this goal, a DNA-CTMA clad inverted ridge waveguide is demonstrated at 633 nm and 1550 nm, the structure of which is patterned directly in the DNA-CTMA cladding by NIL. Additionally, EO modulation is demonstrated in a slab waveguide structure with DNA-CTMA cladding and SEO110 EO polymer core. Marine-derived deoxyribonucleic acid biopolymer (DNA-CTMA) is a green, nontoxic, low cost optical polymer material derived from waste products of the salmon fishing industry. It exhibits low optical loss at 1550 nm, forms a thin flexible film, is compatible with existing poled polymer technologies, increases the poling efficiency when used as a low resistivity cladding layer, and is thermally stable to 200 oC. Due to chemical incompatibility with the photoresists and the associated solvents, NIL has been developed for patterning the DNA biopolymer cladding to form an inverted ridge waveguide for the basis of the Mach Zehnder modulator. While DNA-CTMA presents significant advantages over other commonly used cladding materials for the 1550 nm wavelength range, one of the commonly used bands for optical communications, the mechanical properties and environmental susceptibility of the material poses significant fabrication challenges. A study of the effects of optical and mechanical effects of environmental humidity exposure are presented for the DNA-CTMA and SEO110 polymers used in the inverted ridge waveguide. While the soft, flexible nature of the DNA-CTMA is desirable for certain applications, this presents a challenge in producing a clean polished window for optical

  16. Isolation and characterization of linear deoxyribonucleic acid plasmids from Kluyveromyces lactis and the plasmid-associated killer character.

    PubMed Central

    Gunge, N; Tamaru, A; Ozawa, F; Sakaguchi, K

    1981-01-01

    Two linear deoxyribonucleic acid plasmids, designated pGK11 and pGK12, were isolated from the yeast Kluyveromyces lactis IFO 1267. pGK11 and pGK12 had molecular weights of 5.4 X 10(6) and 8.4 X 10(6), respectively. Both plasmids possessed the same density of 1.687 g/cm3, lighter than the densities of mitochondrial (1.692 g/cm3) and nuclear (1.699 g/cm3) deoxyribonucleic acids. A restriction map of pGK11 was constructed from digestions by EcoRI, HindIII, PstI, and BamHI. pGK12 was cleaved by EcoRI into seven fragments and by BamHI into two fragments K. lactis IFO 1267 killed Saccharomyces cerevisiae sensitive and killer strains and certain strains of Saccharomyces italicus, K. lactis, Kluyveromyces thermotolerans, and K. vanudenii. All K. lactis strains lacking the pGK1 plasmids were nonkillers. A hybrid was constructed between K. lactis IFO 1267 and a nonkiller K. lactis strain lacking the plasmids and subjected to tetrad analysis after sporulation. The killer character was extrachromosomally transmitted in all tetrads in association with the pGK1 plasmids. The double-stranded ribonucleic acid killer plasmid could not be detected in any K. lactis killer strains. It is thus highly probable that the killer character is mediated by the linear deoxyribonucleic acid plasmids. A single chromosomal gene was found which was responsible for the resistance to the K. lactis killer. Images PMID:6257636

  17. Self-assembled ternary complexes of neutral liposomes, deoxyribonucleic acid, and bivalent metal cations. Promising vectors for gene transfer?

    NASA Astrophysics Data System (ADS)

    Bruni, P.; Pisani, M.; Amici, A.; Marchini, C.; Montani, M.; Francescangeli, O.

    2006-02-01

    By means of synchrotron x-ray diffraction we demonstrate the self-assembled formation of the neutral ternary dioleoyl-phosphatidylcholine-deoxyribonucleic acid (plasmid)-Me2+ (Me=Ca and Mn) complexes in the liquid-crystalline Lα phase. We also report an attempt of an in vitro transfection on mouse fibroplast NIH 3T3 cell lines, which shows the capability of these complexes to transfect DNA. Based on the reported results, efficient encapsulation of DNA plasmids in these ternary neutral complexes may represent an important alternative to current systemic gene approaches.

  18. Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses

    PubMed Central

    Sheth, Bhavisha P.; Thaker, Vrinda S.

    2015-01-01

    Background: Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. Objective: To identify a herbal powder obtained from a herbalist in the local vicinity of Rajkot, Gujarat, using deoxyribonucleic acid (DNA) barcoding and molecular tools. Materials and Methods: The DNA was extracted from a herbal powder and selected Cassia species, followed by the polymerase chain reaction (PCR) and sequencing of the rbcL barcode locus. Thereafter the sequences were subjected to National Center for Biotechnology Information (NCBI) basic local alignment search tool (BLAST) analysis, followed by the protein three-dimension structure determination of the rbcL protein from the herbal powder and Cassia species namely Cassia fistula, Cassia tora and Cassia javanica (sequences obtained in the present study), Cassia Roxburghii, and Cassia abbreviata (sequences retrieved from Genbank). Further, the multiple and pairwise structural alignment were carried out in order to identify the herbal powder. Results: The nucleotide sequences obtained from the selected species of Cassia were submitted to Genbank (Accession No. JX141397, JX141405, JX141420). The NCBI BLAST analysis of the rbcL protein from the herbal powder showed an equal sequence similarity (with reference to different parameters like E value, maximum identity, total score, query coverage) to C. javanica and C. roxburghii. In order to solve the ambiguities of the BLAST result, a protein structural approach was implemented. The protein homology models obtained in the present study were submitted to the protein model database (PM0079748-PM0079753). The pairwise structural alignment of the herbal powder (as template) and C. javanica and C. roxburghii (as targets individually) revealed a close similarity of the herbal powder with C. javanica. Conclusion: A strategy as used here, incorporating the integrated use of DNA

  19. Ribonucleic Acid, Deoxyribonucleic Acid, and Protein Content of Cells of Different Ages of Mycobacterium tuberculosis and the Relationship to Immunogenicity

    PubMed Central

    Youmans, Anne S.; Youmans, Guy P.

    1968-01-01

    The amount of ribonucleic acid (RNA), protein, and deoxyribonucleic acid (DNA) was determined in pellicle cultures of different ages of the H37Ra strain of Mycobacterium tuberculosis, grown on a synthetic medium. We found that the highest content of RNA and protein was present in 2-week-old cultures, indicating that these cells were in the logarithmic phase of growth. DNA content was highest at 1 and 2 weeks. The amount of all three compounds then decreased about 50% during the following 6 weeks. Two-week-old cells should therefore be used for preparation of the immunogenic ribosomal fraction. The optimal concentration of zinc chloride increased RNA and protein synthesis, and also improved the appearance of the pellicle growth. Two-week-old cells, which contained the largest amount of RNA and protein, immunized mice significantly better than older cells. Since protein and DNA are not involved in the production of immunity, a correlation could be made between amount of RNA and the capacity of viable H37Ra cells to immunize mice. The immunizing capacity of these cells was not affected by ribonuclease, probably because the ribonuclease did not penetrate into the whole cells. PMID:4966539

  20. Association of mitochondrial deoxyribonucleic acid mutation with polymorphism in CYP2E1 gene in oral carcinogenesis

    PubMed Central

    Pandey, Rahul; Mehrotra, Divya; Catapano, Carlo; Choubey, Vimal; Sarin, Rajiv; Mahdi, Abbas Ali; Singh, Stuti

    2012-01-01

    Background Oral carcinogenesis is a complex process affected by genetic as well as environmental factors. CYP2E1 gene is involved in metabolism of number of compounds and carcinogens. Its normal functioning is required for homeostasis of free radical. Mitochondrial deoxyribonucleic acid (mtDNA) is 10–100 times more susceptible to damage than nuclear DNA. Mitochondrial DNA large scale deletions are well documented in oral cancer. However, the relationship between CYP2E1 gene polymorphisms and mtDNA damage is still not documented in literature. Materials and Methods Case–control study involving 50 subjects was carried out. Deoxyribonucleic acid extraction was done from study subject tissue samples. Restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR) amplification was done to confirm CYP2E1 gene polymorphisms. The PCR amplification was done for mtDNA 4977 bp deletion. Statistical analysis was carried out using SPSS version 11.5 with χ2 tests. Results c1c1 and DD polymorphisms are prevalent in North Indian population having oral cancer. These polymorphisms are significantly associated with mtDNA 4977 bp deletion. Conclusion Mitochondrial DNA damage induced by wild CYP2E1 forms and imperfect DNA repair in mtDNA may act synergistically to greatly enhance oral cancer risk. PMID:25756024

  1. High mobility organic field-effect transistor based on water-soluble deoxyribonucleic acid via spray coating

    SciTech Connect

    Shi, Wei; Han, Shijiao; Huang, Wei; Yu, Junsheng

    2015-01-26

    High mobility organic field-effect transistors (OFETs) by inserting water-soluble deoxyribonucleic acid (DNA) buffer layer between electrodes and pentacene film through spray coating process were fabricated. Compared with the OFETs incorporated with DNA in the conventional organic solvents of ethanol and methanol: water mixture, the water-soluble DNA based OFET exhibited an over four folds enhancement of field-effect mobility from 0.035 to 0.153 cm{sup 2}/Vs. By characterizing the surface morphology and the crystalline structure of pentacene active layer through atomic force microscope and X-ray diffraction, it was found that the adoption of water solvent in DNA solution, which played a key role in enhancing the field-effect mobility, was ascribed to both the elimination of the irreversible organic solvent-induced bulk-like phase transition of pentacene film and the diminution of a majority of charge trapping at interfaces in OFETs.

  2. Evaluation of deoxyribonucleic acid (DNA) isolated from human bloodstains exposed to ultraviolet light, heat, humidity, and soil contamination

    SciTech Connect

    McNally, L.; Shaler, R.C.; Baird, M.; Balazs, I.; De Forest, P.; Kobilinsky, L. )

    1989-09-01

    This study was designed to analyze the effects of common environmental insults on the ability to obtain deoxyribonucleic acid (DNA) restriction fragment-length polymorphisms (RFLP) patterns from laboratory prepared specimens. The environmental conditions studied include the exposure of dried bloodstains to varying amounts of relative humidity (0, 33, 67, and 98%), heat (37{degree}C), and ultraviolet light for periods of up to five days. In addition, the effect of drying over a four-day period in whole blood collected with and without ethylenediaminetetraacetate (EDTA) was examined. The results of the study showed that, under the conditions studied, the integrity of DNA is not altered such that false RFLP patterns are obtained. The only effect observed was that the overall RFLP pattern becomes weaker, but individual RFLP fragments are neither created nor destroyed.

  3. Adenovirus-associated virus multiplication. VI. Base compostion of the deoxyribonucleic acid strand species and strand-specific in vivo transcription.

    PubMed

    Rose, J A; Koczot, F

    1971-11-01

    The two complementary strand species of 5-bromodeoxyuridine-substituted, adenovirus-associated virus type 2 (AAV-2) deoxyribonucleic acid were preparatively separated in CsCl density gradients and further purified by sedimentation through 5 to 20% sucrose. The base composition of each strand species was determined, and it was found that the species banding at a greater density in CsCl (heavy strands) had an expected higher thymidine content (26.5%) than that 21.7%) of the less dense species (light strands). Furthermore, the base composition of in vivo-synthesized, AAV-specific ribonucleic acid was similar to that of light-strand deoxyribonucleic acid, and this ribonucleic acid apparently hybridized only with heavy strands. These observations indicate that the heavy-strand species alone serves as the transcriptional template in vivo. This study represents the first instance in which the base composition and specificity of in vivo transcription have been determined for each of the complementary strands of an animal virus deoxyribonucleic acid.

  4. Long-Term Control of Human Immunodeficiency Virus-1 Replication Despite Extensive Resistance to Current Antiretroviral Regimens: Clonal Analysis of Resistance Mutations in Proviral Deoxyribonucleic Acid

    PubMed Central

    Stella-Ascariz, Natalia; Montejano, Rocio; Martin-Vicente, María; Mingorance, Jesús; Pérez-Valero, Ignacio; Bernardino, José I.; Arribas, Jose R.

    2016-01-01

    Archived resistance mutations compromise antiretroviral treatment. We have investigated 3 selected aviremic patients who had extensive historical resistance to their current regimen. All 3 patients underwent unstructured treatment interruptions associated to the re-emergence of wild-type virus before starting their current suppressive regimes. Almost all historical resistance mutations detected in plasma were found in circulating proviral deoxyribonucleic acid. None of the clones analyzed was fully resistant to the current antiretroviral regimen. PMID:27006965

  5. The effect of deoxyribonucleic acid extraction methods from lymphoid tissue on the purity, content, and amplifying ability

    PubMed Central

    Ayatollahi, Hossein; Sadeghian, Mohammad Hadi; Keramati, Mohammad Reza; Ayatollahi, Ali; Shajiei, Arezoo; Sheikhi, Maryam; Bakhshi, Samane

    2016-01-01

    Background: Nowadays, definitive diagnosis of numerous diseases is based on the genetic and molecular findings. Therefore, preparation of fundamental materials for these evaluations is necessary. Deoxyribonucleic acid (DNA) is the first material for the molecular pathology and genetic analysis, and better results need more pure DNA. Furthermore, higher concentration of achieved DNA causes better results and higher amplifying ability for subsequent steps. We aim to evaluate five DNA extraction methods to compare DNA intimacy including purity, concentration, and amplifying ability with each other. Materials and Methods: The lymphoid tissue DNA was extracted from formalin-fixed, paraffin embedded (FFPE) tissue through five different methods including phenol-chloroform as the reference method, DNA isolation kit (QIAamp DNA FFPE Tissue Kit, Qiagen, Germany), proteinase K and xylol extraction and heat alkaline plus mineral oil extraction as authorship innovative method. Finally, polymerase chain reaction (PCR) and real-time PCR method were assessed to compare each following method consider to DNA purity and its concentration. Results: Among five different applied methods, the highest mean of DNA purity was related to heat alkaline method. Moreover, the highest mean of DNA concentration was related to heat alkaline plus mineral oil. Furthermore, the best result in quantitative PCR was in proteinase K method that had the lowest cycle threshold averages among the other extraction methods. Conclusion: We concluded that our innovative method for DNA extraction (heat alkaline plus mineral oil) achieved high DNA purity and concentration. PMID:27630381

  6. The effect of deoxyribonucleic acid extraction methods from lymphoid tissue on the purity, content, and amplifying ability

    PubMed Central

    Ayatollahi, Hossein; Sadeghian, Mohammad Hadi; Keramati, Mohammad Reza; Ayatollahi, Ali; Shajiei, Arezoo; Sheikhi, Maryam; Bakhshi, Samane

    2016-01-01

    Background: Nowadays, definitive diagnosis of numerous diseases is based on the genetic and molecular findings. Therefore, preparation of fundamental materials for these evaluations is necessary. Deoxyribonucleic acid (DNA) is the first material for the molecular pathology and genetic analysis, and better results need more pure DNA. Furthermore, higher concentration of achieved DNA causes better results and higher amplifying ability for subsequent steps. We aim to evaluate five DNA extraction methods to compare DNA intimacy including purity, concentration, and amplifying ability with each other. Materials and Methods: The lymphoid tissue DNA was extracted from formalin-fixed, paraffin embedded (FFPE) tissue through five different methods including phenol-chloroform as the reference method, DNA isolation kit (QIAamp DNA FFPE Tissue Kit, Qiagen, Germany), proteinase K and xylol extraction and heat alkaline plus mineral oil extraction as authorship innovative method. Finally, polymerase chain reaction (PCR) and real-time PCR method were assessed to compare each following method consider to DNA purity and its concentration. Results: Among five different applied methods, the highest mean of DNA purity was related to heat alkaline method. Moreover, the highest mean of DNA concentration was related to heat alkaline plus mineral oil. Furthermore, the best result in quantitative PCR was in proteinase K method that had the lowest cycle threshold averages among the other extraction methods. Conclusion: We concluded that our innovative method for DNA extraction (heat alkaline plus mineral oil) achieved high DNA purity and concentration.

  7. Nature of Transient Inhibition of Deoxyribonucleic Acid Synthesis in HeLa Cells by Parainfluenza Virus 1 (Sendai)

    PubMed Central

    Fuchs, Pinhas; Kohn, Alexander

    1971-01-01

    Adsorption of ultraviolet-inactivated Sendai virus, at high or low multiplicity, to HeLa cells caused a transient increased incorporation of 3H-thymidine into the cellular deoxyribonucleic acid (DNA). In HeLa cells synchronized by a double-thymidine block, this increased incorporation of thymidine during the S phase lasted from about 30 to 90 min after virus adsorption. The observations that the kinetics of accumulation of radioactive thymidine in the nucleotide pool did not differ in control and in the virus-treated cells and that the 32P incorporation into the DNA of the virus-treated cells was inhibited at the same time indicate that the augmented incorporation of 3H-thymidine into DNA results from a transient block in the endogenous pathway of thymidine synthesis. Chromatographic analysis of the nucleotide pool of the virus-treated cells labeled with 14C-formate indicates that methylation of deoxyuridine monophosphate to thymidine monophosphate is inhibited. It is suggested that the inhibition is caused by a block of either the thymidilate synthetase or some step in the tetrahydrofolate cycle. PMID:4332139

  8. Rapid concentration of deoxyribonucleic acid via Joule heating induced temperature gradient focusing in poly-dimethylsiloxane microfluidic channel.

    PubMed

    Ge, Zhengwei; Wang, Wei; Yang, Chun

    2015-02-01

    This paper reports rapid microfluidic electrokinetic concentration of deoxyribonucleic acid (DNA) with the Joule heating induced temperature gradient focusing (TGF) by using our proposed combined AC and DC electric field technique. A peak of 480-fold concentration enhancement of DNA sample is achieved within 40s in a simple poly-dimethylsiloxane (PDMS) microfluidic channel of a sudden expansion in cross-section. Compared to a sole DC field, the introduction of an AC field can reduce DC field induced back-pressure and produce sufficient Joule heating effects, resulting in higher concentration enhancement. Within such microfluidic channel structure, negative charged DNA analytes can be concentrated at a location where the DNA electrophoretic motion is balanced with the bulk flow driven by DC electroosmosis under an appropriate temperature gradient field. A numerical model accounting for a combined AC and DC field and back-pressure driven flow effects is developed to describe the complex Joule heating induced TGF processes. The experimental observation of DNA concentration phenomena can be explained by the numerical model. PMID:25597807

  9. Molecular aspects on the interaction of phenosafranine to deoxyribonucleic acid: Model for intercalative drug DNA binding

    NASA Astrophysics Data System (ADS)

    Das, Suman; Kumar, Gopinatha Suresh

    2008-01-01

    The mode, mechanism and energetics of interaction of phenosafranine, the planar, cationic and rigid phenazium dye to calf thymus DNA was investigated from absorption, fluorescence, circular dichroism, isothermal titration calorimetry, thermal melting, and viscosity. The study revealed non-cooperative binding of the dye to DNA with an affinity in the range (3.81-4.22) × 10 5 M -1 as observed from diverse techniques and obeying neighbor exclusion principle. The stoichiometry of binding was characterized to be one phenosafranine molecule per two base pairs. The binding was characterized by strong stabilization of DNA against thermal strand separation, large intrinsic circular dichroic changes of DNA by itself and the generation of induced circular dichroism for the optically inactive phenosafranine molecules. Hydrodynamic and fluorescence quenching studies revealed strong evidence that the phenosafranine molecules are intercalated between every alternate base pairs of calf thymus DNA. Isothermal titration calorimetry studies suggested that the binding was exothermic and favoured by both negative enthalpy and positive entropy changes. This study for the first time presents the complete molecular aspects and energetics of phenosafranine complexation to DNA as model for intercalative drug-DNA interaction.

  10. Spectroscopic and microcalorimetric studies on the molecular binding of food colorant acid red 27 with deoxyribonucleic acid.

    PubMed

    Basu, Anirban; Kumar, Gopinatha Suresh

    2016-08-01

    Interaction of the food colorant acid red 27 with double stranded DNA was investigated using spectroscopic and calorimetric methods. Absorbance and fluorescence studies suggested an intimate binding interaction between the dye and DNA. The quantum efficiency value testified an effective energy transfer from the DNA base pairs to the dye molecules. Minor groove displacement assay with Hoechst 33258 revealed that the binding occurs in the minor groove of DNA. Circular dichroism studies revealed that acid red 27 induces moderate conformational perturbations in DNA. Results of calorimetric studies suggested that the complexation process was driven largely by positive entropic contribution with a smaller favorable enthalpy contribution. The equilibrium constant of the binding was calculated to be (3.04 ± 0.09) × 10(4)  M(-1) at 298.15 K. Negative heat capacity value along with the enthalpy-entropy compensation phenomenon established the involvement of dominant hydrophobic forces in the binding process. Differential scanning calorimetry studies presented evidence for an increased thermal stability of DNA on binding of acid red 27. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26846192

  11. Assessment of the deoxyribonucleic acid damage caused by occupational exposure to chemical compounds in Isfahan Polyacryl Company

    PubMed Central

    Etebari, Mahmoud; Jafarian-Dehkordi, Abbas; Kahookar, Ahmad; Moradi, Shahla

    2014-01-01

    Background: Chemical pollutants found in industrial environments can cause chronic genotoxicity in vulnerable individuals during the long-term exposure. The primary purpose of the present study was to assess the deoxyribonucleic acid (DNA) damage caused by occupational exposure to industrial chemicals and secondary purpose is to investigate the effect of possible risk factors of genotoxicity. Materials and Methods: The blood samples of the workers of Isfahan Polyacryl Company were evaluated in terms of genotoxicity using the comet assay method. The percentage of DNA in the tail and tail moment were measured and DNA damage was evaluated. Furthermore, the effect of age, smoking, duration of working in the company and working in two parts of the company on the degree of vulnerability to genotoxicity was assessed. Results: The amount of DNA damage in the target group (the production line workers) was significantly higher than the control group (the staffs), 3.87 versus 1.52 as tail moment, (P < 0.0001). DNA damage was significantly higher in smoker groups compared with non-smoker target group and control group, 4.18 versus 3.07 and 1.52 respectively as tail moment, (P < 0.0001). Furthermore, it was higher in person working in two different parts of the company compared to those work in one part and control group, 4.63 versus 3.74 and 1.52 respectively as tail moment, (P < 0.0001). Conclusion: Occupational exposure to Polyacryl caused DNA damage. Smoking and working in two parts of the company may have a significant role in DNA damage. PMID:25197297

  12. Detection of deoxyribonucleic acid (DNA) targets using polymerase chain reaction (PCR) and paper surface-enhanced Raman spectroscopy (SERS) chromatography.

    PubMed

    Hoppmann, Eric P; Yu, Wei W; White, Ian M

    2014-01-01

    Surface-enhanced Raman spectroscopy (SERS) enables multiplex detection of analytes using simple, portable equipment consisting of a single excitation source and detector. Thus, in theory, SERS is ideally suited to replace fluorescence in assays that screen for numerous deoxyribonucleic acid (DNA) targets, but in practice, SERS-based assays have suffered from complexity and elaborate processing steps. Here, we report an assay in which a simple inkjet-fabricated plasmonic paper device enables SERS-based detection of multiple DNA targets within a single polymerase chain reaction (PCR). In prior work, we demonstrated the principles of chromatographic separation and SERS-based detection on inkjet-fabricated plasmonic paper. The present work extends that capability for post-PCR gene sequence detection. In this design, hydrolysis DNA probes with 5' Raman labels are utilized; if the target is present, the probe is hydrolyzed during PCR, freeing the reporter. After applying the PCR sample to a paper SERS device, an on-device chromatographic separation and concentration is conducted to discriminate between hydrolyzed and intact probes. SERS is then used to detect the reporter released by the hydrolyzed probes. This simple separation and detection on paper eliminates the need for complex sample processing steps. In this work, we simultaneously detect the methicillin-resistant Staphylococcus aureus genes mecA and femB to illustrate the concept. We envision that this approach could contribute to the development of multiplex DNA diagnostic tests enabling screening for several target sequences within a single reaction, which is necessary for cases in which sample volume and resources are limited.

  13. Determination of deoxyribonucleic acids by a resonance light scattering technique and its application

    NASA Astrophysics Data System (ADS)

    Jie, Nianqin; Jia, Guifang; Hou, Shicong; Xiong, Yanmei; Dong, Yanhong

    2003-12-01

    For the first time, acetamiprid has been used to determine nucleic acid (DNA) using the resonance light scattering (RLS). The RLS of acetamiprid was greatly enhanced by DNA in the range of pH 1.6-1.8. A RLS peak at 313 nm was found, and the enhanced intensity of RLS at this wavelength was proportional to the concentration of DNA. The linear range of the calibration curve was 0-11.0 μg ml -1 with the detection limit of 20 ng ml -1. The nucleic acids in synthetic sample and in rice seedling extraction were determined satisfactorily. The interaction mechanism of acetamiprid and DNA is discussed. Mechanism studies show that the enhanced RLS is due to the aggregation of acetamiprid in the presence of DNA.

  14. DNA Tetrominoes: The Construction of DNA Nanostructures Using Self-Organised Heterogeneous Deoxyribonucleic Acids Shapes

    PubMed Central

    Ong, Hui San; Rahim, Mohd Syafiq; Firdaus-Raih, Mohd; Ramlan, Effirul Ikhwan

    2015-01-01

    The unique programmability of nucleic acids offers alternative in constructing excitable and functional nanostructures. This work introduces an autonomous protocol to construct DNA Tetris shapes (L-Shape, B-Shape, T-Shape and I-Shape) using modular DNA blocks. The protocol exploits the rich number of sequence combinations available from the nucleic acid alphabets, thus allowing for diversity to be applied in designing various DNA nanostructures. Instead of a deterministic set of sequences corresponding to a particular design, the protocol promotes a large pool of DNA shapes that can assemble to conform to any desired structures. By utilising evolutionary programming in the design stage, DNA blocks are subjected to processes such as sequence insertion, deletion and base shifting in order to enrich the diversity of the resulting shapes based on a set of cascading filters. The optimisation algorithm allows mutation to be exerted indefinitely on the candidate sequences until these sequences complied with all the four fitness criteria. Generated candidates from the protocol are in agreement with the filter cascades and thermodynamic simulation. Further validation using gel electrophoresis indicated the formation of the designed shapes. Thus, supporting the plausibility of constructing DNA nanostructures in a more hierarchical, modular, and interchangeable manner. PMID:26258940

  15. The deoxyribonucleic acid unwinding protein of Escherichia coli. Properties and functions in replication.

    PubMed

    Weiner, J H; Bertsch, L L; Kornberg, A

    1975-03-25

    The DNA unwinding protein of Escherichia coli (Sigal, N., Delius, H., Kornberg, T., Gefter, M., and Alberts, B. (1972) Proc. Nat. Acad. Sci. U.S.A. 69, 3537-3541) has been purified to homogeneity by a simple procedure which utilizes its stability to heating. The protein is an asymmetric tetramer of 18,500 dalton subunits which binds preferentially to single-stranded DNA at a ratio of one protein molecule per 32 nucleotides. Binding to DNA is complete in less than 10 s at 0 degrees while release of the protein from single-stranded DNA is relatively slow even at 37 degrees. A simple functional assay for unwinding protein depends on its essential role in the conversion of phage G4 single-stranded DNA to the replicative form. Unwinding protein stimulates initiation of replication of all single-stranded phage DNAs. Approximately 300 copies of unwinding protein are present per cell, as estimated by antibody titration, an amount sufficient to cover substantial lengths of DNA in several replicating forks.

  16. Effect of Ethylene on Cell Division and Deoxyribonucleic Acid Synthesis in Pisum sativum1

    PubMed Central

    Apelbaum, Akiva; Burg, Stanley P.

    1972-01-01

    Ethylene and supraoptimal levels of 2,4-dichlorophenoxyacetic acid inhibit the growth of the apical hook region of etiolated Pisum sativum (var. Alaska) seedlings by stopping almost all cell divisions. Cells are prevented from entering prophase. The hormones also retard cell division in intact root tips and completely stop the process in lateral buds. The latter inhibition is reversed partially by benzyl adenine. In root tips and the stem plumular and subhook regions, ethylene inhibits DNA synthesis. The magnitude of this inhibition is correlated with the degree of repression of cell division in meristematic tissue, suggesting that the effect on cell division results from a lack of DNA synthesis. Ethylene inhibits cell division within a few hours with a dose-response curve similar to that for most other actions of the gas. Experiments with seedlings grown under hypobaric conditions suggest that the gas naturally controls plumular expansion and cell division in the apical region. Images PMID:16658105

  17. Inhibition of Hsp27 Radiosensitizes Head-and-Neck Cancer by Modulating Deoxyribonucleic Acid Repair

    SciTech Connect

    Guttmann, David M.; Hart, Lori; Du, Kevin; Seletsky, Andrew; Koumenis, Constantinos

    2013-09-01

    Purpose: To present a novel method of tumor radiosensitization through Hsp27 knockdown using locked nucleic acid (LNA) and to investigate the role of Hsp27 in DNA double strand break (DSB) repair. Methods and Materials: Clonogenic survival assays, immunoblotting, the proximity ligation assay, and γH2AX foci analysis were conducted in SQ20B and FaDu human head-and-neck cancer cell lines treated with Hsp27 LNA and Hsp27 short hairpin RNA (shRNA). Additionally, nude mice with FaDu flank tumors were treated with fractionated radiation therapy after pretreatment with Hsp27 LNA and monitored for tumor growth. Results: Hsp27 LNA and Hsp27 shRNA radiosensitized head-and-neck cancer cell lines in an Hsp27-dependent manner. Ataxia-Telangectasia Mutated-mediated DNA repair signaling was impaired in irradiated cells with Hsp27 knockdown. ATM kinase inhibition abrogated the radiosensitizing effect of Hsp27. Furthermore, Hsp27 LNA and shRNA both attenuated DNA repair kinetics after radiation, and Hsp27 was found to colocalize with ATM in both untreated and irradiated cells. Last, combined radiation and Hsp27 LNA treatment in tumor xenografts in nude mice suppressed tumor growth compared with either treatment alone. Conclusions: These results support a radiosensitizing property of Hsp27 LNA in vitro and in vivo, implicate Hsp27 in double strand break repair, and suggest that Hsp27 LNA might eventually serve as an effective clinical agent in the radiotherapy of head-and-neck cancer.

  18. Enzymatic DNA molecules

    NASA Technical Reports Server (NTRS)

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

    1998-01-01

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

  19. Reversible phospholipid nanogels for deoxyribonucleic acid fragment size determinations up to 1500 base pairs and integrated sample stacking.

    PubMed

    Durney, Brandon C; Bachert, Beth A; Sloane, Hillary S; Lukomski, Slawomir; Landers, James P; Holland, Lisa A

    2015-06-23

    Phospholipid additives are a cost-effective medium to separate deoxyribonucleic acid (DNA) fragments and possess a thermally-responsive viscosity. This provides a mechanism to easily create and replace a highly viscous nanogel in a narrow bore capillary with only a 10°C change in temperature. Preparations composed of dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) self-assemble, forming structures such as nanodisks and wormlike micelles. Factors that influence the morphology of a particular DMPC-DHPC preparation include the concentration of lipid in solution, the temperature, and the ratio of DMPC and DHPC. It has previously been established that an aqueous solution containing 10% phospholipid with a ratio of [DMPC]/[DHPC]=2.5 separates DNA fragments with nearly single base resolution for DNA fragments up to 500 base pairs in length, but beyond this size the resolution decreases dramatically. A new DMPC-DHPC medium is developed to effectively separate and size DNA fragments up to 1500 base pairs by decreasing the total lipid concentration to 2.5%. A 2.5% phospholipid nanogel generates a resolution of 1% of the DNA fragment size up to 1500 base pairs. This increase in the upper size limit is accomplished using commercially available phospholipids at an even lower material cost than is achieved with the 10% preparation. The separation additive is used to evaluate size markers ranging between 200 and 1500 base pairs in order to distinguish invasive strains of Streptococcus pyogenes and Aspergillus species by harnessing differences in gene sequences of collagen-like proteins in these organisms. For the first time, a reversible stacking gel is integrated in a capillary sieving separation by utilizing the thermally-responsive viscosity of these self-assembled phospholipid preparations. A discontinuous matrix is created that is composed of a cartridge of highly viscous phospholipid assimilated into a separation matrix

  20. Detection of toxins in single molecule level using deoxyribonucleic acid aptamers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Toxins in foodstuffs are always a threat to food safety Among many toxins related to food, ricin (category B toxin) from castor beans has been mentioned in some poisoning cases happened. Atomic Force Microscopy (AFM) is a widely used nanotechnology to detect biospecies in vitro and in situ. The AFM...

  1. The estimation of deoxyribonucleic acid in the presence of sialic acid: application to analysis of human gastric washings

    PubMed Central

    Croft, D. N.; Lubran, M.

    1965-01-01

    1. Sialic acid has been found to interfere with three colorimetric reactions used for the estimation of DNA: a modified diphenylamine reaction at 100° (Dische, 1930), the nitrophenylhydrazine method (Webb & Levy, 1955) and the diphenylamine reaction at 30° (Burton, 1956). 2. Evidence is presented that sialic acid is present in hydrolysates obtained from gastric wash-out material. 3. A mathematical method for correcting for interference from sialic acid in the diphenylamine reaction at 30° is described. 4. The diphenylamine reaction has been modified to make it suitable for the estimation of DNA in the presence of sialic acid. The modifications are to increase the concentration of diphenylamine to 2% and to perform the reaction at 6–13° for 48hr. These modifications increase the sensitivity 25% above Burton's (1956) modification of the diphenylamine reaction. 5. The precipitation, extraction and recovery of DNA from gastric wash-out material have been investigated. PMID:14342494

  2. Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same

    DOEpatents

    Croteau, Rodney Bruce; Burke, Charles Cullen

    2008-06-24

    In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

  3. Structural studies of lambda transducing bacteriophage carrying bacterial deoxyribonucleic acid from the metBJLF region of the Escherichia coli chromosome.

    PubMed Central

    Krueger, J H; Johnson, J R; Greene, R C; Dresser, M

    1981-01-01

    The structures of several lambda dmet and related lambda darg transducing phage were studied by restriction fragment mapping and electron microscopic measurements of homoduplexes and heteroduplexes. A new transducing phage (lambda dmet141), in which metF is the only functional gene of the cluster, was isolated. In contrast, lambda dmet117, which expresses the entire metBJLF cluster, has only 3 kilobases more bacterial deoxyribonucleic acid (DNA) than lambda dmet141. An EcoRI restriction fragment of lambda dmet117, which carries the leftmost 6 kilobases of the bacterial DNA insert, was isolated and shown to contain a functional copy of metB. Small structural differences at the attachment sites of some of the phage were shown to result from different sites of lambda integration in the two parent insertion lysogens. Images PMID:6267016

  4. Application of an enzyme-based biofuel cell containing a bioelectrode modified with deoxyribonucleic acid-wrapped single-walled carbon nanotubes to serum.

    PubMed

    Lee, Jin Young; Shin, Hyun Yong; Kang, Seong Woo; Park, Chulhwan; Kim, Seung Wook

    2011-01-01

    Enzyme-based biofuel cells (EFCs) are a form of biofuel cells (BFCs) that can utilize redox enzymes as biocatalysts. Applications of an EFC to an implantable system are evaluated under mild conditions, such as ambient temperature or neutral pH. In the present study, an EFC containing a bioelectrode modified with deoxyribonucleic acid (DNA)-wrapped single-walled carbon nanotubes (SWNTs) was applied to a serum system. The protection of immobilized glucose oxidase (GOD) using DNA-wrapped SWNTs was investigated in a trypsin environment, which can exist in a serum. GOD is immobilized by masking the active site onto the anode electrode. The anode/cathode system in the cell was composed of GOD/laccase as the biocatalysts and glucose/oxygen as the substrates in serum. The electrical properties of the anode in serum according to cyclic voltammetry (CV cycle) were improved using the DNA-wrapped SWNTs. Overall, an EFC that employed DNA-wrapped SWNTs and GOD immobilization in conjunction with protection of the active site increased the stability of GOD in serum, which enabled a high level of power production (ca. 190 μW/cm(2)) for up to 1 week.

  5. Physiological Modifications in the Production and Repair of Methyl Methane Sulfonate-Induced Breaks in the Deoxyribonucleic Acid of Escherichia coli K-12

    PubMed Central

    Scudiero, Dominic A.; Friesen, Benjamin S.; Baptist, Jeremy E.

    1973-01-01

    The medium in which Rec+ strains of Escherichia coli K-12 are grown affected their sensitivity to treatment with methyl methane sulfonate (MMS). Rec+ cells grown to the stationary phase in glucose-enriched nutrient broth (GNB) were more resistant to MMS than cells grown in nutrient broth (NB). The repair of MMS-induced breaks (or alkali-labile bonds) in the deoxyribonucleic acid (DNA) from E. coli K-12 strains AB1157, AB1886 uvrA6, and SR111 recA13 recB21 grown in GNB and NB media was examined by means of alkaline sucrose gradient centrifugation. It appeared that essentially all of the repair of breaks that occurred, as evidenced by an increase in “molecular weight,” took place within 10 min after treatment with MMS under our conditions. Cell survival was highest in cells for which the size of the DNA after the post-treatment incubation was the largest. The largest DNA after post-treatment incubation was found in Rec+ cells grown in GNB medium. The results suggest that these cells may have an enhanced capacity for repairing breaks in DNA. PMID:4349030

  6. Carcinogenic damage to deoxyribonucleic acid is induced by near-infrared laser pulses in multiphoton microscopy via combination of two- and three-photon absorption

    NASA Astrophysics Data System (ADS)

    Nadiarnykh, Oleg; Thomas, Giju; Van Voskuilen, Johan; Sterenborg, Henricus J. C. M.; Gerritsen, Hans C.

    2012-11-01

    Nonlinear optical imaging modalities (multiphoton excited fluorescence, second and third harmonic generation) applied in vivo are increasingly promising for clinical diagnostics and the monitoring of cancer and other disorders, as they can probe tissue with high diffraction-limited resolution at near-infrared (IR) wavelengths. However, high peak intensity of femtosecond laser pulses required for two-photon processes causes formation of cyclobutane-pyrimidine-dimers (CPDs) in cellular deoxyribonucleic acid (DNA) similar to damage from exposure to solar ultraviolet (UV) light. Inaccurate repair of subsequent mutations increases the risk of carcinogenesis. In this study, we investigate CPD damage that results in Chinese hamster ovary cells in vitro from imaging them with two-photon excited autofluorescence. The CPD levels are quantified by immunofluorescent staining. We further evaluate the extent of CPD damage with respect to varied wavelength, pulse width at focal plane, and pixel dwell time as compared with more pronounced damage from UV sources. While CPD damage has been expected to result from three-photon absorption, our results reveal that CPDs are induced by competing two- and three-photon absorption processes, where the former accesses UVA absorption band. This finding is independently confirmed by nonlinear dependencies of damage on laser power, wavelength, and pulse width.

  7. Development of a chamber system for rapid, high yield and cost-effective purification of deoxyribonucleic acid fragments from agarose gel

    PubMed Central

    Eslami, Gilda; Salehi, Rasoul

    2014-01-01

    Background: There are several methods commonly practicing for deoxyribonucleic acid (DNA) purification from agarose gel. In most laboratories, especially in developing countries, present methods for recovering of DNA fragments from the gel are mostly involved organic solvents. However, manual purification using organic solvents are toxic, labor intensive, time consuming and prone to contamination owing to several handling steps. The above mentioned burdens as well as cost and long time to import them, especially in developing countries, prompted us to design and develop a chamber system for rapid, non-toxic, cost-effective and user friendly device for polymerase chain reaction (PCR) products purification from agarose gel. Materials and Methods: The device was made from plexiglass plates. After amplification of two fragments of 250 and 850 bp, PCR products were electrophoresed. Subsequently, the desired bands were excised and purified with three method: HiPer Mini chamber, phenol extraction method and spin column procedure. To assess the suitability of the purified DNAs, restriction digestion was applied. Results: Results showed that the yield of recovered DNA in our method was above 95%, whereas the yields obtained with conventional phenol extraction and spin column methods were around 60%. Conclusion: In conclusion, the current method for DNA elution is quick, inexpensive and robust and it does not require the use of toxic organic solvents. In addition, the purified DNA was well has suited for further manipulations such as restriction digestion, ligation, cloning, sequencing and hybridization. PMID:24761386

  8. Nucleic Acids as Information Molecules.

    ERIC Educational Resources Information Center

    McInerney, Joseph D.

    1996-01-01

    Presents an activity that aims at enabling students to recognize that DNA and RNA are information molecules whose function is to store, copy, and make available the information in biological systems, without feeling overwhelmed by the specialized vocabulary and the minutia of the central dogma. (JRH)

  9. Method for sequencing nucleic acid molecules

    DOEpatents

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2006-06-06

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  10. Method for sequencing nucleic acid molecules

    DOEpatents

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2006-05-30

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  11. Induction of human choriogonadotropin in HeLa-cell cultures by aliphatic monocarboxylates and inhibitors of deoxyribonucleic acid synthesis

    PubMed Central

    Ghosh, Nimai K.; Rukenstein, Adriana; Cox, Rody P.

    1977-01-01

    The ectopic production of the glycopeptide hormone human placental choriogonadotropin by HeLa65 cells was measured by radioimmunoassay with antiserum against the β-subunit of choriogonadotropin and with the 125I-labelled β-subunit as a tracer antigen. Choriogonadotropin synthesis was markedly (500-fold) stimulated by sodium butyrate. Kinetic studies and the use of an inhibitor of protein synthesis, cycloheximide, indicated that protein synthesis was required for this induction. Investigation of the efficiency of 22 aliphatic short-chain fatty acids and derivatives in causing increased choriogonadotropin synthesis by HeLa cells showed stringent structural requirements. Induction of choriogonadotropin synthesis in HeLa cells was not restricted to butyrate. Other aliphatic acids (propionate, isobutyrate, valerate and hexanoate) were also capable of inducing choriogonadotropin synthesis at 10–50% of the efficiency of butyrate. Hydroxy derivatives of monocarboxylate inducers, related mono- and di-carboxylic acids, alcohols, amines, ketones, esters and sulphoxide were ineffective in increasing choriogonadotropin production by HeLa cells. A saturated C4 straight-chain acid without substituent hydroxyl groups but with a methyl group at one end and a carboxyl moiety at the other appeared to be most efficient in activating choriogonadotropin production. A second clonal line of HeLa cells, HeLa71, showed a higher constitutive synthesis of choriogonadotropin than HeLa65 cells, which was also markedly increased by butyrate. Butyrate and other aliphatic monocarboxylate inducers of choriogonadotropin synthesis inhibited HeLa-cell growth and DNA synthesis. This inhibition of DNA replication may be related to the mechanism of choriogonadotropin synthesis, since two well-characterized anti-neoplastic inhibitors of DNA synthesis, hydroxyurea and 1-β-d-arabinofuranosylcytosine, also stimulated a 300-fold increase in choriogonadotropin synthesis in HeLa cells and were synergistic

  12. Floral Induction of Vegetative Plants Supplied a Purified Fraction of Deoxyribonucleic Acid from Stems of Flowering Plants 1

    PubMed Central

    Wardell, William L.

    1977-01-01

    It has been found that floral induced stems of flowering tobacco (Nicotiana tabacum cv. Wis. 38) plants contain large amounts of rapidly renaturing DNA, whereas noninduced stems of vegetative plants contain only small amounts. In addition, it has been shown that the striking qualitative difference in DNA between stems of flowering and vegetative plants mimics the over-all quantitative difference in DNA content (on a fresh weight basis). Therefore, the extra DNA in stems of flowering plants seems, at least in part, to represent preferential synthesis of rapidly renaturing DNA. Rapidly renatured DNA (flowering plants) has been purified (cesium chloride gradients) from heated-cooled DNA solution and under noninductive conditions has been tested for floral activity. It has been found that when rapidly renatured DNA in buffer solution is supplied to axillary vegetative buds of vegetative plants and then the axillary buds are defoliated every 4th day for 12 days, the treated buds change into flower buds. On the other hand, control axillary buds supplied buffer solution alone remain vegetative. In stem segments from flowering plants, the concept, discussed in previous reports, that indole-3-acetic acid may modify in vitro bud expression by directly affecting DNA synthesis has been reviewed. On the basis of this report, the concept is elaborated by proposing here that indole-3-acetic acid may act partially in bud expression by directly suppressing synthesis of rapidly renaturing DNA. PMID:16660207

  13. Bovine thrombospondin-2: complete complementary deoxyribonucleic acid sequence and immunolocalization in the external zones of the adrenal cortex.

    PubMed

    Danik, M; Chinn, A M; Lafeuillade, B; Keramidas, M; Aguesse-Germon, S; Penhoat, A; Chen, H; Mosher, D F; Chambaz, E M; Feige, J J

    1999-06-01

    Given the variety of biological functions in the adrenal cortex that are controlled by ACTH, we hypothesized that some extracellular proteins act as biological relays for this systemic hormone. One candidate protein [corticotropin-induced secreted protein (CISP)] was purified from the conditioned medium of bovine adrenocortical cells on the basis of a 5- to 14-fold increase in its synthesis after the addition of ACTH. We report here the cloning of overlapping complementary DNAs that span the sequence encoding the full-length protein (1170 amino acids). The deduced CISP protein sequence is 89% identical to that of human thrombospondin-2 (TSP2), but only 61% identical to that of bovine TSP1, confirming that CISP is the bovine ortholog of TSP2. The bovine TSP2 sequence aligned perfectly with human, mouse, and chicken TSP2 sequences, except for a gap of 2 amino acids located in a linker region. All 58 cysteine residues that are conserved in other species were present in the bovine sequence as well as most of the functional domains. Most endocrine tissues (adrenal cortex, testis, ovary, and placenta) appeared to express TSP2, as determined by Western blot analysis. The highest levels of TSP2 protein were found in the adrenal cortex, followed by the heart, spleen, brain, and kidney. A differential extent of N-glycosylation or tissular proteolytic maturation may be responsible for the mol wt differences observed between bovine TSP2 detected in the medium from primary cultures and that in fresh tissue extracts. The immunohistochemical analysis of the distribution of TSP2 in the bovine adrenal gland revealed that the protein is much more abundant in the external zones (zona glomerulosa and zona fasciculata) than in the internal reticularis zone, a pattern similar to that reported for ACTH receptors. This distribution clearly suggests that TSP2 is a candidate relay protein for a subset of ACTH actions in the adrenal cortex. PMID:10342868

  14. Cell cytotoxicity and serum albumin binding capacity of the morin-Cu(ii) complex and its effect on deoxyribonucleic acid.

    PubMed

    Roy, Atanu Singha; Samanta, Sintu Kumar; Ghosh, Pooja; Tripathy, Debi Ranjan; Ghosh, Sudip Kumar; Dasgupta, Swagata

    2016-08-16

    The dietary components, flavonoids, are important for their anti-oxidant properties and the ability to act as metal ion chelators. The characterization of the morin-Cu(ii) complex is executed using elemental analysis, FTIR and mass spectroscopy. DNA cleaving and cell cytotoxicity properties followed by serum albumin binding have been investigated in this report. The morin-Cu(ii) complex was found to cleave plasmid pBR322 DNA via an oxidative pathway as revealed by agarose gel based assay performed in the presence of some scavengers and reactive oxygen species. The breaking of the deoxyribose ring of calf thymus DNA (ct-DNA) was also confirmed by the formation of thiobarbituric acid reacting species (TBARS) between thiobarbituric acid and malonaldehyde. The morin-Cu(ii) complex is able to inhibit the growth of human HeLa cells. Fluorescence studies revealed that the morin-Cu(ii) complex can quench the intrinsic fluorescence of serum albumins (SAs) via a static quenching method. The binding constants were found to be in the order of 10(5) M(-1) and observed to increase with temperature. Both ΔH° and ΔS° are positive for the binding of the morin-Cu(ii) complex with serum albumins which indicated the presence of hydrophobic forces. Site-selectivity studies reveal that the morin-Cu(ii) complex binds to both site 1 (subdomain IIA) and site 2 (subdomain IIIA) of human serum albumin (HSA) and bovine serum albumin (BSA). Circular dichroism (CD) studies showed the structural perturbation of SAs during binding with the morin-Cu(ii) complex. The results from binding studies confirmed that after complexation with the Cu(ii) ion, morin alters its mode of interaction with SAs which could have differential implications on its other biological and pharmaceutical properties.

  15. Cell cytotoxicity and serum albumin binding capacity of the morin-Cu(ii) complex and its effect on deoxyribonucleic acid.

    PubMed

    Roy, Atanu Singha; Samanta, Sintu Kumar; Ghosh, Pooja; Tripathy, Debi Ranjan; Ghosh, Sudip Kumar; Dasgupta, Swagata

    2016-08-16

    The dietary components, flavonoids, are important for their anti-oxidant properties and the ability to act as metal ion chelators. The characterization of the morin-Cu(ii) complex is executed using elemental analysis, FTIR and mass spectroscopy. DNA cleaving and cell cytotoxicity properties followed by serum albumin binding have been investigated in this report. The morin-Cu(ii) complex was found to cleave plasmid pBR322 DNA via an oxidative pathway as revealed by agarose gel based assay performed in the presence of some scavengers and reactive oxygen species. The breaking of the deoxyribose ring of calf thymus DNA (ct-DNA) was also confirmed by the formation of thiobarbituric acid reacting species (TBARS) between thiobarbituric acid and malonaldehyde. The morin-Cu(ii) complex is able to inhibit the growth of human HeLa cells. Fluorescence studies revealed that the morin-Cu(ii) complex can quench the intrinsic fluorescence of serum albumins (SAs) via a static quenching method. The binding constants were found to be in the order of 10(5) M(-1) and observed to increase with temperature. Both ΔH° and ΔS° are positive for the binding of the morin-Cu(ii) complex with serum albumins which indicated the presence of hydrophobic forces. Site-selectivity studies reveal that the morin-Cu(ii) complex binds to both site 1 (subdomain IIA) and site 2 (subdomain IIIA) of human serum albumin (HSA) and bovine serum albumin (BSA). Circular dichroism (CD) studies showed the structural perturbation of SAs during binding with the morin-Cu(ii) complex. The results from binding studies confirmed that after complexation with the Cu(ii) ion, morin alters its mode of interaction with SAs which could have differential implications on its other biological and pharmaceutical properties. PMID:27345944

  16. Sugar amino acids in designing new molecules.

    PubMed

    Chakraborty, Tushar Kanti; Srinivasu, Pothukanuri; Tapadar, Subhasish; Mohan, Bajjuri Krishna

    2005-03-01

    Emulating the basic principles followed by nature to build its vast repertoire of biomolecules, organic chemists are developing many novel multifunctional building blocks and using them to create 'nature-like' and yet unnatural organic molecules. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl termini provide an excellent opportunity to organic chemists to create structural diversities akin to Nature's molecular arsenal. This article describes some of our works on various sugar amino acids and many other related building blocks, like furan amino acids, pyrrole amino acids etc. used in wide-ranging peptidomimetic studies. PMID:16133829

  17. Featured Molecules: Ascorbic Acid and Methylene Blue

    NASA Astrophysics Data System (ADS)

    Coleman, William F.; Wildman, Randall J.

    2003-05-01

    The WebWare molecules of the month for May are featured in several articles in this issue. "Arsenic: Not So Evil After All?" discusses the pharmaceutical uses of methylene blue and its development as the first synthetic drug used against a specific disease. The JCE Classroom Activity "Out of the Blue" and the article "Greening the Blue Bottle" feature methylene blue and ascorbic acid as two key ingredients in the formulation of the blue bottle. You can also see a colorful example of these two molecules in action on the cover. "Sailing on the 'C': A Vitamin Titration with a Twist" describes an experiment to determine the vitamin C (ascorbic acid) content of citrus fruits and challenges students, as eighteenth-century sea captains, to decide the best fruit to take on a long voyage. Fully manipulable (Chime) versions of these and other molecules are available at Only@JCE Online.

  18. Nanoconstructions Based on Spatially Ordered Nucleic Acid Molecules

    NASA Astrophysics Data System (ADS)

    Yevdokimov, Yu. M.

    Different strategies for the design of nanoconstructions whose building blocks are both linear molecules of double-stranded nucleic acids and nucleic acid molecules fixed in the spatial structure of particles of liquid-crystalline dispersions are described.

  19. Cloning and characterization of a complementary deoxyribonucleic acid encoding haploid-specific alanine-rich acidic protein located on chromosome-X.

    PubMed

    Uchida, K; Tsuchida, J; Tanaka, H; Koga, M; Nishina, Y; Nozaki, M; Yoshinaga, K; Toshimori, K; Matsumiya, K; Okuyama, A; Nishimune, Y

    2000-10-01

    We have isolated a cDNA clone encoding a germ cell-specific protein from an expression cDNA library prepared from the mouse testis using testis-specific polyclonal antibodies. Northern blot analysis showed a transcript of 1.1 kilobases exclusively expressed in haploid germ cells of the testis. Sequence analysis of the cDNA revealed one long open reading frame consisting of 238 deduced amino acids, rich in basic amino acids in the N-terminal one-third that also contained the nuclear localization signal, and rich in acidic amino acids, including two type of acidic alanine-rich repeats, in the rest of the deduced protein. The protein having a molecular weight of approximately 55 kDa and an isoelectric point of pH 4.3-4.7 was also exclusively detected in the testis by Western blot analysis. As the cDNA was located on chromosome-X, Halap-X (haploid-specific alanine-rich acidic protein located on chromosome-X) was proposed for the name of the protein encoded by the cDNA. Immunohistochemical observation revealed that the Halap-X protein was predominantly present in the nucleoplasm of round spermatids but gradually decreased as spermatids matured, followed by the subsequent appearance in the cytoplasm of elongating spermatids. Thus, the Halap-X protein was transferred from the nuclei to the cytoplasm during the spermatid maturation when the chromatin condensation and transformation of the nuclei occurred. The Halap-X may facilitate specific association of nuclear DNA with some basic chromosomal proteins and play important roles in the process of chromatin condensation. PMID:10993819

  20. Molecular cloning of otoconin-22 complementary deoxyribonucleic acid in the bullfrog endolymphatic sac: effect of calcitonin on otoconin-22 messenger ribonucleic acid levels.

    PubMed

    Yaoi, Yuichi; Suzuki, Masakazu; Tomura, Hideaki; Sasayama, Yuichi; Kikuyama, Sakae; Tanaka, Shigeyasu

    2003-08-01

    Anuran amphibians have a special organ called the endolymphatic sac (ELS), containing many calcium carbonate crystals, which is believed to have a calcium storage function. The major protein of aragonitic otoconia, otoconin-22, which is considered to be involved in the formation of calcium carbonate crystals, has been purified from the saccule of the Xenopus inner ear. In this study, we cloned a cDNA encoding otoconin-22 from the cDNA library constructed for the paravertebral lime sac (PVLS) of the bullfrog, Rana catesbeiana, and sequenced it. The bullfrog otoconin-22 encoded a protein consisting of 147 amino acids, including a signal peptide of 20 amino acids. The protein had cysteine residues identical in a number and position to those conserved among the secretory phospholipase A(2) family. The mRNA of bullfrog otoconin-22 was expressed in the ELS, including the PVLS and inner ear. This study also revealed the presence of calcitonin receptor-like protein in the ELS, with the putative seven-transmembrane domains of the G protein-coupled receptors. The ultimobranchialectomy induced a prominent decrease in the otoconin-22 mRNA levels of the bullfrog PVLS. Supplementation of the ultimobranchialectomized bullfrogs with synthetic salmon calcitonin elicited a significant increase in the mRNA levels of the sac. These findings suggest that calcitonin secreted from the ultimobranchial gland, regulates expression of bullfrog otoconin-22 mRNA via calcitonin receptor-like protein on the ELS, thereby stimulating the formation of calcium carbonate crystals in the lumen of the ELS. PMID:12865304

  1. Recent Advances in Developing Small Molecules Targeting Nucleic Acid

    PubMed Central

    Wang, Maolin; Yu, Yuanyuan; Liang, Chao; Lu, Aiping; Zhang, Ge

    2016-01-01

    Nucleic acids participate in a large number of biological processes. However, current approaches for small molecules targeting protein are incompatible with nucleic acids. On the other hand, the lack of crystallization of nucleic acid is the limiting factor for nucleic acid drug design. Because of the improvements in crystallization in recent years, a great many structures of nucleic acids have been reported, providing basic information for nucleic acid drug discovery. This review focuses on the discovery and development of small molecules targeting nucleic acids. PMID:27248995

  2. Repair of Radiation-Induced Damage in Escherichia coli II. Effect of rec and uvr Mutations on Radiosensitivity, and Repair of X-Ray-Induced Single-Strand Breaks in Deoxyribonucleic Acid1

    PubMed Central

    Kapp, Daniel S.; Smith, Kendric C.

    1970-01-01

    Strains of Escherichia coli K-12 mutant in the genes controlling excision repair (uvr) and genetic recombination (rec) have been studied with reference to their radiosensitivity and their ability to repair X-ray-induced single-strand breaks in deoxyribonucleic acid (DNA). Mutations in the rec genes appreciably increase the radiosensitivity of E. coli K-12, whereas uvr mutations produce little if any increase in radiosensitivity. For a given dose of X-rays, the yield of single-strand breaks has been shown by alkaline sucrose gradient studies to be largely independent of the presence of rec or uvr mutations. The rec+ cells (including those carrying the uvrB5 mutation) could efficiently rejoin X-ray-induced single-strand breaks in DNA, whereas recA56 mutants could not repair these breaks to any great extent. The recB21 and recC22 mutants showed some indication of repair capacity. From these studies, it is concluded that a correlation exists between the inability to repair single-strand breaks and the radiosensitivity of the rec mutants of E. coli K-12. This suggests that unrepaired single-strand breaks may be lethal lesions in E. coli. PMID:4912530

  3. Isolated menthone reductase and nucleic acid molecules encoding same

    DOEpatents

    Croteau, Rodney B; Davis, Edward M; Ringer, Kerry L

    2013-04-23

    The present invention provides isolated menthone reductase proteins, isolated nucleic acid molecules encoding menthone reductase proteins, methods for expressing and isolating menthone reductase proteins, and transgenic plants expressing elevated levels of menthone reductase protein.

  4. Cigarette smoking complements the prognostic value of baseline plasma Epstein-Barr virus deoxyribonucleic acid in patients with nasopharyngeal carcinoma undergoing intensity-modulated radiation therapy: a large-scale retrospective cohort study.

    PubMed

    Lv, Jia-Wei; Chen, Yu-Pei; Zhou, Guan-Qun; Tang, Ling-Long; Mao, Yan-Ping; Li, Wen-Fei; Guo, Rui; Lin, Ai-Hua; Ma, Jun; Sun, Ying

    2016-03-29

    We evaluated the combined prognostic value of cigarette smoking and baseline plasma Epstein-Barr virus deoxyribonucleic acid (EBV DNA) in patients with nasopharyngeal carcinoma (NPC) treated with intensity-modulated radiation therapy (IMRT). Of consecutive patients, 1501 with complete data were eligible for retrospective analysis. Smoking index (SI; cigarette packs per day times smoking duration [years]), was used to evaluate the cumulative effect of smoking. Primary end-point was overall survival (OS); progression-free survival (PFS), distant metastasis-free survival (DMFS) and locoregional relapse-free survival (LRFS) were secondary end-points. Both cigarette smoking and baseline plasma EBV DNA load were associated with poorer survival (P <0.001). Patients were divided into four groups: low EBV DNA and light smoker (LL), low EBV DNA and heavy smoker (LH), high EBV DNA and light smoker (HL), and high EBV DNA and heavy smoker (HH). The respective 5-year survival rates were: OS (93.1%, 87.2%, 82.9%, and 76.3%, P<0.001), PFS (87.0%, 84.0%, 73.9%, and 64.6%, P<0.001), DMFS (94.1%, 92.1%, 82.4%, and72.5%, P<0.001), and LRFS (92.8%, 92.4%, 88.7%, and 84.0%, P=0.012).OS and PFS were significantly different between the LH and HL groups and HL and HH groups, but not LL and LH groups (pairwise comparisons). The combined risk stratification remained an independent prognostic factor for all endpoints (all Ptrend<0.001; multivariate analysis). Both cigarette smoking and baseline plasma EBV DNA were independent prognostic factors for survival outcomes. Combined interpretation of EBV DNA with smoking led to the refinement of the risks stratification for patient subsets, especially with improved risk discrimination in patients with high baseline plasma EBV DNA. PMID:26919237

  5. Bilateral lesions of suprachiasmatic nuclei affect circadian rhythms in (/sup 3/H)-thymidine incorporation into deoxyribonucleic acid in mouse intestinal tract, mitotic index of corneal epithelium, and serum corticosterone

    SciTech Connect

    Scheving, L.E.; Tsai, T.H.; Powell, E.W.; Pasley, J.N.; Halberg, F.; Dunn, J.

    1983-03-01

    Investigations into the role of the suprachiasmatic nuclei (SCN) in the coordination of circadian rhythms have presented differing results. Several reports have shown that ablation of the suprachiasmatic nuclei (SCNA) alters the phase and amplitude of rhythms but does not abolish them. The present study investigates the effect of SCNA on the rhythms in cell proliferation in various regions of the intestinal tract as measured by the incorporation of (/sup 3/H)-thymidine into deoxyribonucleic acid, in the mitotic activity of the corneal epithelium, and in serum corticosterone levels. The study involved mice with verified lesions of the SCN (six to 13 mice per time point) and control groups of both sham-operated and unoperated mice (seven of each per time point). The mice were killed in groups that represented seven time points over a single 24 hr span (3 hr intervals with the 0800 hr sampled both at start and end of the series). The tissues examined were the tongue, esophagus, gastric stomach, and colon for DNA synthesis, the corneal epithelium for mitotic index, and blood serum for corticosterone level. The most consistent result of SCNA was a phase advance in the rhythms in cell proliferation in the tongue, esophagus, gastric stomach, colon, and corneal epithelium. A reduction in rhythm amplitude occurred in the tongue, esophagus, and corneal epithelium; however, there was an amplitude increase for the stomach, colon, and serum corticosterone. The mesor (rhythm-adjusted mean) was increased by SCNA in all tissues except the corneal epithelium. These findings further support the role of the suprachiasmatic nuclear area in the control of rhythms in cell proliferation and corticosterone production, by acting as a ''phase-resetter'' and as a modulator of rhythm amplitude.

  6. Methods And Devices For Characterizing Duplex Nucleic Acid Molecules

    DOEpatents

    Akeson, Mark; Vercoutere, Wenonah; Haussler, David; Winters-Hilt, Stephen

    2005-08-30

    Methods and devices are provided for characterizing a duplex nucleic acid, e.g., a duplex DNA molecule. In the subject methods, a fluid conducting medium that includes a duplex nucleic acid molecule is contacted with a nanopore under the influence of an applied electric field and the resulting changes in current through the nanopore caused by the duplex nucleic acid molecule are monitored. The observed changes in current through the nanopore are then employed as a set of data values to characterize the duplex nucleic acid, where the set of data values may be employed in raw form or manipulated, e.g., into a current blockade profile. Also provided are nanopore devices for practicing the subject methods, where the subject nanopore devices are characterized by the presence of an algorithm which directs a processing means to employ monitored changes in current through a nanopore to characterize a duplex nucleic acid molecule responsible for the current changes. The subject methods and devices find use in a variety of applications, including, among other applications, the identification of an analyte duplex DNA molecule in a sample, the specific base sequence at a single nulceotide polymorphism (SNP), and the sequencing of duplex DNA molecules.

  7. 2-hydroxyoleic acid: a new hypotensive molecule.

    PubMed

    Alemany, Regina; Terés, Silvia; Baamonde, Carmela; Benet, Mikhail; Vögler, Oliver; Escribá, Pablo V

    2004-02-01

    Recent studies have shown that diets rich in monounsaturated fatty acids (MUFAs) from olive oil, a natural source of oleic acid, have beneficial effects on blood pressure (BP) in hypertensive patients. With this in mind, we investigated whether a synthetic derivative of the MUFA oleic acid, 2-hydroxyoleic acid (2-OHOA), was capable of regulating the BP of Sprague-Dawley rats. Intraperitoneal and oral administration of 2-OHOA to rats induced significant and sustained decreases in BP in a time-dependent manner. Without affecting heart rate, treatments for 7 days provoked reductions in systolic BP of 20 to 26 mm Hg. At the molecular level, the density of Galpha(s), but not Galpha(i2) or Galpha(o), increased in membranes from the hearts and aortas of 2-OHOA-treated rats, whereas in heart membranes, the density of Galpha(q)/11 and protein kinase Calpha proteins was also augmented. These molecular alterations were reflected in the increase in cAMP levels after Galpha(s) protein and beta-adrenergic receptor stimulation. On the contrary, inhibitory hormones reduced adenylyl cyclase activity to the same extent in 2-OHOA-treated rats as in vehicle-treated ones. Our results indicate that cardiovascular tissues from 2-OHOA-treated rats exhibited increased cAMP production in response to Galpha(s) activation, which might be attributed to enhanced expression of Galpha(s) proteins. As a result of this change, a significant reduction in systolic BP was observed. Therefore, BP can be lowered by administration of 2-OHOA, which might represent the first member of a new family of antihypertensive drugs.

  8. Deoxyribonucleic acid directed metallization of platinum nanoparticles on graphite nanofibers as a durable oxygen reduction catalyst for polymer electrolyte fuel cells

    NASA Astrophysics Data System (ADS)

    Peera, S. Gouse; Sahu, A. K.; Arunchander, A.; Nath, Krishna; Bhat, S. D.

    2015-11-01

    Effective surface functionalization to the hydrophobic graphite nanofibers (GNF) is performed with the biomolecule, namely deoxy-ribo-nucleic-acid (DNA) via π-π interactions. Pt nanoparticles are impregnated on GNF-DNA composite by ethylene glycol reduction method (Pt/GNF-DNA) and its effect on electro catalytic activity for oxygen reduction reaction (ORR) is systemically studied. Excellent dispersion of Pt nanoparticles over GNF-DNA surfaces with no evidence on particle aggregation is a remarkable achievement in this study. This result in higher electro chemical surface area of the catalyst, enhanced ORR behavior with significant enhancement in mass activity. The catalyst is validated in H2-O2 polymer electrolyte fuel cell (PEFC) and a peak power density of 675 mW cm-2 is achieved at a load current density of 1320 mA cm-2 with a minimal catalyst loading of 0.1 mg cm-2 at a cell temperature of 70 °C and 2 bar absolute pressure. Repeated potential cycling up to 10000 cycles in acidic media is also performed for this catalyst and found excellent stability with only 60 mV drop in the ORR half wave potential. The superior behavior of Pt/GNF-DNA catalyst is credited to the robust fibrous structure of GNF and its effective surface functionalization process via π-π interaction.

  9. Purification of closed circular lambda deoxyribonucleic acid and its sedimentation properties as a function of Sodium chloride concentration and ethidium binding.

    PubMed

    Hinton, D M; Bode, V C

    1975-02-10

    The sedimentation of circular lambda DNA suggests that the molecular undergoes significant changes in shape and super-coiling as the NaC1 concentration increases. Closed circular lambda DNA, species I, isolated and purified from superinfected immune bacteria, sediments in sucrose gradients of low ionic strength at a rate 2.0 times faster than linear lambda DNA, species III. The addition of ethidium causes the sedimentation rate of species I DNA to decrease until enough dye is bound to remove 121 supercoils per molecule. At this point, species I co-sediments with nicked and nonsupercoiled species II. Futher additions of ethidium cause the sedimentation rate to increase until the relative rate of species I is again at least twice that of species III. This classical behavior is altered when NaC1 is present in the buffer. In 1.0 M NaC1 the changes in S are complex. Initially, species I sediments 1.55 times faster than species III. Titration with ethidium caused a decrease in S to an early minimum value, than an increase to a first maximum, followed by a decrease to the S of species II. At this point enough dye has intercalated to remove 208 superhelical turns. Further additions of dye introduce supercoils and cause S to increase again. In 0.1 to 0.4 M NaC1 the relative S of species I is 1.69 and 1.59, respectively. If titrated with ethidium, S first increases to a maximum value then decreases to the minimum rate when enough dye is bound to remove 158 and 183 supercoils, respectively. The results indicate an increase in the superhelix density from 0.026 turns per 10 base pairs in buffer alone to 0.045 in the same buffer with 1.0 M NaC1. If this change in superhelix density results from a concomitant change in the average rotation angle between base pairs in the Watson-Crick helix, the addition of 1.0 M NaC1 alters the rotation angle by 0.68 degrees per base pair.

  10. p53-Dependent and p53-independent induction of insulin-like growth factor binding protein-3 by deoxyribonucleic acid damage and hypoxia.

    PubMed

    Grimberg, Adda; Coleman, Carrie M; Burns, Timothy F; Himelstein, Bruce P; Koch, Cameron J; Cohen, Pinchas; El-Deiry, Wafik S

    2005-06-01

    IGF binding protein (IGFBP)-3, the principal carrier of IGFs in the circulation, contributes to both endocrine and autocrine/paracrine growth control; it can be induced by GH, cytokines, retinoic acid, and tumor suppressors. Induction of IGFBP-3 by the tumor suppressor p53 has been shown in various models that directly manipulate p53 activity. However, the physiologic settings under which this induction occurs have not been established. DNA damage and hypoxia are two important physiologic activators of p53. We have demonstrated for the first time that IGFBP-3 is an in vivo target of p53 in response to ionizing radiation. This effect was tissue specific. Furthermore, we demonstrated that genotoxic drugs could increase IGFBP-3 protein levels and secretion in tumor cell lines in a p53-independent manner. Finally, we have established that IGFBP-3 induction under hypoxic conditions is independent of p53 in tumor cell lines derived form multiple tissue types. Thus, IGFBP-3 is induced by physiologic conditions that also induce p53, although p53 is not always required. Because IGFBP-3 can inhibit growth and induce apoptosis in IGF-dependent and IGF-independent manners, its induction by DNA damage and hypoxia suggest IGFBP-3 plays a role in the physiologic protection against aberrant cell growth.

  11. Oxidized fatty acids as inter-kingdom signaling molecules.

    PubMed

    Pohl, Carolina H; Kock, Johan L F

    2014-01-20

    Oxylipins or oxidized fatty acids are a group of molecules found to play a role in signaling in many different cell types. These fatty acid derivatives have ancient evolutionary origins as signaling molecules and are ideal candidates for inter-kingdom communication. This review discusses examples of the ability of organisms from different kingdoms to "listen" and respond to oxylipin signals during interactions. The interactions that will be looked at are signaling between animals and plants; between animals and fungi; between animals and bacteria and between plants and fungi. This will aid in understanding these interactions, which often have implications in ecology, agriculture as well as human and animal health.

  12. Analysis of single nucleic acid molecules with protein nanopores

    PubMed Central

    Maglia, Giovanni; Heron, Andrew J.; Stoddart, David; Japrung, Deanpen; Bayley, Hagan

    2011-01-01

    We describe the methods used in our laboratory for the analysis of single nucleic acid molecules with protein nanopores. The technical section is preceded by a review of the variety of experiments that can be done with protein nanopores. The end goal of much of this work is single-molecule DNA sequencing, although sequencing is not discussed explicitly here. The technical section covers the equipment required for nucleic acid analysis, the preparation and storage of the necessary materials, and aspects of signal processing and data analysis. PMID:20627172

  13. Deoxyribonucleic acid base compositions of dermatophytes.

    PubMed

    Davison, F D; Mackenzie, D W; Owen, R J

    1980-06-01

    DNA was extracted and purified from 55 dermatophyte isolates representing 34 species of Trichophyton, Microsporum and Epidermophyton. The base compositions of the chromosomal DNA were determined by CsCl density gradient centrifugation and were found to be in the narrow range of 48.7 to 50.3 mol % G + C. A satellite DNA component assumed to be of mitochondrial origin was present in most strains, with a G + C content ranging from 14.7 to 30.8 mol % G + C. Heterogeneity in microscopic and colonial characteristics was not reflected in differences in the mean G + C content of the chromosomal DNAs. Strains varied in the G + C contents of satelite DNA, but these did not correlate with traditional species concepts.

  14. Nucleotide `maps' of digests of deoxyribonucleic acid

    PubMed Central

    Murray, K.

    1970-01-01

    Various digests of 32P-labelled DNA were examined by two-dimensional ionophoresis on cellulose acetate and DEAE-cellulose paper. The products from digestion with pancreatic deoxyribonuclease and Neurospora crassa endonuclease were qualitatively closely similar, but very complex, and were used to investigate the mapping behaviour of nucleotides in various ionophoretic systems. Ionophoresis on DEAE-cellulose paper in triethylamine carbonate, pH 9.7, followed by ionophoresis in the second dimension at pH1.9 gave high resolution of nucleotides in very complex mixtures and permitted the fractionation of larger quantities than is possible on cellulose acetate. High resolution of nucleotides in compact spots was obtained with two-dimensional ionophoresis on cellulose acetate and AE-cellulose paper, a system that is a useful supplement to those based on DEAE-cellulose paper. ImagesPLATE 7PLATE 1PLATE 2PLATE 3PLATE 4PLATE 5PLATE 6 PMID:5476726

  15. DETECTION OF A NEW INTERSTELLAR MOLECULE: THIOCYANIC ACID HSCN

    SciTech Connect

    Halfen, D. T.; Ziurys, L. M.; Bruenken, S.; Gottlieb, C. A.; McCarthy, M. C.; Thaddeus, P. E-mail: lziurys@as.arizona.edu E-mail: cgottlieb@cfa.harvard.edu E-mail: pthaddeus@cfa.harvard.edu

    2009-09-10

    A new interstellar molecule, HSCN (thiocyanic acid), an energetic isomer of the well-known species HNCS, has been detected toward Sgr B2(N) with the Arizona Radio Observatory 12 m telescope. Eight rotational transitions in the K{sub a} = 0 ladder were observed in the 2 mm and 3 mm bands. Five consecutive transitions in the 3 mm band are unblended, but three in the 2 mm band are partially masked by lines of other molecules. The peak intensity of all eight transitions are well described by a rotational temperature that is in very good agreement with that of many other molecules in this source. The line width and radial velocity of HSCN match closely with those of the ground state isomer HNCS (isothiocyanic acid), HNCO (isocyanic acid), and HOCN (cyanic acid); preliminary maps indicate that all four molecules are similarly distributed in Sgr B2. Although HSCN is calculated to lie over 3000 K higher in energy than HNCS, its column density of 1.3 x 10{sup 13} cm{sup -2} in Sgr B2(N) is only three times lower than that of HNCS. The fractional abundances of HSCN and HNCS relative to H{sub 2} are 4.5 x 10{sup -12} and 1.1 x 10{sup -11}. By analogy with the isomeric pair HCN and HNC, these two sulfur-bearing isomers are plausibly formed from a common cation precursor.

  16. Sugar amino acids and their uses in designing bioactive molecules.

    PubMed

    Chakraborty, Tushar K; Ghosh, Subhash; Jayaprakash, Sarva

    2002-02-01

    In search of new molecular entities for discovering new drugs and materials, organic chemists are looking for innovative approaches that try to imitate nature in assembling quickly large number of distinct and diverse molecular structures from 'nature-like' and yet unnatural designer building blocks using combinatorial approach. The main objective in developing such libraries is to mimic the diversities displayed in structures and properties of natural products. The unnatural building blocks used in these assemblies are carefully designed to manifest the structural diversities of the monomeric units used by nature like amino acids, carbohydrates and nucleosides to build its arsenal. Compounds made of such unnatural building blocks are also expected to be more stable toward proteolytic cleavage in physiological systems than their natural counterparts. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl termini provide an excellent opportunity to organic chemists to create structural diversities akin to nature's molecular arsenal. Recent advances in the area of combinatorial chemistry give an unprecedented technological support for rapid compilations of sugar amino acid-based libraries exploiting the diversities of carbohydrate molecules and well-developed solid-phase peptide synthesis methods. This review describes the development of sugar amino acids as a novel class of peptidomimetic building blocks and their applications in creating large number of structurally diverse peptide-based molecules many of which display interesting three-dimensional structures as well as useful biological properties. PMID:11945118

  17. Anion photoelectron spectroscopy of acid-base systems, solvated molecules and MALDI matrix molecules

    NASA Astrophysics Data System (ADS)

    Eustis, Soren Newman

    Gas phase, mass-selected, anion photoelectron spectroscopic studies were performed on a variety of molecular systems. These studies can be grouped into three main themes: acid-base interactions, solvation, and ions of analytical interest. Acid-base interactions represent some of the most fundamental processes in chemistry. The study of these processes elucidates elementary principles such as inner and outer sphere complexes, hard and soft ions, and salt formation---to name a few. Apart from their appeal from a pedagogical standpoint, the ubiquity of chemical reactions which involve acids, bases or the resulting salts makes the study of their fundamental interactions both necessary and fruitful. With this in mind, the neutral and anionic series (NH3···HX) (X= F, Cl, Br, I) were examined experimentally and theoretically. The relatively small size of these systems, combined with the advances in computational methods, allowed our experimental results to be compared with very high level ab initio theoretical results. The synergy between theory and experiment yielded an understanding of the nature of the complexes that could not be achieved with either method in isolation. The second theme present in this body or work is molecular solvation. Solvation is a phenomenon which is present in biology, chemistry and physics. Many biological molecules do not become 'active' until they are solvated by water. Thus, the study of biologically relevant species solvated by water is one step in a bottom up approach to studying the biochemical interactions in living organisms. Furthermore, the hydration of acidic molecules in the atmosphere is what drives the formation of 'free' protons or hydronium ions which are the key players in acid driven chemistry. Here are presented two unique solvation studies, Adenine(H2O)-n and C6F6(H2O)-n, these systems are very distinct, but show somewhat similar responses to hydration. The last theme presented in this work is the electronic properties

  18. Pharmacology of bile acid receptors: Evolution of bile acids from simple detergents to complex signaling molecules.

    PubMed

    Copple, Bryan L; Li, Tiangang

    2016-02-01

    For many years, bile acids were thought to only function as detergents which solubilize fats and facilitate the uptake of fat-soluble vitamins in the intestine. Many early observations; however, demonstrated that bile acids regulate more complex processes, such as bile acids synthesis and immune cell function through activation of signal transduction pathways. These studies were the first to suggest that receptors may exist for bile acids. Ultimately, seminal studies by many investigators led to the discovery of several bile acid-activated receptors including the farnesoid X receptor, the vitamin D receptor, the pregnane X receptor, TGR5, α5 β1 integrin, and sphingosine-1-phosphate receptor 2. Several of these receptors are expressed outside of the gastrointestinal system, indicating that bile acids may have diverse functions throughout the body. Characterization of the functions of these receptors over the last two decades has identified many important roles for these receptors in regulation of bile acid synthesis, transport, and detoxification; regulation of glucose utilization; regulation of fatty acid synthesis and oxidation; regulation of immune cell function; regulation of energy expenditure; and regulation of neural processes such as gastric motility. Through these many functions, bile acids regulate many aspects of digestion ranging from uptake of essential vitamins to proper utilization of nutrients. Accordingly, within a short time period, bile acids moved beyond simple detergents and into the realm of complex signaling molecules. Because of the important processes that bile acids regulate through activation of receptors, drugs that target these receptors are under development for the treatment of several diseases, including cholestatic liver disease and metabolic syndrome. In this review, we will describe the various bile acid receptors, the signal transduction pathways activated by these receptors, and briefly discuss the physiological processes that

  19. Control of Biofilms with the Fatty Acid Signaling Molecule cis-2-Decenoic Acid

    PubMed Central

    Marques, Cláudia N. H.; Davies, David G.; Sauer, Karin

    2015-01-01

    Biofilms are complex communities of microorganisms in organized structures attached to surfaces. Importantly, biofilms are a major cause of bacterial infections in humans, and remain one of the most significant challenges to modern medical practice. Unfortunately, conventional therapies have shown to be inadequate in the treatment of most chronic biofilm infections based on the extraordinary innate tolerance of biofilms to antibiotics. Antagonists of quorum sensing signaling molecules have been used as means to control biofilms. QS and other cell-cell communication molecules are able to revert biofilm tolerance, prevent biofilm formation and disrupt fully developed biofilms, albeit with restricted effectiveness. Recently however, it has been demonstrated that Pseudomonas aeruginosa produces a small messenger molecule cis-2-decenoic acid (cis-DA) that shows significant promise as an effective adjunctive to antimicrobial treatment of biofilms. This molecule is responsible for induction of the native biofilm dispersion response in a range of Gram-negative and Gram-positive bacteria and in yeast, and has been shown to reverse persistence, increase microbial metabolic activity and significantly enhance the cidal effects of conventional antimicrobial agents. In this manuscript, the use of cis-2-decenoic acid as a novel agent for biofilm control is discussed. Stimulating the biofilm dispersion response as a novel antimicrobial strategy holds significant promise for enhanced treatment of infections and in the prevention of biofilm formation. PMID:26610524

  20. NALDB: nucleic acid ligand database for small molecules targeting nucleic acid.

    PubMed

    Kumar Mishra, Subodh; Kumar, Amit

    2016-01-01

    Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php.

  1. NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

    PubMed Central

    Kumar Mishra, Subodh; Kumar, Amit

    2016-01-01

    Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php PMID:26896846

  2. Nucleic acid detection technologies and marker molecules in bacterial diagnostics.

    PubMed

    Scheler, Ott; Glynn, Barry; Kurg, Ants

    2014-05-01

    There is a growing need for quick and reliable methods for microorganism detection and identification worldwide. Although traditional culture-based technologies are trustworthy and accurate at a relatively low cost, they are also time- and labor-consuming and are limited to culturable bacteria. Those weaknesses have created a necessity for alternative technologies that are capable for faster and more precise bacterial identification from medical, food or environmental samples. The most common current approach is to analyze the nucleic acid component of analyte solution and determine the bacterial composition according to the specific nucleic acid profiles that are present. This review aims to give an up-to-date overview of different nucleic acid target sequences and respective analytical technologies.

  3. 2-Fatty acrylic acids: new highly derivatizable lipophilic platform molecules

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This paper reports the incorporation of an alpha-methylene unit into fatty acid skeletons. Since the new olefin is conjugated with the carboxylate, it is susceptible to 1,4- (Michael) additions. We have used multifunctional thiols and amines for additions at the methylene. The resulting products ...

  4. Electric Dipole Moments of Nanosolvated Acid Molecules in Water Clusters

    NASA Astrophysics Data System (ADS)

    Guggemos, Nicholas; Slavíček, Petr; Kresin, Vitaly V.

    2015-01-01

    The electric dipole moments of (H2O)nDCl (n =3 - 9 ) clusters have been measured by the beam-deflection method. Reflecting the (dynamical) charge distribution within the system, the dipole moment contributes information about the microscopic structure of nanoscale solvation. The addition of a DCl molecule to a water cluster results in a strongly enhanced susceptibility. There is evidence for a noticeable rise in the dipole moment occurring at n ≈5 - 6 . This size is consistent with predictions for the onset of ionic dissociation. Additionally, a molecular-dynamics model suggests that even with a nominally bound impurity an enhanced dipole moment can arise due to the thermal and zero-point motion of the proton and the water molecules. The experimental measurements and the calculations draw attention to the importance of fluctuations in defining the polarity of water-based nanoclusters and generally to the essential role played by motional effects in determining the response of fluxional nanoscale systems under realistic conditions.

  5. Surface functionalization of bioactive glasses with natural molecules of biological significance, Part I: Gallic acid as model molecule

    NASA Astrophysics Data System (ADS)

    Zhang, Xin; Ferraris, Sara; Prenesti, Enrico; Verné, Enrica

    2013-12-01

    Gallic acid (3,4,5-trihydroxybenzoic acid, GA) and its derivatives are a group of biomolecules (polyphenols) obtained from plants. They have effects which are potentially beneficial to heath, for example they are antioxidant, anticarcinogenic and antibacterial, as recently investigated in many fields such as medicine, food and plant sciences. The main drawbacks of these molecules are both low stability and bioavailability. In this research work the opportunity to graft GA to bioactive glasses is investigated, in order to deliver the undamaged biological molecule into the body, using the biomaterial surfaces as a localized carrier. GA was considered for functionalization since it is a good model molecule for polyphenols and presents several interesting biological activities, like antibacterial, antioxidant and anticarcinogenic properties. Two different silica based bioactive glasses (SCNA and CEL2), with different reactivity, were employed as substrates. UV photometry combined with the Folin&Ciocalteu reagent was adopted to test the concentration of GA in uptake solution after functionalization. This test verified how much GA consumption occurred with surface modification and it was also used on solid samples to test the presence of GA on functionalized glasses. XPS and SEM-EDS techniques were employed to characterize the modification of material surface properties and functional group composition before and after functionalization.

  6. An on-line high-performance liquid chromatography-diode-array detector-multi-stage mass spectrometry-deoxyribonucleic acid-4',6-diamidino-2-phenylindole-fluorescence detector system for screening the DNA-binding active compounds in Fufang Banbianlian Injection.

    PubMed

    Li, Sensen; Jiang, Haixiu; Lin, Zongtao; Deng, Shanshan; Guan, Yanqing; Wang, Hong; Chen, Shizhong

    2015-12-11

    Fufang Banbianlian Injection (FBI), a well-known traditional Chinese medicine formula, has been recently approved and extensively used as a newly anti-inflammatory and anti-tumor drug. This prescription comprises an equal ratio of three traditional Chinese herbs, Lobelia chinensis Lour, Scutellaria barbata D. Don and Hedyotis diffusa Willd. The relationships between its chemical compositions and activities have not been understood well yet. To investigate the ingredients and their DNA-binding activities in FBI, an on-line high-performance liquid chromatography-diode-array detector-multi-stage mass spectrometry-deoxyribonucleic acid-4',6-diamidino-2-phenylindole-fluorescence detector (HPLC-DAD-MS(n)-DNA-DAPI-FLD) system was developed using a combination of chromatographic, mass spectrometric and fluorescent detection techniques. 4',6-Diamidino-2-phenylindole (DAPI) specifically binds to three ATT base pairs on the DNA minor groove, and thus can be used as a fluorescent probe for screening active compounds that compete ATT sequences with DAPI. Using this system, 21 of 58 identified or tentatively characterized compounds in FBI showed DNA-binding activities, with most of the active compounds being flavone glycosides. In addition, the structure-activity relationships of these active compounds suggested that conjugated planar structures are favorable for DNA-binding activities, and adjacent hydroxyl groups in flavonoids can significantly improve their activities. This is, to the best of our knowledge, the first application of DAPI as a fluorescent probe for the screening of DNA-binding active compounds in complex samples. PMID:26592560

  7. Acid properties of solid acid catalysts characterized by solid-state 31P NMR of adsorbed phosphorous probe molecules.

    PubMed

    Zheng, Anmin; Huang, Shing-Jong; Liu, Shang-Bin; Deng, Feng

    2011-09-01

    A brief review is presented on acidity characterization of solid acid catalysts by means of solid-state phosphor-31 magic-angle-spinning nuclear magnetic resonance ((31)P MAS NMR) spectroscopy using phosphor-containing molecules as probes. It is emphasized that such a simple approach using (31)P MAS NMR of adsorbed phosphorous probe molecules, namely trimethylphosphine (TMP) and trialkylphosphine oxides (R(3)PO), represents a unique technique in providing detailed qualitative and quantitative features, viz. type, strength, distribution, and concentration of acid sites in solid acid catalysts. In particular, it will be shown that when applied with a proper choice of probe molecules with varied sizes and results obtained from elemental analysis, the amounts and locations (intracrystalline vs. extracrystalline) of different types (Brønsted vs. Lewis) of acid sites may be determined. In addition, by incorporating the NMR results with that obtained from theoretical density functional theory (DFT) calculations, correlations between the (31)P chemical shifts (δ(31)P) and acidic strengths of Brønsted and Lewis acid sites may also be derived, facilitating a suitable acidity scale for solid acid catalysts.

  8. Stardust and the Molecules of Life (Why are the Amino Acids Left-Handed?)

    SciTech Connect

    Boyd, R N; Kajino, T; Onaka, T

    2010-04-02

    A mechanism for creating and selecting amino acid chirality is identified, and subsequent chemical replication and galactic mixing that would populate the galaxy with the predominant species will be described. This involves: (1) the spin of the {sup 14}N in the amino acids, or in precursor molecules from which amino acids might be formed, coupling to the chirality of the molecules; (2) the neutrinos emitted from the supernova, together with magnetic field from the nascent neutron star or black hole from the supernova selectively destroying one orientation of the {sup 14}N, thereby selecting the chirality associated with the other {sup 14}N orientation; (3) amplification by chemical evolution, by which the molecules replicate on a relatively short timescale; and (4) galactic mixing on a longer timescale mixing the selected molecules throughout the galaxy.

  9. Adsorption of monomers on microspherical structures of thermal heterocomplex molecules from amino ACIDS

    NASA Astrophysics Data System (ADS)

    Honda, Hajime; Sakurazawa, Shigeru; Dekikimura, H.; Imai, Eiichi; Matsuno, Koichiro

    1995-10-01

    The surface of a microspherical structure formed in the aqueous suspension of thermal heterocomplex molecules made by heating aspartic acid and proline can adsorb basic amino acids such as histidine, lysine and arginine. It can also adsorb adenine, cytosine, adenosine and cytidine. Electrostatic interactions acting between those monomers to be adsorbed and the adsorbing surface are responsible for the adsorption.

  10. Dissociative attachment reactions of electrons with strong acid molecules

    SciTech Connect

    Adams, N.G.; Smith, D.; Viggiano, A.A.; Paulson, J.F.; Henchman, M.J.

    1986-06-15

    Using the flowing afterglow/Langmuir probe (FALP) technique, we have determined (at variously 300 and 570 K) the dissociative attachment coefficients ..beta.. for the reactions of electrons with the common acids HNO/sub 3/ (producing NO/sup -//sub 2/) and H/sub 2/SO/sub 4/ (HSO/sup -//sub 4/), the superacids FSO/sub 3/H (FSO/sup -//sub 3/), CF/sub 3/SO/sub 3/H (CF/sub 3/SO/sup -//sub 3/), ClSO/sub 3/H (ClSO/sup -//sub 3/,Cl/sup -/), the acid anhydride (CF/sub 3/SO/sub 2/)/sub 2/O (CF/sub 3/SO/sup -//sub 3/), and the halogen halides HBr (Br/sup -/) and HI (I/sup -/). The anions formed in the reactions are those given in the parentheses. The reactions with HF and HCl were investigated, but did not occur at a measurable rate since they are very endothermic. Dissociative attachment is rapid for the common acids, the superacids, and the anhydride, the measured ..beta.. being appreciable fractions of the theoretical maximum ..beta.. for such reactions, ..beta../sub max/. The HI reaction is very fast ( ..beta..approx...beta../sub max/) but the HBr reaction occurs much more slowly because it is significantly endothermic. The data indicate that the extreme acidity of the (Bronsted-type) superacids has its equivalence in the very efficient gas-phase dissociative attachment which these species undergo when reacting with free electrons. The anions of the superacids generated in these reactions, notably FSO/sup -//sub 3/ and CF/sub 3/SO/sup -//sub 3/, are very stable (unreactive) implying exceptionally large electron affinities for the FSO/sub 3/ and CF/sub 3/SO/sub 3/ radicals.

  11. Analysis of single nucleic acid molecules in micro- and nano-fluidics.

    PubMed

    Friedrich, Sarah M; Zec, Helena C; Wang, Tza-Huei

    2016-03-01

    Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano-fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano-fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano-structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.

  12. Activation of Carbonyl-Containing Molecules with Solid Lewis Acids in Aqueous Media

    SciTech Connect

    Román-Leshkov, Yuriy; Davis, Mark E.

    2011-09-28

    Current interest in reacting carbonyl-containing molecules in aqueous media is primarily due to the growing emphasis on conversion of biomass to fuels and chemicals. Recently, solid Lewis acids have been shown to perform catalytic reactions with carbonyl-containing molecules such as sugars in aqueous media. Here, catalysis mediated by Lewis acids is briefly discussed, Lewis acid solids that perform catalysis in aqueous media are then described, and the review is concluded with a few comments on the outlook for the future.

  13. Hydration of biological molecules: lipids versus nucleic acids.

    PubMed

    Pohle, W; Gauger, D R; Dornberger, U; Birch-Hirschfeld, E; Selle, C; Rupprecht, A; Bohl, M

    2002-01-01

    We used FTIR spectroscopy to comparatively study the hydration of films prepared from nucleic acids (DNA and double-stranded RNA) and lipids (phosphatidylcholines and phosphatidylethanolamines chosen as the most abundant ones) at room temperature by varying the ambient relative humidity in terms of solvent-induced structural changes. The nucleic acids and phospholipids both display examples of polymorphism on the one hand and structural conservatism on the other; even closely related representatives behave differently in this respect. DNA undergoes a hydration-driven A-B conformational transition, but RNA maintains an A-like structure independently of the water activity. Similarly, a main transition between the solid and liquid-crystalline phases can be induced lyotropically in certain phosphatidylcholines, while their phosphatidylethanolamine counterparts do not exhibit chain melting under the same conditions. A principal difference concerning the structural changes that occur in the studied biomolecules is given by the relevant water-substrate stoichiometries. These are rather high in DNA and often low in phospholipids, suggesting different mechanisms of action of the hydration water that appears to induce structural changes on global- and local-mode levels, respectively.

  14. Acidity characterization of heterogeneous catalysts by solid-state NMR spectroscopy using probe molecules.

    PubMed

    Zheng, Anmin; Liu, Shang-Bin; Deng, Feng

    2013-01-01

    Characterization of the surface acidic properties of solid acid catalysts is a key issue in heterogeneous catalysis. Important acid features of solid acids, such as their type (Brønsted vs. Lewis acid), distribution and accessibility (internal vs. external sites), concentration (amount), and strength of acid sites are crucial factors dictating their reactivity and selectivity. This short review provides information on different solid-state NMR techniques used for acidity characterization of solid acid catalysts. In particular, different approaches using probe molecules containing a specific nucleus of interest, such as pyridine-d5, 2-(13)C-acetone, trimethylphosphine, and trimethylphosphine oxide, are compared. Incorporation of valuable information (such as the adsorption structure, deprotonation energy, and NMR parameters) from density functional theory (DFT) calculations can yield explicit correlations between the chemical shift of adsorbed probe molecules and the intrinsic acid strength of solid acids. Methods that combine experimental NMR data with DFT calculations can therefore provide both qualitative and quantitative information on acid sites.

  15. Single-molecule pull-down for investigating protein-nucleic acid interactions.

    PubMed

    Fareh, Mohamed; Loeff, Luuk; Szczepaniak, Malwina; Haagsma, Anna C; Yeom, Kyu-Hyeon; Joo, Chirlmin

    2016-08-01

    The genome and transcriptome are constantly modified by proteins in the cell. Recent advances in single-molecule techniques allow for high spatial and temporal observations of these interactions between proteins and nucleic acids. However, due to the difficulty of obtaining functional protein complexes, it remains challenging to study the interactions between macromolecular protein complexes and nucleic acids. Here, we combined single-molecule fluorescence with various protein complex pull-down techniques to determine the function and stoichiometry of ribonucleoprotein complexes. Through the use of three examples of protein complexes from eukaryotic cells (Drosha, Dicer, and TUT4 protein complexes), we provide step-by-step guidance for using novel single-molecule techniques. Our single-molecule methods provide sub-second and nanometer resolution and can be applied to other nucleoprotein complexes that are essential for cellular processes. PMID:27017911

  16. Comparative Study on Single-Molecule Junctions of Alkane- and Benzene-Based Molecules with Carboxylic Acid/Aldehyde as the Anchoring Groups.

    PubMed

    Chen, Fang; Peng, Lin-Lu; Hong, Ze-Wen; Mao, Jin-Chuan; Zheng, Ju-Fang; Shao, Yong; Niu, Zhen-Jiang; Zhou, Xiao-Shun

    2016-12-01

    We have measured the alkane and benzene-based molecules with aldehyde and carboxylic acid as anchoring groups by using the electrochemical jump-to-contact scanning tunneling microscopy break junction (ECSTM-BJ) approach. The results show that molecule with benzene backbone has better peak shape and intensity than those with alkane backbone. Typically, high junction formation probability for same anchoring group (aldehyde and carboxylic acid) with benzene backbone is found, which contributes to the stronger attractive interaction between Cu and molecules with benzene backbone. The present work shows the import role of backbone in junction, which can guide the design molecule to form effective junction for studying molecular electronics. PMID:27566686

  17. Comparative Study on Single-Molecule Junctions of Alkane- and Benzene-Based Molecules with Carboxylic Acid/Aldehyde as the Anchoring Groups

    NASA Astrophysics Data System (ADS)

    Chen, Fang; Peng, Lin-Lu; Hong, Ze-Wen; Mao, Jin-Chuan; Zheng, Ju-Fang; Shao, Yong; Niu, Zhen-Jiang; Zhou, Xiao-Shun

    2016-08-01

    We have measured the alkane and benzene-based molecules with aldehyde and carboxylic acid as anchoring groups by using the electrochemical jump-to-contact scanning tunneling microscopy break junction (ECSTM-BJ) approach. The results show that molecule with benzene backbone has better peak shape and intensity than those with alkane backbone. Typically, high junction formation probability for same anchoring group (aldehyde and carboxylic acid) with benzene backbone is found, which contributes to the stronger attractive interaction between Cu and molecules with benzene backbone. The present work shows the import role of backbone in junction, which can guide the design molecule to form effective junction for studying molecular electronics.

  18. Effects of corn silage derived from a genetically modified variety containing two transgenes on feed intake, milk production, and composition, and the absence of detectable transgenic deoxyribonucleic acid in milk in Holstein dairy cows.

    PubMed

    Calsamiglia, S; Hernandez, B; Hartnell, G F; Phipps, R

    2007-10-01

    The objectives were to compare the chemical composition, nutritive value, feed intake, milk production and composition, and presence in milk of transgenic DNA and the encoded protein Cry1Ab when corn silages containing 2 transgenes (2GM: herbicide tolerance: mepsps and insect resistance: cry1Ab) were fed as part of a standard total mixed ration (TMR) compared with a near isogenic corn silage (C) to 8 multiparous lactating Holstein dairy cows in a single reversal design study. Cows were fed a TMR ration ad libitum and milked twice daily. Diets contained [dry matter (DM) basis] 45% corn silage, 10% alfalfa hay, and 45% concentrate (1.66 Mcal of net energy for lactation/kg of DM, 15.8% crude protein, 35% neutral detergent fiber, and 4.1% fat). Each period was 28-d long. During the last 4 d of each period, feed intake and milk production data were recorded and milk samples taken for compositional analysis, including the presence of transgenic DNA and Cry1Ab protein. There was no significant difference in the chemical composition between C and 2GM silages, and both were within the expected range (37.6% DM, 1.51 Mcal of net energy for lactation/kg, 8.6% crude protein, 40% neutral detergent fiber, 19.6% acid detergent fiber, pH 3.76, and 62% in vitro DM digestibility). Cows fed the 2GM silage produced milk with slightly higher protein (3.09 vs. 3.00%), lactose (4.83 vs. 4.72%) and solids-not-fat (8.60 vs. 8.40%) compared with C. However, the yield (kg/d) of milk (36.5), 3.5% fat-corrected milk (34.4), fat (1.151), protein (1.106), lactose (1.738), and solids-not-fat (3.094), somatic cell count (log10: 2.11), change in body weight (+7.8 kg), and condition score (+0.09) were not affected by type of silage, indicating no overall production difference. All milk samples were negative for the presence of transgenic DNA from either trait or the Cry1Ab protein. Results indicate that the 2GM silage modified with 2 transgenes did not affect nutrient composition of the silages and

  19. Syntheses of biodiesel precursors: sulfonic acid catalysts for condensation of biomass-derived platform molecules.

    PubMed

    Balakrishnan, Madhesan; Sacia, Eric R; Bell, Alexis T

    2014-04-01

    Synthesis of transportation fuel from lignocellulosic biomass is an attractive solution to the green alternative-energy problem. The production of biodiesel, in particular, involves the process of upgrading biomass-derived small molecules to diesel precursors containing a specific carbon range (C11 -C23). Herein, a carbon-upgrading process utilizing an acid-catalyzed condensation of furanic platform molecules from biomass is described. Various types of sulfonic acid catalysts have been evaluated for this process, including biphasic and solid supported catalysts. A silica-bound alkyl sulfonic acid catalyst has been developed for promoting carbon-carbon bond formation of biomass-derived carbonyl compounds with 2-methylfuran. This hydrophobic solid acid catalyst exhibits activity and selectivity that are comparable to those of a soluble acid catalyst. The catalyst can be readily recovered and recycled, possesses appreciable hydrolytic stability in the presence of water, and retains its acidity over multiple reaction cycles. Application of this catalyst to biomass-derived platform molecules led to the synthesis of a variety of furanic compounds, which are potential biodiesel precursors.

  20. The deoxyribonucleic acid polymerases of non-vertebrate eukaryotes.

    PubMed

    McLennan, A G; Keir, H M

    1977-01-01

    DNA-dependent DNA polymerases have now been purified from a number of invertebrate animals, protists, higher plants and fungi. In this article we review the properties of these enzymes and compare them with the better-known enzymes of vertebrate animals and prokaryotes. Three facts emerge. Firstly, plants, protists and fungi contain high-molecular-weight DNA polymerases which may be capable of categorization into two groups on the basis of their properties in vitro. Secondly, no enzyme analogous to the vertebrate polymerase-beta has yet been found in such organisms, and thirdly, many of these enzymes possess associated exonuclease activities like those of the bacterial DNA polymerases. On the basis of these findings, some tentative proposals are made about the evolution of DNA polymerases.

  1. Sustained Small Molecule Delivery from Injectable Hyaluronic Acid Hydrogels through Host-Guest Mediated Retention

    PubMed Central

    Mealy, Joshua E.; Rodell, Christopher B.; Burdick, Jason A.

    2015-01-01

    Self-assembled and injectable hydrogels have many beneficial properties for the local delivery of therapeutics; however, challenges still exist in the sustained release of small molecules from these highly hydrated networks. Host-guest chemistry between cyclodextrin and adamantane has been used to create supramolecular hydrogels from modified polymers. Beyond assembly, this chemistry may also provide increased drug retention and sustained release through the formation of inclusion complexes between drugs and cyclodextrin. Here, we engineered a two-component system from adamantane-modified and β-cyclodextrin (CD)-modified hyaluronic acid (HA), a natural component of the extracellular matrix, to produce hydrogels that are both injectable and able to sustain the release of small molecules. The conjugation of cyclodextrin to HA dramatically altered its affinity for hydrophobic small molecules, such as tryptophan. This interaction led to lower molecule diffusivity and the release of small molecules for up to 21 days with release profiles dependent on CD concentration and drug-CD affinity. There was significant attenuation of release from the supramolecular hydrogels (~20% release in 24h) when compared to hydrogels without CD (~90% release in 24h). The loading of small molecules also had no effect on hydrogel mechanics or self-assembly properties. Finally, to illustrate this controlled delivery approach with clinically used small molecule pharmaceuticals, we sustained the release of two widely used drugs (i.e., doxycycline and doxorubicin) from these hydrogels. PMID:26693019

  2. Single molecule DNA interaction kinetics of retroviral nucleic acid chaperone proteins

    NASA Astrophysics Data System (ADS)

    Williams, Mark

    2010-03-01

    Retroviral nucleocapsid (NC) proteins are essential for several viral replication processes including specific genomic RNA packaging and reverse transcription. The nucleic acid chaperone activity of NC facilitates the latter process. In this study, we use single molecule biophysical methods to quantify the DNA interactions of wild type and mutant human immunodeficiency virus type 1 (HIV-1) NC and Gag and human T-cell leukemia virus type 1 (HTLV-1) NC. We find that the nucleic acid interaction properties of these proteins differ significantly, with HIV-1 NC showing rapid protein binding kinetics, significant duplex destabilization, and strong DNA aggregation, all properties that are critical components of nucleic acid chaperone activity. In contrast, HTLV-1 NC exhibits significant destabilization activity but extremely slow DNA interaction kinetics and poor aggregating capability, which explains why HTLV-1 NC is a poor nucleic acid chaperone. To understand these results, we developed a new single molecule method for quantifying protein dissociation kinetics, and applied this method to probe the DNA interactions of wild type and mutant HIV-1 and HTLV-1 NC. We find that mutations to aromatic and charged residues strongly alter the proteins' nucleic acid interaction kinetics. Finally, in contrast to HIV-1 NC, HIV-1 Gag, the nucleic acid packaging protein that contains NC as a domain, exhibits relatively slow binding kinetics, which may negatively impact its ability to act as a nucleic acid chaperone.

  3. Investigation of pyridine carboxylic acids in CM2 carbonaceous chondrites: Potential precursor molecules for ancient coenzymes

    NASA Astrophysics Data System (ADS)

    Smith, Karen E.; Callahan, Michael P.; Gerakines, Perry A.; Dworkin, Jason P.; House, Christopher H.

    2014-07-01

    The distribution and abundances of pyridine carboxylic acids (including nicotinic acid) in eight CM2 carbonaceous chondrites (ALH 85013, DOM 03183, DOM 08003, EET 96016, LAP 02333, LAP 02336, LEW 85311, and WIS 91600) were investigated by liquid chromatography coupled to UV detection and high resolution Orbitrap mass spectrometry. We find that pyridine monocarboxylic acids are prevalent in CM2-type chondrites and their abundance negatively correlates with the degree of pre-terrestrial aqueous alteration that the meteorite parent body experienced. We also report the first detection of pyridine dicarboxylic acids in carbonaceous chondrites. Additionally, we carried out laboratory studies of proton-irradiated pyridine in carbon dioxide-rich ices (a 1:1 mixture) to serve as a model of the interstellar ice chemistry that may have led to the synthesis of pyridine carboxylic acids. Analysis of the irradiated ice residue shows that a comparable suite of pyridine mono- and dicarboxylic acids was produced, although aqueous alteration may still play a role in the synthesis (and ultimate yield) of these compounds in carbonaceous meteorites. Nicotinic acid is a precursor to nicotinamide adenine dinucleotide, a likely ancient molecule used in cellular metabolism in all of life, and its common occurrence in CM2 chondrites may indicate that meteorites may have been a source of molecules for the emergence of more complex coenzymes on the early Earth.

  4. Investigation of Pyridine Carboxylic Acids in CM2 Carbonaceous Chondrites: Potential Precursor Molecules for Ancient Coenzymes

    NASA Technical Reports Server (NTRS)

    Smith, Karen E.; Callahan, Michael P.; Gerakines, Perry A.; Dworkin, Jason P.; House, Christopher H.

    2014-01-01

    The distribution and abundances of pyridine carboxylic acids (including nicotinic acid) in eight CM2 carbonaceous chondrites (ALH 85013, DOM 03183, DOM 08003, EET 96016, LAP 02333, LAP 02336, LEW 85311, and WIS 91600) were investigated by liquid chromatography coupled to UV detection and high resolution Orbitrap mass spectrometry. We find that pyridine monocarboxylic acids are prevalent in CM2-type chondrites and their abundance negatively correlates with the degree of pre-terrestrial aqueous alteration that the meteorite parent body experienced. We lso report the first detection of pyridine dicarboxylic acids in carbonaceous chondrites. Additionally, we carried out laboratory studies of proton-irradiated pyridine in carbon dioxide-rich ices (a 1:1 mixture) to serve as a model of the interstellar ice chemistry that may have led to the synthesis of pyridine carboxylic acids. Analysis of the irradiated ice residue shows that a comparable suite of pyridine mono- and dicarboxylic acids was produced, although aqueous alteration may still play a role in the synthesis (and ultimate yield) of these compounds in carbonaceous meteorites. Nicotinic acid is a precursor to nicotinamide adenine dinucleotide, a likely ancient molecule used in cellular metabolism in all of life, and its common occurrence in CM2 chondrites may indicate that meteorites may have been a source of molecules for the emergence of more complex coenzymes on the early Earth.

  5. Investigation of Pyridine Carboxylic Acids in CM2 Carbonaceous Chondrites: Potential Precursor Molecules for Ancient Coenzymes

    NASA Technical Reports Server (NTRS)

    Smith, Karen E.; Callahan, Michael P.; Gerakines, Perry A.; Dworkin, Jason P.; House, Christopher H.

    2014-01-01

    The distribution and abundances of pyridine carboxylic acids (including nicotinic acid) in eight CM2 carbonaceous chondrites (ALH 85013, DOM 03183, DOM 08003, EET 96016, LAP 02333, LAP 02336, LEW 85311, and WIS 91600) were investigated by liquid chromatography coupled to UV detection and high resolution Orbitrap mass spectrometry. We find that pyridine monocarboxylic acids are prevalent in CM2-type chondrites and their abundance negatively correlates with the degree of pre-terrestrial aqueous alteration that the meteorite parent body experienced. We also report the first detection of pyridine dicarboxylic acids in carbonaceous chondrites. Additionally, we carried out laboratory studies of proton-irradiated pyridine in carbon dioxide-rich ices (a 1:1 mixture) to serve as a model of the interstellar ice chemistry that may have led to the synthesis of pyridine carboxylic acids. Analysis of the irradiated ice residue shows that a comparable suite of pyridine mono- and dicarboxylic acids was produced, although aqueous alteration may still play a role in the synthesis (and ultimate yield) of these compounds in carbonaceous meteorites. Nicotinic acid is a precursor to nicotinamide adenine dinucleotide, a likely ancient molecule used in cellular metabolism in all of life, and its common occurrence in CM2 chondrites may indicate that meteorites may have been a source of molecules for the emergence of more complex coenzymes on the early Earth.

  6. The activity of deoxyribonucleic acid polymerase and deoxyribonucleic acid synthesis in nuclei from brain fractionated by zonal centrifugation

    PubMed Central

    Stambolova, M. A.; Cox, D.; Mathias, A. P.

    1973-01-01

    1. The DNA polymerase (EC 2.7.7.7) activity in purified intact brain nuclei from infant rats was investigated. The effects of pH, Mg2+, glycerol, sonication and storage of the nuclei under different conditions were examined and a suitable assay system was established. 2. The nuclei from infant brain cells were fractionated by zonal centrifugation in a discontinuous sucrose gradient into five zones: zone (I) contained neuronal nuclei (59%) and astrocytic nuclei (41%); zone (II) contained astrocytic nuclei (81%) and neuronal nuclei (19%); zone (III) contained astrocytic nuclei (82%) and oligodendrocytic nuclei (18%); zone (IV) contained oligodendrocytic nuclei (92%) and zone (V) contained oligodendrocytic nuclei (100%). 3. The content of DNA, RNA and protein for each fraction was measured. 4. The distribution of DNA polymerase activity in the fractionated infant and adult rat brain nuclei was determined. The highest activity was found in the neuronal nuclei from zone (I) and the following zones exhibited a progressive decline. In contrast with the nuclei from infant rats those from adults had a much higher activity and expressed a preference for native DNA as template. 5. The deoxyribonuclease activity in all classes of nuclei was measured with [3H]DNA as substrate. A general correspondence in the pattern of the relative activities in the nuclear fractions with the distribution of DNA polymerase was found. 6. The incorporation of [3H]thymidine into nuclear DNA in infant and adult rat brain was investigated. The specific radioactivity of the DNA in the 10-day-old rats was highest in zone (V) whereas in the nuclei of adult rats, which exhibited a comparatively low incorporation, the highest specific radioactivity was associated with zones (I) and (V). PMID:4780694

  7. Characterization of deoxyribonucleic Acid species from castor bean endosperm: inability to detect a unique deoxyribonucleic Acid species associated with glyoxysomes.

    PubMed

    Douglass, S A; Criddle, R S; Breidenbach, R W

    1973-05-01

    Three DNA buoyant density species (nuclear, 1.692 g cm(-3); mitochondria 1.705 g cm(-3); and proplastid, 1.713 g cm(-3)) can be detected in extracts from castor bean endosperm. No other buoyant density species can be identified. DNA extracts from sucrose density gradient purified glyoxysomes exhibit varying amounts of each of the three identified DNAs but no other distinguishable DNA species. RNA synthesized in vitro by Escherichia coli RNA polymerase using purified castor bean nuclear DNA as a template, hybridizes equally well with its template and with the 1.692 g cm(-3) species from glyoxysome fractions. These results are discussed in terms of their relevance to microbody biogenesis.

  8. L-Ascorbic Acid: A Multifunctional Molecule Supporting Plant Growth and Development

    PubMed Central

    Gallie, Daniel R.

    2013-01-01

    L-Ascorbic acid (vitamin C) is as essential to plants as it is to animals. Ascorbic acid functions as a major redox buffer and as a cofactor for enzymes involved in regulating photosynthesis, hormone biosynthesis, and regenerating other antioxidants. Ascorbic acid regulates cell division and growth and is involved in signal transduction. In contrast to the single pathway responsible for ascorbic acid biosynthesis in animals, plants use multiple pathways to synthesize ascorbic acid, perhaps reflecting the importance of this molecule to plant health. Given the importance of ascorbic acid to human nutrition, several technologies have been developed to increase the ascorbic acid content of plants through the manipulation of biosynthetic or recycling pathways. This paper provides an overview of these approaches as well as the consequences that changes in ascorbic acid content have on plant growth and function. Discussed is the capacity of plants to tolerate changes in ascorbic acid content. The many functions that ascorbic acid serves in plants, however, will require highly targeted approaches to improve their nutritional quality without compromising their health. PMID:24278786

  9. Conformational dynamics of nucleic acid molecules studied by PELDOR spectroscopy with rigid spin labels

    NASA Astrophysics Data System (ADS)

    Prisner, T. F.; Marko, A.; Sigurdsson, S. Th.

    2015-03-01

    Nucleic acid molecules can adopt a variety of structures and exhibit a large degree of conformational flexibility to fulfill their various functions in cells. Here we describe the use of Pulsed Electron-Electron Double Resonance (PELDOR or DEER) to investigate nucleic acid molecules where two cytosine analogs have been incorporated as spin probes. Because these new types of spin labels are rigid and incorporated into double stranded DNA and RNA molecules, there is no additional flexibility of the spin label itself present. Therefore the magnetic dipole-dipole interaction between both spin labels encodes for the distance as well as for the mutual orientation between the spin labels. All of this information can be extracted by multi-frequency/multi-field PELDOR experiments, which gives very precise and valuable information about the structure and conformational flexibility of the nucleic acid molecules. We describe in detail our procedure to obtain the conformational ensembles and show the accuracy and limitations with test examples and application to double-stranded DNA.

  10. Small molecule- and amino acid-induced aggregation of gold nanoparticles.

    PubMed

    Zakaria, Hesham M; Shah, Akash; Konieczny, Michael; Hoffmann, Joan A; Nijdam, A Jasper; Reeves, M E

    2013-06-25

    To understand which organic molecules are capable of binding to gold nanoparticles and/or inducing nanoparticle aggregation, we investigate the interaction of gold nanoparticles with small molecules and amino acids at variable pH. Dynamic Light Scattering (DLS) and ultraviolet-visible (UV-vis) spectra were measured on mixtures of colloidal gold with small molecules to track the progression of the aggregation of gold nanoparticles. We introduce the 522 to 435 nm UV-vis absorbance ratio as a sensitive method for the detection of colloidal gold aggregation, whereby we delineate the ability of thiol, amine, and carboxylic acid functional groups to bind to the surfaces of gold nanoparticles and investigate how combinations of these functional groups affect colloidal stability. We present models for mechanisms of aggregation of colloidal gold, including surface charge reduction and bridging linkers. For all molecules whose addition leads to the aggregation of gold nanoparticles, the aggregation kinetics were accelerated at acidic pH values. Colloidal gold is maintained only in the presence of anionic carboxyl groups, which are neutralized by protonation at lower pH. The overall reduced charge on the stabilizing carboxyl groups accounts for the accelerated aggregation at lower pH values. PMID:23718319

  11. On the influence of low-energy ionizing radiation on the amino acid molecule: proline

    NASA Astrophysics Data System (ADS)

    Tamuliene, Jelena; Romanova, Liudmila; Vukstich, Vasyl; Papp, Alexander; Shkurin, Serhiy; Baliulyte, Laura; Snegursky, Alexander

    2016-06-01

    New data on the electron-impact fragmentation of the amino acid proline molecule are presented as being related to the formation of the ionized products due to the influence of low-energy ionizing radiation on the above molecule. An extensive DFT-theory based on the theoretical approach enabled the main pathways of the proline molecules fragmentation to be elucidated. A series of the produced fragments have been identified. The absolute appearance energies for some of them have been both measured experimentally and calculated theoretically. The data of the experimental studies and theoretical calculations are compared and analyzed. Contribution to the Topical Issue "Low-Energy Interactions related to Atmospheric and Extreme Conditions", edited by S. Ptasinska, M. Smialek-Telega, A. Milosavljevic, B. Sivaraman.

  12. Sequential photochemical and microbial degradation of organic molecules bound to humic acid

    SciTech Connect

    Amador, J.A.; Zika, R.G. ); Alexander, M. )

    1989-11-01

    We studied the effects of photochemical processes on the mineralization by soil microorganisms of (2-{sup 14}C)glycine bound to soil humic acid. Microbial mineralization of these complexes in the dark increased inversely with the molecular weight of the complex molecules. Sunlight irradiation of glycine-humic acid complexes resulted in loss of absorbance in the UV range and an increase in the amount of {sup 14}C-labeled low-molecular-weight photoproducts and the rate and extent of mineralization. More than half of the radioactivity in the low-molecular-weight photoproducts appears to be associated with carboxylic acids. Microbial mineralization of the organic carbon increased with solar flux and was proportional to the loss of A{sub 330}. Mineralization was proportional to the percentage of the original complex that was converted to low-molecular-weight photoproducts. Only light at wavelengths below 380 nm had an effect on the molecular weight distribution of the products formed from the glycine-humic acid complexes and on the subsequent microbial mineralization. Our results indicate that photochemical processes generate low-molecular-weight, readily biodegradable molecules from high-molecular-weight complexes of glycine with humic acid.

  13. Sequential photochemical and microbial degradation of organic molecules bound to humic Acid.

    PubMed

    Amador, J A; Alexander, M; Zika, R G

    1989-11-01

    We studied the effects of photochemical processes on the mineralization by soil microorganisms of [2-C]glycine bound to soil humic acid. Microbial mineralization of these complexes in the dark increased inversely with the molecular weight of the complex molecules. Sunlight irradiation of glycine-humic acid complexes resulted in loss of absorbance in the UV range and an increase in the amount of C-labeled low-molecular-weight photoproducts and the rate and extent of mineralization. More than half of the radioactivity in the low-molecular-weight photoproducts appears to be associated with carboxylic acids. Microbial mineralization of the organic carbon increased with solar flux and was proportional to the loss of A(330). Mineralization was proportional to the percentage of the original complex that was converted to low-molecular-weight photoproducts. Only light at wavelengths below 380 nm had an effect on the molecular weight distribution of the products formed from the glycine-humic acid complexes and on the subsequent microbial mineralization. Our results indicate that photochemical processes generate low-molecular-weight, readily biodegradable molecules from high-molecular-weight complexes of glycine with humic acid.

  14. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling

    NASA Astrophysics Data System (ADS)

    Zhao, Yanan; Ashcroft, Brian; Zhang, Peiming; Liu, Hao; Sen, Suman; Song, Weisi; Im, Jongone; Gyarfas, Brett; Manna, Saikat; Biswas, Sovan; Borges, Chad; Lindsay, Stuart

    2014-06-01

    The human proteome has millions of protein variants due to alternative RNA splicing and post-translational modifications, and variants that are related to diseases are frequently present in minute concentrations. For DNA and RNA, low concentrations can be amplified using the polymerase chain reaction, but there is no such reaction for proteins. Therefore, the development of single-molecule protein sequencing is a critical step in the search for protein biomarkers. Here, we show that single amino acids can be identified by trapping the molecules between two electrodes that are coated with a layer of recognition molecules, then measuring the electron tunnelling current across the junction. A given molecule can bind in more than one way in the junction, and we therefore use a machine-learning algorithm to distinguish between the sets of electronic `fingerprints' associated with each binding motif. With this recognition tunnelling technique, we are able to identify D and L enantiomers, a methylated amino acid, isobaric isomers and short peptides. The results suggest that direct electronic sequencing of single proteins could be possible by sequentially measuring the products of processive exopeptidase digestion, or by using a molecular motor to pull proteins through a tunnel junction integrated with a nanopore.

  15. Difficulties in Laboratory Studies and Astronomical Observations of Organic Molecules: Hydroxyacetone and Lactic Acid

    NASA Technical Reports Server (NTRS)

    Apponi, A. J.; Brewster, M. A.; Hoy, J.; Ziurys, L. M.

    2006-01-01

    For the past 35 years, radio astronomy has revealed a rich organic chemistry in the interstellar gas, which is exceptionally complex towards active star-forming regions. New solar systems condense out of this gas and may influence the evolution of life on newly formed planets. Much of the biologically important functionality is present among the some 130 gas-phase molecules found to date, including alcohols, aldehydes, ketones, acids, amines, amides and even the simplest sugar - glycolaldehyde. Still, many unidentified interstellar radio signals remain, and their identification relies on further laboratory study. The molecules hydroxyacetone and lactic acid are relatively small organic molecules, but possess rather complex rotational spectra owing to their high asymmetry. Hydroxyacetone is particularly problematic because it possess a very low barrier to internal rotation, and exhibits strong coupling of the free-rotor states with the overall rotation of the molecule. As in the case of acetamide, a full decomposition method was employed to order the resultant eigenstates onto normal asymmetric top eigenvectors.

  16. Nucleic acid molecules conferring enhanced ethanol tolerance and microorganisms having enhanced tolerance to ethanol

    SciTech Connect

    Brown, Steven; Guss, Adam; Yang, Shihui; Karpinets, Tatiana; Lynd, Lee; Shao, Xiongjun

    2014-01-14

    The present invention provides isolated nucleic acid molecules which encode a mutant acetaldehyde-CoA/alcohol dehydrogenase or mutant alcohol dehydrogenase and confer enhanced tolerance to ethanol. The invention also provides related expression vectors, genetically engineered microorganisms having enhanced tolerance to ethanol, as well as methods of making and using such genetically modified microorganisms for production of biofuels based on fermentation of biomass materials.

  17. Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants.

    PubMed

    Kelly, Casey P; Cramer, Christopher J; Truhlar, Donald G

    2006-02-23

    Aqueous acid dissociation free energies for a diverse set of 57 monoprotic acids have been calculated using a combination of experimental and calculated gas and liquid-phase free energies. For ionic species, aqueous solvation free energies were calculated using the recently developed SM6 continuum solvation model. This model combines a dielectric continuum with atomic surface tensions to account for bulk solvent effects. For some of the acids studied, a combined approach that involves attaching a single explicit water molecule to the conjugate base (anion), and then surrounding the resulting anion-water cluster by a dielectric continuum, significantly improves the agreement between the calculated pK(a) value and experiment. This suggests that for some anions, particularly those concentrating charge on a single exposed heteroatom, augmenting implicit solvent calculations with a single explicit water molecule is required, and adequate, to account for strong short-range hydrogen bonding interactions between the anion and the solvent. We also demonstrate the effect of adding several explicit waters by calculating the pK(a) of bicarbonate (HCO(3)(-)) using as the conjugate base carbonate (CO(3)(2-)) bound by up to three explicit water molecules.

  18. Investigating organic molecules responsible of auxin-like activity of humic acid fraction extracted from vermicompost.

    PubMed

    Scaglia, Barbara; Nunes, Ramom Rachide; Rezende, Maria Olímpia Oliveira; Tambone, Fulvia; Adani, Fabrizio

    2016-08-15

    This work studied the auxin-like activity of humic acids (HA) obtained from vermicomposts produced using leather wastes plus cattle dung at different maturation stages (fresh, stable and mature). Bioassays were performed by testing HA concentrations in the range of 100-6000mgcarbonL(-1). (13)C CPMAS-NMR and GC-MS instrumental methods were used to assess the effect of biological processes and starting organic mixtures on HA composition. Not all HAs showed IAA-like activity and in general, IAA-like activity increased with the length of the vermicomposting process. The presence of leather wastes was not necessary to produce the auxin-like activity of HA, since HA extracted from a mix of cattle manure and sawdust, where no leather waste was added, showed IAA-like activity as well. CPMAS (13)CNMR revealed that HAs were similar independently of the mix used and that the humification process involved the increasing concentration of pre-existing alkali soluble fractions in the biomass. GC/MS allowed the identification of the molecules involved in IAA-like effects: carboxylic acids and amino acids. The concentration of active molecules, rather than their simple presence in HA, determined the bio-stimulating effect, and a good linear regression between auxin-like activity and active stimulating molecules concentration was found (R(2)=-0.85; p<0.01, n=6). PMID:27100009

  19. Investigating organic molecules responsible of auxin-like activity of humic acid fraction extracted from vermicompost.

    PubMed

    Scaglia, Barbara; Nunes, Ramom Rachide; Rezende, Maria Olímpia Oliveira; Tambone, Fulvia; Adani, Fabrizio

    2016-08-15

    This work studied the auxin-like activity of humic acids (HA) obtained from vermicomposts produced using leather wastes plus cattle dung at different maturation stages (fresh, stable and mature). Bioassays were performed by testing HA concentrations in the range of 100-6000mgcarbonL(-1). (13)C CPMAS-NMR and GC-MS instrumental methods were used to assess the effect of biological processes and starting organic mixtures on HA composition. Not all HAs showed IAA-like activity and in general, IAA-like activity increased with the length of the vermicomposting process. The presence of leather wastes was not necessary to produce the auxin-like activity of HA, since HA extracted from a mix of cattle manure and sawdust, where no leather waste was added, showed IAA-like activity as well. CPMAS (13)CNMR revealed that HAs were similar independently of the mix used and that the humification process involved the increasing concentration of pre-existing alkali soluble fractions in the biomass. GC/MS allowed the identification of the molecules involved in IAA-like effects: carboxylic acids and amino acids. The concentration of active molecules, rather than their simple presence in HA, determined the bio-stimulating effect, and a good linear regression between auxin-like activity and active stimulating molecules concentration was found (R(2)=-0.85; p<0.01, n=6).

  20. Mycosporine-like amino acids are multifunctional molecules in sea hares and their marine community.

    PubMed

    Kicklighter, Cynthia E; Kamio, Michiya; Nguyen, Linh; Germann, Markus W; Derby, Charles D

    2011-07-12

    Molecules of keystone significance are relatively rare, yet mediate a variety of interactions between organisms. They influence the distribution and abundance of species, the transfer of energy across multiple trophic levels, and thus they play significant roles in structuring ecosystems. Despite their potential importance in facilitating our understanding of ecological systems, only three molecules thus far have been proposed as molecules of keystone significance: saxitoxin and dimethyl sulfide in marine communities and tetrodotoxin in riparian communities. In the course of studying the neuroecology of chemical defenses, we identified three mycosporine-like amino acids (MAAs)--N-ethanol palythine (= asterina-330), N-isopropanol palythine (= aplysiapalythine A), and N-ethyl palythine (= aplysiapalythine B)--as intraspecific alarm cues for sea hares (Aplysia californica). These alarm cues are released in the ink secretion of sea hares and cause avoidance behaviors in neighboring conspecifics. Further, we show that these three bioactive MAAs, two [aplysiapalythine A (APA) and -B (APB)] being previously unknown molecules, are present in the algal diet of sea hares and are concentrated in their defensive secretion as well as in their skin. MAAs are known to be produced by algae, fungi, and cyanobacteria and are acquired by many aquatic animals through trophic interactions. MAAs are widely used as sunscreens, among other uses, but sea hares modify their function to serve a previously undocumented role, as intraspecific chemical cues. Our findings highlight the multifunctionality of MAAs and their role in ecological connectivity, suggesting that they may function as molecules of keystone significance in marine ecosystems.

  1. Scanning Tunneling Microscopy Observations of Benzoic Acid Molecules Coadsorbed with Single-Walled Carbon Nanotubes on Au(111) surface

    NASA Astrophysics Data System (ADS)

    Rabot, Caroline; Clair, Sylvain; Kim, Yousoo; Kawai, Maki

    2007-08-01

    We investigated the interaction of single-walled carbon nanotubes (SWCNTs) with benzoic acid molecules coadsorbed on a Au(111) surface by scanning tunneling microscopy (STM). We studied the self-assembly of the benzoic acid overlayer on Au(111) terraces and along Au(111) step edges and compared the structure of this layer with the benzoic acid molecular structure along SWCNTs.

  2. A Small Molecule Inhibits Virion Attachment to Heparan Sulfate- or Sialic Acid-Containing Glycans

    PubMed Central

    Colpitts, Che C.

    2014-01-01

    ABSTRACT Primary attachment to cellular glycans is a critical entry step for most human viruses. Some viruses, such as herpes simplex virus type 1 (HSV-1) and hepatitis C virus (HCV), bind to heparan sulfate, whereas others, such as influenza A virus (IAV), bind to sialic acid. Receptor mimetics that interfere with these interactions are active against viruses that bind to either heparan sulfate or to sialic acid. However, no molecule that inhibits the attachment of viruses in both groups has yet been identified. Epigallocatechin gallate (EGCG), a green tea catechin, is active against many unrelated viruses, including several that bind to heparan sulfate or to sialic acid. We sought to identify the basis for the broad-spectrum activity of EGCG. Here, we show that EGCG inhibits the infectivity of a diverse group of enveloped and nonenveloped human viruses. EGCG acts directly on the virions, without affecting the fluidity or integrity of the virion envelopes. Instead, EGCG interacts with virion surface proteins to inhibit the attachment of HSV-1, HCV, IAV, vaccinia virus, adenovirus, reovirus, and vesicular stomatitis virus (VSV) virions. We further show that EGCG competes with heparan sulfate for binding of HSV-1 and HCV virions and with sialic acid for binding of IAV virions. Therefore, EGCG inhibits unrelated viruses by a common mechanism. Most importantly, we have identified EGCG as the first broad-spectrum attachment inhibitor. Our results open the possibility for the development of small molecule broad-spectrum antivirals targeting virion attachment. IMPORTANCE This study shows that it is possible to develop a small molecule antiviral or microbicide active against the two largest groups of human viruses: those that bind to glycosaminoglycans and those that bind to sialoglycans. This group includes the vast majority of human viruses, including herpes simplex viruses, cytomegalovirus, influenza virus, poxvirus, hepatitis C virus, HIV, and many others. PMID

  3. Intracellular delivery of peptide nucleic acid and organic molecules using zeolite-L nanocrystals.

    PubMed

    Bertucci, Alessandro; Lülf, Henning; Septiadi, Dedy; Manicardi, Alex; Corradini, Roberto; De Cola, Luisa

    2014-11-01

    The design and synthesis of smart nanomaterials can provide interesting potential applications for biomedical purposes from bioimaging to drug delivery. Manufacturing multifunctional systems in a way to carry bioactive molecules, like peptide nucleic acids able to recognize specific targets in living cells, represents an achievement towards the development of highly selective tools for both diagnosis and therapeutics. This work describes a very first example of the use of zeolite nanocrystals as multifunctional nanocarriers to deliver simultaneously PNA and organic molecules into living cells. Zeolite-L nanocrystals are functionalized by covalently attaching the PNA probes onto the surface, while the channel system is filled with fluorescent guest molecules. The cellular uptake of the PNA/Zeolite-L hybrid material is then significantly increased by coating the whole system with a thin layer of biodegradable poly-L-lysine. The delivery of DAPI as a model drug molecule, inserted into the zeolite pores, is also demonstrated to occur in the cells, proving the multifunctional ability of the system. Using this zeolite nanosystem carrying PNA probes designed to target specific RNA sequences of interest in living cells could open new possibilities for theranostic and gene therapy applications. PMID:24789252

  4. Intracellular delivery of peptide nucleic acid and organic molecules using zeolite-L nanocrystals.

    PubMed

    Bertucci, Alessandro; Lülf, Henning; Septiadi, Dedy; Manicardi, Alex; Corradini, Roberto; De Cola, Luisa

    2014-11-01

    The design and synthesis of smart nanomaterials can provide interesting potential applications for biomedical purposes from bioimaging to drug delivery. Manufacturing multifunctional systems in a way to carry bioactive molecules, like peptide nucleic acids able to recognize specific targets in living cells, represents an achievement towards the development of highly selective tools for both diagnosis and therapeutics. This work describes a very first example of the use of zeolite nanocrystals as multifunctional nanocarriers to deliver simultaneously PNA and organic molecules into living cells. Zeolite-L nanocrystals are functionalized by covalently attaching the PNA probes onto the surface, while the channel system is filled with fluorescent guest molecules. The cellular uptake of the PNA/Zeolite-L hybrid material is then significantly increased by coating the whole system with a thin layer of biodegradable poly-L-lysine. The delivery of DAPI as a model drug molecule, inserted into the zeolite pores, is also demonstrated to occur in the cells, proving the multifunctional ability of the system. Using this zeolite nanosystem carrying PNA probes designed to target specific RNA sequences of interest in living cells could open new possibilities for theranostic and gene therapy applications.

  5. Acceleration of suspending single-walled carbon nanotubes in BSA aqueous solution induced by amino acid molecules.

    PubMed

    Kato, Haruhisa; Nakamura, Ayako; Horie, Masanori

    2015-01-01

    Single-walled carbon nanotube (SWCNT) suspensions in aqueous media were prepared using bovine serum albumin (BSA) and amino acid molecules. It was found that the amino acid molecules clearly decreased the time required for suspending the SWCNTs in BSA aqueous solutions. Dynamic light scattering measurements revealed that the particle sizes of the SWCNTs suspended in aqueous media with and without amino acid molecules were approximately the same and stable for more than one week. The zeta potential values of the BSA molecules in pure water and amino acid aqueous solutions were different, and these values were also reflected in the surface potential of colloidal SWCNT particles in the corresponding aqueous media, thus inducing different dispersibility of SWCNTs in aqueous media. Pulsed field gradient nuclear magnetic resonance measurements showed that the interactions between the SWCNTs and the amino acid molecules are weak and comprise chemical exchange interactions and not bonding interactions. Amino acid molecules play a fascinating role in the preparation of SWCNT suspensions in BSA aqueous media by increasing electrostatic repulsive interactions between SWCNT colloidal particles and consequently enhancing the dispersion ability of the BSA molecules.

  6. Controlled synthesis and inclusion ability of a hyaluronic acid derivative bearing beta-cyclodextrin molecules.

    PubMed

    Charlot, Aurélia; Heyraud, Alain; Guenot, Pierre; Rinaudo, Marguerite; Auzély-Velty, Rachel

    2006-03-01

    A new synthetic route to beta-cyclodextrin-linked hyaluronic acid (HA-CD) was developed. This was based on the preparation of a HA derivative selectively modified with adipic dihydrazide (HA-ADH) and a beta-cyclodextrin derivative possessing an aldehyde function on the primary face, followed by their coupling by a reductive amination-type reaction. The CD-polysaccharide was fully characterized in terms of chemical integrity and purity by high-resolution NMR spectroscopy. The complexation ability of the grafted CD was further demonstrated by isothermal titration calorimetry using sodium adamantane acetate (ADAc) and Ibuprofen as model guest molecules. The thermodynamic parameters for the complexation of these negatively charged guest molecules by the beta-CD grafted on negatively charged HA were shown to be largely influenced by the ionic strength of the aqueous medium. PMID:16529430

  7. An acidic microenvironment sets the humoral pattern recognition molecule PTX3 in a tissue repair mode.

    PubMed

    Doni, Andrea; Musso, Tiziana; Morone, Diego; Bastone, Antonio; Zambelli, Vanessa; Sironi, Marina; Castagnoli, Carlotta; Cambieri, Irene; Stravalaci, Matteo; Pasqualini, Fabio; Laface, Ilaria; Valentino, Sonia; Tartari, Silvia; Ponzetta, Andrea; Maina, Virginia; Barbieri, Silvia S; Tremoli, Elena; Catapano, Alberico L; Norata, Giuseppe D; Bottazzi, Barbara; Garlanda, Cecilia; Mantovani, Alberto

    2015-06-01

    Pentraxin 3 (PTX3) is a fluid-phase pattern recognition molecule and a key component of the humoral arm of innate immunity. In four different models of tissue damage in mice, PTX3 deficiency was associated with increased fibrin deposition and persistence, and thicker clots, followed by increased collagen deposition, when compared with controls. Ptx3-deficient macrophages showed defective pericellular fibrinolysis in vitro. PTX3-bound fibrinogen/fibrin and plasminogen at acidic pH and increased plasmin-mediated fibrinolysis. The second exon-encoded N-terminal domain of PTX3 recapitulated the activity of the intact molecule. Thus, a prototypic component of humoral innate immunity, PTX3, plays a nonredundant role in the orchestration of tissue repair and remodeling. Tissue acidification resulting from metabolic adaptation during tissue repair sets PTX3 in a tissue remodeling and repair mode, suggesting that matrix and microbial recognition are common, ancestral features of the humoral arm of innate immunity. PMID:25964372

  8. An acidic microenvironment sets the humoral pattern recognition molecule PTX3 in a tissue repair mode

    PubMed Central

    Doni, Andrea; Musso, Tiziana; Morone, Diego; Bastone, Antonio; Zambelli, Vanessa; Sironi, Marina; Castagnoli, Carlotta; Cambieri, Irene; Stravalaci, Matteo; Pasqualini, Fabio; Laface, Ilaria; Valentino, Sonia; Tartari, Silvia; Ponzetta, Andrea; Maina, Virginia; Barbieri, Silvia S.; Tremoli, Elena; Catapano, Alberico L.; Norata, Giuseppe D.; Bottazzi, Barbara; Garlanda, Cecilia

    2015-01-01

    Pentraxin 3 (PTX3) is a fluid-phase pattern recognition molecule and a key component of the humoral arm of innate immunity. In four different models of tissue damage in mice, PTX3 deficiency was associated with increased fibrin deposition and persistence, and thicker clots, followed by increased collagen deposition, when compared with controls. Ptx3-deficient macrophages showed defective pericellular fibrinolysis in vitro. PTX3-bound fibrinogen/fibrin and plasminogen at acidic pH and increased plasmin-mediated fibrinolysis. The second exon-encoded N-terminal domain of PTX3 recapitulated the activity of the intact molecule. Thus, a prototypic component of humoral innate immunity, PTX3, plays a nonredundant role in the orchestration of tissue repair and remodeling. Tissue acidification resulting from metabolic adaptation during tissue repair sets PTX3 in a tissue remodeling and repair mode, suggesting that matrix and microbial recognition are common, ancestral features of the humoral arm of innate immunity. PMID:25964372

  9. Molecular understanding of atmospheric particle formation from sulfuric acid and large oxidized organic molecules.

    PubMed

    Schobesberger, Siegfried; Junninen, Heikki; Bianchi, Federico; Lönn, Gustaf; Ehn, Mikael; Lehtipalo, Katrianne; Dommen, Josef; Ehrhart, Sebastian; Ortega, Ismael K; Franchin, Alessandro; Nieminen, Tuomo; Riccobono, Francesco; Hutterli, Manuel; Duplissy, Jonathan; Almeida, João; Amorim, Antonio; Breitenlechner, Martin; Downard, Andrew J; Dunne, Eimear M; Flagan, Richard C; Kajos, Maija; Keskinen, Helmi; Kirkby, Jasper; Kupc, Agnieszka; Kürten, Andreas; Kurtén, Theo; Laaksonen, Ari; Mathot, Serge; Onnela, Antti; Praplan, Arnaud P; Rondo, Linda; Santos, Filipe D; Schallhart, Simon; Schnitzhofer, Ralf; Sipilä, Mikko; Tomé, António; Tsagkogeorgas, Georgios; Vehkamäki, Hanna; Wimmer, Daniela; Baltensperger, Urs; Carslaw, Kenneth S; Curtius, Joachim; Hansel, Armin; Petäjä, Tuukka; Kulmala, Markku; Donahue, Neil M; Worsnop, Douglas R

    2013-10-22

    Atmospheric aerosols formed by nucleation of vapors affect radiative forcing and therefore climate. However, the underlying mechanisms of nucleation remain unclear, particularly the involvement of organic compounds. Here, we present high-resolution mass spectra of ion clusters observed during new particle formation experiments performed at the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Research. The experiments involved sulfuric acid vapor and different stabilizing species, including ammonia and dimethylamine, as well as oxidation products of pinanediol, a surrogate for organic vapors formed from monoterpenes. A striking resemblance is revealed between the mass spectra from the chamber experiments with oxidized organics and ambient data obtained during new particle formation events at the Hyytiälä boreal forest research station. We observe that large oxidized organic compounds, arising from the oxidation of monoterpenes, cluster directly with single sulfuric acid molecules and then form growing clusters of one to three sulfuric acid molecules plus one to four oxidized organics. Most of these organic compounds retain 10 carbon atoms, and some of them are remarkably highly oxidized (oxygen-to-carbon ratios up to 1.2). The average degree of oxygenation of the organic compounds decreases while the clusters are growing. Our measurements therefore connect oxidized organics directly, and in detail, with the very first steps of new particle formation and their growth between 1 and 2 nm in a controlled environment. Thus, they confirm that oxidized organics are involved in both the formation and growth of particles under ambient conditions.

  10. Amino acid-bile acid based molecules: extremely narrow surfactant nanotubes formed by a phenylalanine-substituted cholic acid.

    PubMed

    Travaglini, Leana; D'Annibale, Andrea; Schillén, Karin; Olsson, Ulf; Sennato, Simona; Pavel, Nicolae V; Galantini, Luciano

    2012-12-21

    An amino acid-substituted bile acid forms tubular aggregates with inner and outer diameters of about 3 and 6 nm. The diameters are unusually small for surfactant self-assembled tubes. The results enhance the spectrum of applications of supramolecular tubules and open up possibilities for investigating a novel class of biological amphiphiles.

  11. Nucleation of Mixed Nitric Acid-Water Ice Nanoparticles in Molecular Beams that Starts with a HNO3 Molecule.

    PubMed

    Lengyel, Jozef; Pysanenko, Andriy; Kočišek, Jaroslav; Poterya, Viktoriya; Pradzynski, Christoph C; Zeuch, Thomas; Slavíček, Petr; Fárník, Michal

    2012-11-01

    Mixed (HNO3)m(H2O)n clusters generated in supersonic expansion of nitric acid vapor are investigated in two different experiments, (1) time-of-flight mass spectrometry after electron ionization and (2) Na doping and photoionization. This combination of complementary methods reveals that only clusters containing at least one acid molecule are generated, that is, the acid molecule serves as the nucleation center in the expansion. The experiments also suggest that at least four water molecules are needed for HNO3 acidic dissociation. The clusters are undoubtedly generated, as proved by electron ionization; however, they are not detected by the Na doping due to a fast charge-transfer reaction between the Na atom and HNO3. This points to limitations of the Na doping recently advocated as a general method for atmospheric aerosol detection. On the other hand, the combination of the two methods introduces a tool for detecting molecules with sizable electron affinity in clusters.

  12. Elastic Properties of Nucleic Acids by Single-Molecule Force Spectroscopy.

    PubMed

    Camunas-Soler, Joan; Ribezzi-Crivellari, Marco; Ritort, Felix

    2016-07-01

    We review the current knowledge on the use of single-molecule force spectroscopy techniques to extrapolate the elastic properties of nucleic acids. We emphasize the lesser-known elastic properties of single-stranded DNA. We discuss the importance of accurately determining the elastic response in pulling experiments, and we review the simplest models used to rationalize the experimental data as well as the experimental approaches used to pull single-stranded DNA. Applications used to investigate DNA conformational transitions and secondary structure formation are also highlighted. Finally, we provide an overview of the effects of salt and temperature and briefly discuss the effects of contour length and sequence dependence. PMID:27145878

  13. Elastic Properties of Nucleic Acids by Single-Molecule Force Spectroscopy.

    PubMed

    Camunas-Soler, Joan; Ribezzi-Crivellari, Marco; Ritort, Felix

    2016-07-01

    We review the current knowledge on the use of single-molecule force spectroscopy techniques to extrapolate the elastic properties of nucleic acids. We emphasize the lesser-known elastic properties of single-stranded DNA. We discuss the importance of accurately determining the elastic response in pulling experiments, and we review the simplest models used to rationalize the experimental data as well as the experimental approaches used to pull single-stranded DNA. Applications used to investigate DNA conformational transitions and secondary structure formation are also highlighted. Finally, we provide an overview of the effects of salt and temperature and briefly discuss the effects of contour length and sequence dependence.

  14. 76 FR 72950 - Draft Guidance for Industry: Use of Nucleic Acid Tests on Pooled and Individual Samples From...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-28

    ... (HBV) deoxyribonucleic acid (DNA) and recommendations for product testing and disposition, donor...- licensed NAT to screen blood donors for HBV DNA. FDA is also providing these blood establishments...

  15. Polyuridylic Acid-directed Phenylalanine Incorporation in Minicell Extracts

    PubMed Central

    Fralick, J. A.; Fisher, W. D.; Adler, H. I.

    1969-01-01

    Cell-free extracts of miniature Escherichia coli cells deficient in deoxyribonucleic acid (DNA) and DNA-dependent ribonucleic acid polymerase have been shown to be capable of polyuridylic acid-directed [14C]phenylalanine incorporation. PMID:4897117

  16. Oxidative diversification of amino acids and peptides by small-molecule iron catalysis

    NASA Astrophysics Data System (ADS)

    Osberger, Thomas J.; Rogness, Donald C.; Kohrt, Jeffrey T.; Stepan, Antonia F.; White, M. Christina

    2016-09-01

    Secondary metabolites synthesized by non-ribosomal peptide synthetases display diverse and complex topologies and possess a range of biological activities. Much of this diversity derives from a synthetic strategy that entails pre- and post-assembly oxidation of both the chiral amino acid building blocks and the assembled peptide scaffolds. The vancomycin biosynthetic pathway is an excellent example of the range of oxidative transformations that can be performed by the iron-containing enzymes involved in its biosynthesis. However, because of the challenges associated with using such oxidative enzymes to carry out chemical transformations in vitro, chemical syntheses guided by these principles have not been fully realized in the laboratory. Here we report that two small-molecule iron catalysts are capable of facilitating the targeted C-H oxidative modification of amino acids and peptides with preservation of α-centre chirality. Oxidation of proline to 5-hydroxyproline furnishes a versatile intermediate that can be transformed to rigid arylated derivatives or flexible linear carboxylic acids, alcohols, olefins and amines in both monomer and peptide settings. The value of this C-H oxidation strategy is demonstrated in its capacity for generating diversity: four ‘chiral pool’ amino acids are transformed to twenty-one chiral unnatural amino acids representing seven distinct functional group arrays; late-stage C-H functionalizations of a single proline-containing tripeptide furnish eight tripeptides, each having different unnatural amino acids. Additionally, a macrocyclic peptide containing a proline turn element is transformed via late-stage C-H oxidation to one containing a linear unnatural amino acid.

  17. Oxidative diversification of amino acids and peptides by small-molecule iron catalysis

    NASA Astrophysics Data System (ADS)

    Osberger, Thomas J.; Rogness, Donald C.; Kohrt, Jeffrey T.; Stepan, Antonia F.; White, M. Christina

    2016-09-01

    Secondary metabolites synthesized by non-ribosomal peptide synthetases display diverse and complex topologies and possess a range of biological activities. Much of this diversity derives from a synthetic strategy that entails pre- and post-assembly oxidation of both the chiral amino acid building blocks and the assembled peptide scaffolds. The vancomycin biosynthetic pathway is an excellent example of the range of oxidative transformations that can be performed by the iron-containing enzymes involved in its biosynthesis. However, because of the challenges associated with using such oxidative enzymes to carry out chemical transformations in vitro, chemical syntheses guided by these principles have not been fully realized in the laboratory. Here we report that two small-molecule iron catalysts are capable of facilitating the targeted C–H oxidative modification of amino acids and peptides with preservation of α-centre chirality. Oxidation of proline to 5-hydroxyproline furnishes a versatile intermediate that can be transformed to rigid arylated derivatives or flexible linear carboxylic acids, alcohols, olefins and amines in both monomer and peptide settings. The value of this C–H oxidation strategy is demonstrated in its capacity for generating diversity: four ‘chiral pool’ amino acids are transformed to twenty-one chiral unnatural amino acids representing seven distinct functional group arrays; late-stage C–H functionalizations of a single proline-containing tripeptide furnish eight tripeptides, each having different unnatural amino acids. Additionally, a macrocyclic peptide containing a proline turn element is transformed via late-stage C–H oxidation to one containing a linear unnatural amino acid.

  18. Single-molecule characterization and engineering of the surfaces of nucleic acid sensors

    NASA Astrophysics Data System (ADS)

    Josephs, Eric Alan

    The advent of personalized medicine will require biosensors capable of reliably detecting small levels of disease biomarkers. In microarrays and sensors for nucleic acids, hybridization events between surface-tethered DNA probes and the nucleic acids of interest (targets) are transduced into a detectable signal. However, target-binding ultimately occurs as a result of molecular motions and interactions between the probe and target at the nanometer scale, and common characterization methods either lack the resolution to characterize the sensors at this scale or provide only limited information about their interactions with their nanoscale chemical environment. In this dissertation I argue that an impediment to the development of more reliable and practical biosensors is the lack of knowledge and control of the nanometer length-scale structure of biosensor surfaces, which has a profound impact on molecular recognition and reactions for detection. After reviewing the fundamental surface chemistry and structural motifs of biosensors in Chapter 1, in Chapter 2 I use electrochemical atomic force microscopy (EC-AFM) to characterize in situ a common class of model nucleic acid sensors---thiolated DNA attached to a gold electrode which has been passivated by an alkanethiol self-assembled monolayer---with single-molecule resolution. This level of detail allows me to observe both the conformations of individual probes and their spatial distribution at the nanoscale, then determine how these are affected by assembly conditions, probe structure, and interactions with co-adsorbates. I also determine how these nanoscale details affect the dynamic response of probes to electric fields, which have been commonly used in sensing schemes, and ultimately the ability of the surface-tethered probes to bind with target nucleic acids. In Chapter 3, I demonstrate and optimize the nanoscale patterning of individual DNA molecules into isolated, chemically well-defined niches on the surface

  19. UV photolysis, organic molecules in young disks, and the origin of meteoritic amino acids

    NASA Astrophysics Data System (ADS)

    Throop, Henry B.

    2011-04-01

    The origin of complex organic molecules such as amino acids and their precursors found in meteorites and comets is unknown. Previous studies have accounted for the complex organic inventory of the Solar System by aqueous chemistry on warm meteoritic parent bodies, or by accretion of organics formed in the interstellar medium. This paper proposes a third possibility: that complex organics were created in situ by ultraviolet light from nearby O/B stars irradiating ices already in the Sun's protoplanetary disk. If the Sun was born in a dense cluster near UV-bright stars, the flux hitting the disk from external stars could be many orders of magnitude higher than that from the Sun alone. Such photolysis of ices in the laboratory can rapidly produce amino acid precursors and other complex organic molecules. I present a simple model coupling grain growth and UV exposure in a young circumstellar disk. It is shown that the production may be sufficient to create the Solar System's entire complex organic inventory within 10 6 yr. Subsequent aqueous alteration on meteoritic parent bodies is not ruled out.

  20. Bioactive Molecules Released in Food by Lactic Acid Bacteria: Encrypted Peptides and Biogenic Amines.

    PubMed

    Pessione, Enrica; Cirrincione, Simona

    2016-01-01

    Lactic acid bacteria (LAB) can produce a huge amount of bioactive compounds. Since their elective habitat is food, especially dairy but also vegetal food, it is frequent to find bioactive molecules in fermented products. Sometimes these compounds can have adverse effects on human health such as biogenic amines (tyramine and histamine), causing allergies, hypertensive crises, and headache. However, some LAB products also display benefits for the consumers. In the present review article, the main nitrogen compounds produced by LAB are considered. Besides biogenic amines derived from the amino acids tyrosine, histidine, phenylalanine, lysine, ornithine, and glutamate by decarboxylation, interesting peptides can be decrypted by the proteolytic activity of LAB. LAB proteolytic system is very efficient in releasing encrypted molecules from several proteins present in different food matrices. Alpha and beta-caseins, albumin and globulin from milk and dairy products, rubisco from spinach, beta-conglycinin from soy and gluten from cereals constitute a good source of important bioactive compounds. These encrypted peptides are able to control nutrition (mineral absorption and oxidative stress protection), metabolism (blood glucose and cholesterol lowering) cardiovascular function (antithrombotic and hypotensive action), infection (microbial inhibition and immunomodulation) and gut-brain axis (opioids and anti-opioids controlling mood and food intake). Very recent results underline the role of food-encrypted peptides in protein folding (chaperone-like molecules) as well as in cell cycle and apoptosis control, suggesting new and positive aspects of fermented food, still unexplored. In this context, the detailed (transcriptomic, proteomic, and metabolomic) characterization of LAB of food interest (as starters, biocontrol agents, nutraceuticals, and probiotics) can supply a solid evidence-based science to support beneficial effects and it is a promising approach as well to obtain

  1. Bioactive Molecules Released in Food by Lactic Acid Bacteria: Encrypted Peptides and Biogenic Amines

    PubMed Central

    Pessione, Enrica; Cirrincione, Simona

    2016-01-01

    Lactic acid bacteria (LAB) can produce a huge amount of bioactive compounds. Since their elective habitat is food, especially dairy but also vegetal food, it is frequent to find bioactive molecules in fermented products. Sometimes these compounds can have adverse effects on human health such as biogenic amines (tyramine and histamine), causing allergies, hypertensive crises, and headache. However, some LAB products also display benefits for the consumers. In the present review article, the main nitrogen compounds produced by LAB are considered. Besides biogenic amines derived from the amino acids tyrosine, histidine, phenylalanine, lysine, ornithine, and glutamate by decarboxylation, interesting peptides can be decrypted by the proteolytic activity of LAB. LAB proteolytic system is very efficient in releasing encrypted molecules from several proteins present in different food matrices. Alpha and beta-caseins, albumin and globulin from milk and dairy products, rubisco from spinach, beta-conglycinin from soy and gluten from cereals constitute a good source of important bioactive compounds. These encrypted peptides are able to control nutrition (mineral absorption and oxidative stress protection), metabolism (blood glucose and cholesterol lowering) cardiovascular function (antithrombotic and hypotensive action), infection (microbial inhibition and immunomodulation) and gut-brain axis (opioids and anti-opioids controlling mood and food intake). Very recent results underline the role of food-encrypted peptides in protein folding (chaperone-like molecules) as well as in cell cycle and apoptosis control, suggesting new and positive aspects of fermented food, still unexplored. In this context, the detailed (transcriptomic, proteomic, and metabolomic) characterization of LAB of food interest (as starters, biocontrol agents, nutraceuticals, and probiotics) can supply a solid evidence-based science to support beneficial effects and it is a promising approach as well to obtain

  2. Bioactive Molecules Released in Food by Lactic Acid Bacteria: Encrypted Peptides and Biogenic Amines.

    PubMed

    Pessione, Enrica; Cirrincione, Simona

    2016-01-01

    Lactic acid bacteria (LAB) can produce a huge amount of bioactive compounds. Since their elective habitat is food, especially dairy but also vegetal food, it is frequent to find bioactive molecules in fermented products. Sometimes these compounds can have adverse effects on human health such as biogenic amines (tyramine and histamine), causing allergies, hypertensive crises, and headache. However, some LAB products also display benefits for the consumers. In the present review article, the main nitrogen compounds produced by LAB are considered. Besides biogenic amines derived from the amino acids tyrosine, histidine, phenylalanine, lysine, ornithine, and glutamate by decarboxylation, interesting peptides can be decrypted by the proteolytic activity of LAB. LAB proteolytic system is very efficient in releasing encrypted molecules from several proteins present in different food matrices. Alpha and beta-caseins, albumin and globulin from milk and dairy products, rubisco from spinach, beta-conglycinin from soy and gluten from cereals constitute a good source of important bioactive compounds. These encrypted peptides are able to control nutrition (mineral absorption and oxidative stress protection), metabolism (blood glucose and cholesterol lowering) cardiovascular function (antithrombotic and hypotensive action), infection (microbial inhibition and immunomodulation) and gut-brain axis (opioids and anti-opioids controlling mood and food intake). Very recent results underline the role of food-encrypted peptides in protein folding (chaperone-like molecules) as well as in cell cycle and apoptosis control, suggesting new and positive aspects of fermented food, still unexplored. In this context, the detailed (transcriptomic, proteomic, and metabolomic) characterization of LAB of food interest (as starters, biocontrol agents, nutraceuticals, and probiotics) can supply a solid evidence-based science to support beneficial effects and it is a promising approach as well to obtain

  3. Identification of small molecule sulfonic acids as ecto-5'-Nucleotidase inhibitors.

    PubMed

    Raza, Rabia; Saeed, Aamer; Lecka, Joanna; Sévigny, Jean; Iqbal, Jamshed

    2012-11-01

    Ecto-5'-Nucleotidase inhibitors have great potential as anti-tumor agents. We have investigated biochemical properties of human and rat ecto-5'-Nucleotidases and characterized 19 small molecule sulfonic acid derivatives as potential inhibitors of ecto-5'-Nucleotidases. We identified 11 potent inhibitors of human and rat ecto-5'-Nucleotidases and checked their selectivity. Compound 10 (Sodium 2,4-dinitrobenzenesulfonate) with K(i) value of 0.66 μM and 19 (N-(4-sulfamoylphenylcarbamothioyl) pivalamide) with K(i) value of 0.78 μM were identified as the most potent inhibitors for human and rat ecto-5'-Nucleotidase, respectively. The present compounds have low molecular weights, water solubility and equal potency as compared to the reported inhibitors.

  4. Ionization-site effects on the photofragmentation of chloro- and bromoacetic acid molecules

    NASA Astrophysics Data System (ADS)

    Levola, Helena; Itälä, Eero; Schlesier, Kim; Kooser, Kuno; Laine, Sanna; Laksman, Joakim; Ha, Dang Trinh; Rachlew, Elisabeth; Tarkanovskaja, Marta; Tanzer, Katrin; Kukk, Edwin

    2015-12-01

    Fragmentation of gas-phase chloro- and bromoacetic acid samples, particularly its dependency on the atomic site of the initial core ionization, was studied in photoelectron-photoion-photoion coincidence (PEPIPICO) measurements. The fragmentation was investigated after ionizing carbon 1 s and bromine 3 d or chlorine 2 p core orbitals. It was observed that the samples had many similar fragmentation pathways and that their relative weights depended strongly on the initial ionization site. Additional Auger PEPIPICO measurements revealed a clear dependence of fragment pair intensities on the kinetic energy of the emitted Auger electrons. The modeled and measured Auger electron spectra indicated that the average internal energy of the molecule was larger following the carbon 1 s core-hole decay than after the decay of the halogen core hole. This difference in the internal energies was found to be the source of the site-dependent photofragmentation behavior.

  5. Single-molecule FRET and crosslinking studies in structural biology enabled by noncanonical amino acids.

    PubMed

    Tyagi, Swati; Lemke, Edward A

    2015-06-01

    Contemporary structural biology research promises more than just static snap-shots of molecular machineries. This goal is not just facilitated by combining different structural biology techniques, but also by new tools from the field of protein and genetic engineering, as well as from chemistry. Genetic encoding of noncanonical amino acids (ncAAs) through codon-suppression technology provides an excellent opportunity to probe biomolecules using different structural biology methods. In this article, we review the applications of ncAA incorporation into proteins for determining structural information through various techniques with the main focus on crosslinking mass spectrometry and single-molecule FRET-based techniques. Furthermore, advances and limitations of the incorporation of multiple ncAAs are discussed, with respect to design of an ideal host organism for modern and integrative structural biology research.

  6. Cross-Linking Poly(lactic acid) Film Surface by Neutral Hyperthermal Hydrogen Molecule Bombardment.

    PubMed

    Du, Wangli; Shao, Hong; He, Zhoukun; Tang, Changyu; Liu, Yu; Shen, Tao; Zhu, Yan; Lau, Woon-ming; Hui, David

    2015-12-16

    Constructing a dense cross-linking layer on a polymer film surface is a good way to improve the water resistance of poly(lactic acid) (PLA). However, conventional plasma treatments have failed to achieve the aim as a result of the unavoidable surface damage arising from the charged species caused by the uncontrolled high energy coming from colliding ions and electrons. In this work, we report a modified plasma method called hyperthermal hydrogen-induced cross-linking (HHIC) technology to construct a dense cross-linking layer on PLA film surfaces. This method produces energy-controlled neutral hyperthermal hydrogen, which selectively cleaves C-H bonds by molecule collision from the PLA film without breaking other bonds (e.g., C-C bonds in the polymer backbone), and results in subsequent cross-linking of the carbon radicals generated from the organic molecules. The formation of a dense cross-linking layer can serve as a barrier layer to significantly improve both the hydrophobicity and water vapor barrier property of the PLA film. Because of the advantage of selective cleavage of C-H bonds by HHIC treatment, the original physical properties (e.g., mechanical strength and light transmittance) of the PLA films are well-preserved. PMID:26594874

  7. Cross-Linking Poly(lactic acid) Film Surface by Neutral Hyperthermal Hydrogen Molecule Bombardment.

    PubMed

    Du, Wangli; Shao, Hong; He, Zhoukun; Tang, Changyu; Liu, Yu; Shen, Tao; Zhu, Yan; Lau, Woon-ming; Hui, David

    2015-12-16

    Constructing a dense cross-linking layer on a polymer film surface is a good way to improve the water resistance of poly(lactic acid) (PLA). However, conventional plasma treatments have failed to achieve the aim as a result of the unavoidable surface damage arising from the charged species caused by the uncontrolled high energy coming from colliding ions and electrons. In this work, we report a modified plasma method called hyperthermal hydrogen-induced cross-linking (HHIC) technology to construct a dense cross-linking layer on PLA film surfaces. This method produces energy-controlled neutral hyperthermal hydrogen, which selectively cleaves C-H bonds by molecule collision from the PLA film without breaking other bonds (e.g., C-C bonds in the polymer backbone), and results in subsequent cross-linking of the carbon radicals generated from the organic molecules. The formation of a dense cross-linking layer can serve as a barrier layer to significantly improve both the hydrophobicity and water vapor barrier property of the PLA film. Because of the advantage of selective cleavage of C-H bonds by HHIC treatment, the original physical properties (e.g., mechanical strength and light transmittance) of the PLA films are well-preserved.

  8. Amino acid conjugated self assembling molecules for enhancing surface wettability of fiber laser treated titanium surfaces

    NASA Astrophysics Data System (ADS)

    Akkan, Cagri K.; Hür, Deniz; Uzun, Lokman; Garipcan, Bora

    2016-03-01

    Surface wetting properties of implants are one of the most critical parameter, which determine the interaction of proteins and cells with the implant surface. In this regards, acid etching and sand blasting are the mostly used methods at surface modification of Titanium (Ti) for enhanced surface wettability. Besides, these kinds of modifications may cause a conflict whether the surface wettability is influenced by the process related surface contaminations or by the surface roughness. In contrast, lasers might be an option for the alteration of surface wetting properties via supporting micro and/or nano surface topographies while preventing surface chemical contaminations. In this work, we focused on two steps of surface processing approaches of Ti surface: physical and chemical modifications. Herein, we hierarchically structured Ti surfaces by using microsecond modulated pulsed fiber laser. Subsequently, laser structured and non-structured Ti surfaces were further modified with novel histidine and leucine Amino Acid conjugated Self-Assembled Molecules (His1-SAMs2 and Leu3-SAMs) to alter the surface wettability by introducing biologically hydrophilic and hydrophobic groups. Modification of Ti surfaces with His-SAMs and Leu-SAMs ended up with stable wetting properties when compared to non-modified surfaces after 7 days which may enhances the cell-surface interaction.

  9. Formation and Fragmentation of Protonated Molecules after Ionization of Amino Acid and Lactic Acid Clusters by Collision with Ions in the Gas Phase.

    PubMed

    Poully, Jean-Christophe; Vizcaino, Violaine; Schwob, Lucas; Delaunay, Rudy; Kocisek, Jaroslav; Eden, Samuel; Chesnel, Jean-Yves; Méry, Alain; Rangama, Jimmy; Adoui, Lamri; Huber, Bernd

    2015-08-01

    Collisions between O(3+) ions and neutral clusters of amino acids (alanine, valine and glycine) as well as lactic acid are performed in the gas phase, in order to investigate the effect of ionizing radiation on these biologically relevant molecular systems. All monomers and dimers are found to be predominantly protonated, and ab initio quantum-chemical calculations on model systems indicate that for amino acids, this is due to proton transfer within the clusters after ionization. For lactic acid, which has a lower proton affinity than amino acids, a significant non-negligible amount of the radical cation monomer is observed. New fragment-ion channels observed from clusters, as opposed to isolated molecules, are assigned to the statistical dissociation of protonated molecules formed upon ionization of the clusters. These new dissociation channels exhibit strong delayed fragmentation on the microsecond time scale, especially after multiple ionization.

  10. Familial amyloid polyneuropathy: alanine-for-threonine substitution in the transthyretin (prealbumin) molecule.

    PubMed

    Koeppen, A H; Wallace, M R; Benson, M D; Altland, K

    1990-11-01

    A previously reported family with amyloid polyneuropathy (FAP) was reinvestigated to determine the type of mutation in the transthyretin (prealbumin) molecule. Transthyretin was isolated from amyloid-laden myocardium and serum, and tryptic peptides were resolved by high-performance liquid chromatography. Amino acid sequencing of an anomalous peptide revealed an alanine-for-threonine substitution corresponding to position No. 60 of the transthyretin monomer. Detection of the FAP gene in asymptomatic carriers was accomplished by hybrid isoelectric focusing of transthyretin in the presence of dithiothreitol and high concentrations of urea, and by Southern blotting of Pvull-digested leukocyte deoxyribonucleic acid. This type of FAP was found to be identical to the previously described Appalachian amyloid. Patients with FAP and their asymptomatic gene-carrying offspring had significantly reduced levels of serum transthyretin and retinol-binding protein.

  11. Nucleation of Mixed Nitric Acid-Water Ice Nanoparticles in Molecular Beams that Starts with a HNO3 Molecule.

    PubMed

    Lengyel, Jozef; Pysanenko, Andriy; Kočišek, Jaroslav; Poterya, Viktoriya; Pradzynski, Christoph C; Zeuch, Thomas; Slavíček, Petr; Fárník, Michal

    2012-11-01

    Mixed (HNO3)m(H2O)n clusters generated in supersonic expansion of nitric acid vapor are investigated in two different experiments, (1) time-of-flight mass spectrometry after electron ionization and (2) Na doping and photoionization. This combination of complementary methods reveals that only clusters containing at least one acid molecule are generated, that is, the acid molecule serves as the nucleation center in the expansion. The experiments also suggest that at least four water molecules are needed for HNO3 acidic dissociation. The clusters are undoubtedly generated, as proved by electron ionization; however, they are not detected by the Na doping due to a fast charge-transfer reaction between the Na atom and HNO3. This points to limitations of the Na doping recently advocated as a general method for atmospheric aerosol detection. On the other hand, the combination of the two methods introduces a tool for detecting molecules with sizable electron affinity in clusters. PMID:26296012

  12. Relationship between ST8SIA2, polysialic acid and its binding molecules, and psychiatric disorders.

    PubMed

    Sato, Chihiro; Hane, Masaya; Kitajima, Ken

    2016-08-01

    Polysialic acid (polySia, PSA) is a unique and functionally important glycan, particularly in vertebrate brains. It is involved in higher brain functions such as learning, memory, and social behaviors. Recently, an association between several genetic variations and single nucleotide polymorphisms (SNPs) of ST8SIA2/STX, one of two polysialyltransferase genes in vertebrates, and psychiatric disorders, such as schizophrenia (SZ), bipolar disorder (BD), and autism spectrum disorder (ASD), was reported based on candidate gene approaches and genome-wide studies among normal and mental disorder patients. It is of critical importance to determine if the reported mutations and SNPs in ST8SIA2 lead to impairments of the structure and function of polySia, which is the final product of ST8SIA2. To date, however, only a few such forward-directed studies have been conducted. In addition, the molecular mechanisms underlying polySia-involved brain functions remain unknown, although polySia was shown to have an anti-adhesive effect. In this report, we review the relationships between psychiatric disorders and polySia and/or ST8SIA2, and describe a new function of polySia as a regulator of neurologically active molecules, such as brain-derived neurotrophic factor (BDNF) and dopamine, which are deeply involved in psychiatric disorders. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.

  13. Relationship between ST8SIA2, polysialic acid and its binding molecules, and psychiatric disorders.

    PubMed

    Sato, Chihiro; Hane, Masaya; Kitajima, Ken

    2016-08-01

    Polysialic acid (polySia, PSA) is a unique and functionally important glycan, particularly in vertebrate brains. It is involved in higher brain functions such as learning, memory, and social behaviors. Recently, an association between several genetic variations and single nucleotide polymorphisms (SNPs) of ST8SIA2/STX, one of two polysialyltransferase genes in vertebrates, and psychiatric disorders, such as schizophrenia (SZ), bipolar disorder (BD), and autism spectrum disorder (ASD), was reported based on candidate gene approaches and genome-wide studies among normal and mental disorder patients. It is of critical importance to determine if the reported mutations and SNPs in ST8SIA2 lead to impairments of the structure and function of polySia, which is the final product of ST8SIA2. To date, however, only a few such forward-directed studies have been conducted. In addition, the molecular mechanisms underlying polySia-involved brain functions remain unknown, although polySia was shown to have an anti-adhesive effect. In this report, we review the relationships between psychiatric disorders and polySia and/or ST8SIA2, and describe a new function of polySia as a regulator of neurologically active molecules, such as brain-derived neurotrophic factor (BDNF) and dopamine, which are deeply involved in psychiatric disorders. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc. PMID:27105834

  14. Polysialic Acid Directs Tumor Cell Growth by Controlling Heterophilic Neural Cell Adhesion Molecule Interactions

    PubMed Central

    Seidenfaden, Ralph; Krauter, Andrea; Schertzinger, Frank; Gerardy-Schahn, Rita; Hildebrandt, Herbert

    2003-01-01

    Polysialic acid (PSA), a carbohydrate polymer attached to the neural cell adhesion molecule (NCAM), promotes neural plasticity and tumor malignancy, but its mode of action is controversial. Here we establish that PSA controls tumor cell growth and differentiation by interfering with NCAM signaling at cell-cell contacts. Interactions between cells with different PSA and NCAM expression profiles were initiated by enzymatic removal of PSA and by ectopic expression of NCAM or PSA-NCAM. Removal of PSA from the cell surface led to reduced proliferation and activated extracellular signal-regulated kinase (ERK), inducing enhanced survival and neuronal differentiation of neuroblastoma cells. Blocking with an NCAM-specific peptide prevented these effects. Combinatorial transinteraction studies with cells and membranes with different PSA and NCAM phenotypes revealed that heterophilic NCAM binding mimics the cellular responses to PSA removal. In conclusion, our data demonstrate that PSA masks heterophilic NCAM signals, having a direct impact on tumor cell growth. This provides a mechanism for how PSA may promote the genesis and progression of highly aggressive PSA-NCAM-positive tumors. PMID:12897159

  15. Visualizing light-triggered release of molecules inside living cells

    PubMed Central

    Barhoumi, Aoune; Halas, Naomi J.

    2013-01-01

    The light-triggered release of deoxyribonucleic acid (DNA) from gold nanoparticle-based, plasmon resonant vectors, such as nanoshells, shows great promise for gene delivery in living cells. Here we show that intracellular light-triggered release can be performed on molecules that associate with the DNA in a DNA host-guest complex bound to nanoshells. DAPI (4′,6-diamidino-2-phenylindole), a bright blue fluorescent molecule that binds reversibly to double-stranded DNA, was chosen to visualize this intracellular light-induced release process. Illumination of nanoshell-dsDNA-DAPI complexes at their plasmon resonance wavelength dehybridizes the DNA, releasing the DAPI molecules within living cells, where they diffuse to the nucleus and associate with the cell's endogenous DNA. The low laser power and irradiation times required for molecular release do not compromise cell viability. This highly controlled co-release of nonbiological molecules accompanying the oligonucleotides could have broad applications in the study of cellular processes and in the development of intracellular targeted therapies. PMID:20857946

  16. DNA curtains: novel tools for imaging protein-nucleic acid interactions at the single-molecule level.

    PubMed

    Collins, Bridget E; Ye, Ling F; Duzdevich, Daniel; Greene, Eric C

    2014-01-01

    Interactions between proteins and nucleic acids are at the molecular foundations of most key biological processes, including DNA replication, genome maintenance, the regulation of gene expression, and chromosome segregation. A complete understanding of these types of biological processes requires tackling questions with a range of different techniques, such as genetics, cell biology, molecular biology, biochemistry, and structural biology. Here, we describe a novel experimental approach called "DNA curtains" that can be used to complement and extend these more traditional techniques by providing real-time information about protein-nucleic acid interactions at the level of single molecules. We describe general features of the DNA curtain technology and its application to the study of protein-nucleic acid interactions in vitro. We also discuss some future developments that will help address crucial challenges to the field of single-molecule biology.

  17. Searching for amino-acid homochirality on Mars with the Mars Organic Molecule Analyzer (MOMA) onboard ExoMars

    NASA Astrophysics Data System (ADS)

    Buch, A.; Freissinet, C.; Sternberg, R.; Brault, A.; Szopa, C.; Claude-Geffroy, C.; Coll, P. J.; Grand, N.; Raulin, F.; Pinick, V.; Goesmann, F.

    2012-12-01

    The joint ESA-Roscosmos Exo-Mars-2018 rover mission plans to seek the signs of a past or a present life on Mars. The Mars Organic Molecule Analyzer (MOMA) experiment onboard theExoMars rover will be a key analytical tool in providing molecular information from Mars solid samples, with a specific focus on the characterization of their organic content. In this purpose, one of MOMA's main instruments is a gas chromatograph-mass spectrometer (GC-MS), which provides a unique ability to characterize a broad range of compounds and allow chemical analyses on volatile and refractory species. The challenge with the analysis of this refractory matter embedded in soil is their primary extraction before their analysis by GC-MS. Since the extraction of organic matter is not possible by liquid solvent extraction, we have developed a method based on the thermodesorption and subsequent derivatization of the organic molecules. The goal of the thermodesorption is to extract the organic matter by heating the sample quickly enough not to degrade its organic content. One of the main focuses is to determine the chirality of this organic matter, notably amino acids. Indeed, on Earth, homochirality of molecules is an indicator for the presence of life. Amino acids appear to bear only the left-handed form (L) in living system. However, other refractory compounds can raise interest: nucleobases, carboxylic acids and PAHs are among molecules supported by life as we know it, and all of them can display chirality. The intrinsic chirality of molecules being thermosensitive, the thermodesorption parameters have been adjusted to occur within a range of temperatures from 150 °C to 300 °C over a period of 30 s to 10 min, depending on the chemical compound. Under these conditions, we have shown that amino acids are not degraded and that their chirality is preserved. Once extracted, refractory molecules with labile hydrogens (e.g. amino acids, nucleobases, carboxylic acids, etc.) are derivatized

  18. Anion Effects on Sodium Ion and Acid Molecule Adduction to Protein Ions in Electrospray Ionization Mass Spectrometry

    PubMed Central

    Flick, Tawnya G.; Merenbloom, Samuel I.; Williams, Evan R.

    2012-01-01

    Gaseous protein–metal ion and protein–molecule complexes can be readily formed by electrospray ionization (ESI) from aqueous solutions containing proteins and millimolar concentrations of sodium salts of various anions. The extent of sodium and acid molecule adduction to multiply charged protein ions is inversely related and depends strongly on the proton affinity (PA) of the anion, with extensive sodium adduction occurring for anions with PA values greater than ~300 kcal·mol−1 and extensive acid molecule adduction occurring for anions with PA values less than 315 kcal·mol−1. The role of the anion on the extent of sodium and acid molecule adduction does not directly follow the Hofmeister series, suggesting that direct protein–ion interactions may not play a significant role in the observed effect of anions on protein structure in solution. These results indicate that salts with anions that have low PA values may be useful solution-phase additives to minimize nonspecific metal ion adduction in ESI experiments designed to identify specific protein-metal ion interactions. PMID:21952761

  19. Expression and Localization of Neural Cell Adhesion Molecule and Polysialic Acid during Chick Corneal Development

    PubMed Central

    Schwend, Tyler; Conrad, Gary W.

    2012-01-01

    Purpose. To assay for expression and localization of neural cell adhesion molecule (NCAM) and polysialic acid (polySia) in the chick cornea during embryonic and postnatal development. Methods. Real time quantitative PCR and Western blot analyses were used to determine NCAM expression and polysiaylation in embryonic, hatchling, and adult chick corneas. Immunofluorescence staining for NCAM and polySia was conducted on cryosections of embryonic and adult corneas, whole embryonic corneas, and trigeminal neurons. Results. NCAM and ST8SiaII mRNA transcripts peaked by embryonic day (E)9, remained steady between E10 and E14 and slowly decreased thereafter during embryonic development. Both gene transcripts showed > 190-fold decline in the adult chick cornea compared with E9. In contrast, ST8SiaIV expression gradually decreased 26.5-fold from E6 to E19, increased thereafter, and rose to the early embryonic level in the adult cornea. Western blot analysis revealed NCAM was polysialylated and its expression developmentally changed. Other polysiaylated proteins aside from NCAM were also detected by Western blot analysis. Five NCAM isoforms including NCAM-120, NCAM-180 and three soluble NCAM isoforms with low molecular weights (87–96 kDa) were present in chick corneas, with NCAM-120 being the predominate isoform. NCAM was localized to the epithelium, stroma, and stromal extracellular matrix (ECM) of the embryonic cornea. In stroma, NCAM expression shifted from anterior to posterior stroma during embryonic development and eventually became undetectable in 20-week-old adult cornea. Additionally, both NCAM and polySia were detected on embryonic corneal and pericorneal nerves. Conclusions. NCAM and polySia are expressed and developmentally regulated in chick corneas. Both membrane-associated and soluble NCAM isoforms are expressed in chick corneas. The distributions of NCAM and polySia in cornea and on corneal nerves suggest their potential functions in corneal innervation. PMID

  20. Surface active molecules: preparation and properties of long chain n-acyl-l-alpha-amino-omega-guanidine alkyl acid derivatives.

    PubMed

    Infante, R; Dominguez, J G; Erra, P; Julia, R; Prats, M

    1984-12-01

    Synopsis A new route for the synthesis of long chain N(alpha)-acyl-l-alpha-amino-omega-guamdine alkyl acid derivatives, with cationic or amphoteric character has been established. The general formula of these compounds is shown below. A physico-chemical and antimicrobial study of these products as a function of the alkyl ester or sodium salt (R), the straight chain length of the fatty acid residue (x) and the number of carbons between the omega-guanidine and omega-carboxyl group (n) has been investigated. The water solubility, surface tension, critical micelle concentration (c.m.c.) and minimum inhibitory concentration (MIC) against Gram-positive and Gram-negative bacteria (including Pseudomonas) has been determined. Dicyclohexylcarbodiimide has been used to condense fatty acids and alpha-amino-omega-guanidine alkyl acids. In these conditions protection of the omega-guanidine group is not necessary. The main characteristic of this synthetic procedure is the use of very mild experimental conditions (temperature, pH) to form the amide linkage which leads to pure optical compounds in high yield in the absence of electrolytes. The results show that some structural modifications, particularly the protection of the carboxyl group, promote variations of the surfactant and antimicrobial properties. Only those molecules with the blocked carboxyl group (cationic molecules, where R = Me, Et or Pr) showed a good surfactant and antimicrobial activity. When the carboxyl group was unprotected (amphoteric molecules, where R = Na(+)) the resulting compounds were inactive.

  1. Quantitative Structure of an Acetate Dye Molecule Analogue at the TiO2–Acetic Acid Interface

    PubMed Central

    2016-01-01

    The positions of atoms in and around acetate molecules at the rutile TiO2(110) interface with 0.1 M acetic acid have been determined with a precision of ±0.05 Å. Acetate is used as a surrogate for the carboxylate groups typically employed to anchor monocarboxylate dye molecules to TiO2 in dye-sensitized solar cells (DSSC). Structural analysis reveals small domains of ordered (2 × 1) acetate molecules, with substrate atoms closer to their bulk terminated positions compared to the clean UHV surface. Acetate is found in a bidentate bridge position, binding through both oxygen atoms to two 5-fold titanium atoms such that the molecular plane is along the [001] azimuth. Density functional theory calculations provide adsorption geometries in excellent agreement with experiment. The availability of these structural data will improve the accuracy of charge transport models for DSSC. PMID:27110318

  2. Low Band Gap Coplanar Conjugated Molecules Featuring Dynamic Intramolecular Lewis Acid-Base Coordination.

    PubMed

    Zhu, Congzhi; Guo, Zi-Hao; Mu, Anthony U; Liu, Yi; Wheeler, Steven E; Fang, Lei

    2016-05-20

    Ladder-type conjugated molecules with a low band gap and low LUMO level were synthesized through an N-directed borylation reaction of pyrazine-derived donor-acceptor-donor precursors. The intramolecular boron-nitrogen coordination bonds played a key role in rendering the rigid and coplanar conformation of these molecules and their corresponding electronic structures. Experimental investigation and theoretical simulation revealed the dynamic nature of such coordination, which allowed for active manipulation of the optical properties of these molecules by using competing Lewis basic solvents. PMID:27096728

  3. Immobilization of biorecognition molecules on O2 plasma-functionalized SWCNT electrodes for biosensors

    NASA Astrophysics Data System (ADS)

    Jin, Joon-Hyung; Kim, Joon Hyub; Lee, Jun-Yong; Min, Nam Ki

    2012-11-01

    Biointerfaces capable of biological recognition and specificity are very important for the development of carbon nanotube based biosensors. Here, we explore experimentally the effects of O2 plasma treatment on the biomolecule immobilization properties of single-walled carbon nanotube (SWCNT) electrodes for electrochemical biosensing. The SWCNT film was integrated into an electrochemical three-electrode system on a glass substrate and then treated with an O2 plasma to improve its electrochemical response. Glucose oxidases, antibodies, and deoxyribonucleic acids (DNAs) were covalently immobilized on the plasma-functionalized (pf) SWCNT working electrodes, and the electrochemical and bioelectrocatalytic properties of three biomolecular assemblies generated on the pf-SWCNT electrodes were investigated using cyclic voltammetry, square-wave voltammetry, and chronoamperometry. The pf-SWCNT films were found to provide electrochemical biosensing electrodes having high electroactivity and sensitivity for detecting glucoses, antigens, and DNA molecules.

  4. Quantitative structure-property relationship studies on amino acid conjugates of jasmonic acid as defense signaling molecules.

    PubMed

    Li, Zu-Guang; Chen, Ke-Xian; Xie, Hai-Ying; Gao, Jian-Rong

    2009-06-01

    Jasmonates and related compounds, including amino acid conjugates of jasmonic acid, have regulatory functions in the signaling pathway for plant developmental processes and responses to the complex equilibrium of biotic and abiotic stress. But the molecular details of the signaling mechanism are still poorly understood. Statistically significant quantitative structure-property relationship models (r(2) > 0.990) constructed by genetic function approximation and molecular field analysis were generated for the purpose of deriving structural requirements for lipophilicity of amino acid conjugates of jasmonic acid. The best models derived in the present study provide some valuable academic information in terms of the 2/3D-descriptors influencing the lipophilicity, which may contribute to further understanding the mechanism of exogenous application of jasmonates in their signaling pathway and designing novel analogs of jasmonic acid as ecological pesticides.

  5. Deoxyribonucleic acid-dependent ribonucleic acid polymerase activity in rat liver after protein restriction.

    PubMed Central

    Andersson, G M; von der Decken, A

    1975-01-01

    Rats were fed for 6 days on a diet containing either 3 or 20% high-quality protein. Nuclei were isolated from liver and DNA-dependent RNA polymerases (EC 2.7.7.6) extracted with 1 M-(NH4)2SO4. The proteins were then precipitated with 3.5 M-(NH4)2SO4 and after dialysis applied to a DEAE-Sephadex column. The column was developed with a gradient of (NH4)2SO4. Polymerase I separated well from alpha-amanitin-sensitive polymerase II. The enzyme activities were compared between the two dietary groups. Rats that had received 3% protein showed a lower polymerase I activity per g wet wt. of liver, per mg of DNA and per mg of protein. Polymerase II was lower in activity per g wet wt. of liver and per mg of DNA, but was higher per mg of protein. Polyacrylamide-gel electrophoretograms showed a higher proportion of contaminating proteins in polymerase II fractions isolated from 20%-protein-fed rats. The data explain the lower activity obtained per mg of protein in these rats. It is concluded that a decrease in dietary protein content from 20 to 3% induces a fall in content and specific activity of RNA polymerase I and II in liver. PMID:1156400

  6. [Significance of electron interactions of fatty acids of phospholipid molecules in the organism adaptation to habitation temperature].

    PubMed

    Zabelinskiĭ, S A; Chebotareva, M A; Arakelova, E S; Shukoliukova, E P; Furaev, V V; Kalandarov, A M; Feĭzulaev, B A; Krivchenko, A I

    2009-01-01

    Data in the fatty acid composition of muscle tissue phospholipids of some representatives of gastropod molluscs (Gastropoda) have been presented for the first time. In the lake phytophagues Lymnaea stagnalis and Lymnaea ovata the long-chained C22-acid was not detected, whereas in the predator common whelk Buccinum undatum, C22:6omega3 was present. Comparison of absorption spectra (240-720 nm) of lipid extracts of the studied invertebrates and of rat has been performed. The obtained data are discussed from the point of view of participation of pi-electrons of phospholipid fatty acid molecules in adaptation of membranes to the habitation temperature, which arises owing to interelectron attraction and to the process of formation of Cooper's pairs.

  7. The botanical molecule p-hydroxycinnamic acid as a new osteogenic agent: insight into the treatment of cancer bone metastases.

    PubMed

    Yamaguchi, Masayoshi

    2016-10-01

    Bone homeostasis is maintained through a balance between osteoblastic bone formation and osteoclastic bone resorption. Bone loss with aging is induced by decreasing in osteoblastic bone formation and increasing in osteoclastic bone resorption, thereby leading to osteoporosis. Osteoporosis with its accompanying decrease in bone mass is widely recognized as a major public heath problem. Pharmacologic and nutritional factors may play a role in the prevention and treatment of bone loss with aging. p-Hydroxycinnamic acid (HCA), which stimulates bone mineralization in mouse bone tissues in vitro, has been found to be present in the leafstalk of wasabi (Wasabi japonica MATSUM) among various food and plants. Other phenolic acids including cinnamic acid, ferulic acid, caffeic acid and 3,4-dimethoxycinnamic acid did not have osteogenic effects. HCA was demonstrated to stimulate osteoblastic bone formation and suppresses osteoclastic bone resorption in vitro by antagonizing activation of the nuclear factor kappa B. Oral administration of HCA was found to exhibit restorative effects on bone loss induced by ovariectomy and diabetic states, supporting a role in the treatment of osteoporosis. Moreover, HCA was demonstrated to prevent the suppressed osteoblastic mineralization and the enhanced osteoclastogenesis in mouse bone marrow cells cocultured with bone metastatic MDA-MB-231 human breast cancer cells in vitro. The botanical molecule HCA, as a new osteogenic agent, is suggested to play a role in the treatment of cancer bone metastases. This review will discuss an advanced recent finding that HCA may be a useful agent to treat bone metabolic disorder. PMID:27573001

  8. Polysialic acid-neural cell adhesion molecule in brain plasticity: from synapses to integration of new neurons.

    PubMed

    Gascon, Eduardo; Vutskits, Laszlo; Kiss, Jozsef Zoltan

    2007-11-01

    Isoforms of the neuronal cell adhesion molecule (NCAM) carrying the linear homopolymer of alpha 2,8-linked sialic acid (polysialic acid, PSA) have emerged as particularly attractive candidates for promoting plasticity in the nervous system. The large negatively charged PSA chain of NCAM is postulated to be a spacer that reduces adhesion forces between cells allowing dynamic changes in membrane contacts. Accumulating evidence also suggests that PSA-NCAM-mediated interactions lead to activation of intracellular signaling cascades that are fundamental to the biological functions of the molecule. An important role of PSA-NCAM appears to be during development, when its expression level is high and where it contributes to the regulation of cell shape, growth or migration. However, PSA-NCAM does persist in adult brain structures such as the hippocampus that display a high degree of plasticity where it is involved in activity-induced synaptic plasticity. Recent advances in the field of PSA-NCAM research have not only consolidated the importance of this molecule in plasticity processes but also suggest a role for PSA-NCAM in the regulation of higher cognitive functions and psychiatric disorders. In this review, we discuss the role and mode of actions of PSA-NCAM in structural plasticity as well as its potential link to cognitive processes.

  9. Discrimination of organic acids using a three molecule array based upon cruciform fluorophores.

    PubMed

    Davey, Evan A; Zucchero, Anthony J; Trapp, Oliver; Bunz, Uwe H F

    2011-05-25

    A small array was obtained from three reactive cruciform fluorophores in six different solvents. The array discerned 10 different aromatic carboxylic acids by protonation-induced fluorescence shifts, which were recorded by digital photography. This simple array can discern acids that have closely spaced pK(a) values.

  10. Enantioselective silyl protection of alcohols catalysed by an amino-acid-based small molecule.

    PubMed

    Zhao, Yu; Rodrigo, Jason; Hoveyda, Amir H; Snapper, Marc L

    2006-09-01

    Reliable, selective and environmentally friendly chemical transformations are crucial to the development of new therapeutics and the design of novel materials. Chiral catalysts that can be easily prepared and used to obtain organic molecules of high enantiomeric purity are critical to modern chemical synthesis. The development of protecting groups that shield reactive functionalities has also proved indispensable in the preparation of complex biologically active molecules. Here we present a chiral catalyst that promotes the enantioselective protection of a secondary alcohol as one of the most commonly used protected forms of an alcohol: a silyl ether. The catalyst is a small, simple molecule that can be prepared in three steps from commercial materials without the need for rigorously controlled conditions. Enantioselective silylations are performed with commercial silyl chlorides and produce yields of up to 96 per cent at an enantiomeric ratio of up to 98:2. Chiral catalysts for selective formation of commonly used protecting groups such as silyl ethers should significantly enhance the ability of chemical synthesis to deliver, in a more practical and efficient manner, important organic molecules.

  11. Two Isomers of Protonated Isocyanic Acid: Evidence for an Ion-Molecule Pathway for HNCO ↔ HOCN Isomerization.

    PubMed

    Lattanzi, Valerio; Thorwirth, Sven; Gottlieb, Carl A; McCarthy, Michael C

    2012-12-01

    Ion-molecule reactions are thought to play a crucial role in the formation of metastable isomers, but relatively few protonated intermediates beyond HNCH(+) have been characterized at high spectral resolution. We present here laboratory measurements of the rotational spectra of protonated isocyanic acid in two isomeric forms, the ground state H2NCO(+) with C2v symmetry and a low-lying bent chain HNCOH(+), guided by coupled cluster calculations of their molecular structure. Somewhat surprisingly, HNCOH(+) is found to be more abundant than H2NCO(+), even though this metastable isomer is calculated to lie approximately 15-20 kcal/mol higher in energy. In the same way that HCNH(+) serves as a key intermediate in ion-molecule reactions that form HNC via dissociative electron recombination in cold dense interstellar molecular clouds, HNCOH(+) may play an analogous role in the conversion of HNCO to HOCN.

  12. Two Isomers of Protonated Isocyanic Acid: Evidence for an Ion-Molecule Pathway for HNCO-HOCN Isomerization

    NASA Astrophysics Data System (ADS)

    Lattanzi, V.; Thorwirth, S.; Gottlieb, C. A.; McCarthy, M. C.

    2012-11-01

    Ion-molecule reactions are thought to play a crucial role in the formation of metastable isomers, but relatively few protonated intermediates beyond HNCH+ have been characterized at high spectral resolution. We present here laboratory measurements of the rotational spectra of protonated isocyanic acid in two isomeric forms, the ground state H2NCO+ with C2v symmetry and a low-lying bent chain HNCOH+, guided by coupled cluster calculations of their molecular structure. Somewhat surprisingly, HNCOH+ is found to be more abundant than H2NCO+, even though this metastable isomer is calculated to lie approximately 15-20 kcal/mol higher in energy. In the same way that HCNH+ serves as a key intermediate in ion-molecule reactions that form HNC via dissociative electron recombination in cold dense interstellar molecular clouds, HNCOH+ may play an analogous role in the conversion of HNCO to HOCN.

  13. Two Isomers of Protonated Isocyanic Acid: Evidence for an Ion-Molecule Pathway for HNCO ↔ HOCN Isomerization.

    PubMed

    Lattanzi, Valerio; Thorwirth, Sven; Gottlieb, Carl A; McCarthy, Michael C

    2012-12-01

    Ion-molecule reactions are thought to play a crucial role in the formation of metastable isomers, but relatively few protonated intermediates beyond HNCH(+) have been characterized at high spectral resolution. We present here laboratory measurements of the rotational spectra of protonated isocyanic acid in two isomeric forms, the ground state H2NCO(+) with C2v symmetry and a low-lying bent chain HNCOH(+), guided by coupled cluster calculations of their molecular structure. Somewhat surprisingly, HNCOH(+) is found to be more abundant than H2NCO(+), even though this metastable isomer is calculated to lie approximately 15-20 kcal/mol higher in energy. In the same way that HCNH(+) serves as a key intermediate in ion-molecule reactions that form HNC via dissociative electron recombination in cold dense interstellar molecular clouds, HNCOH(+) may play an analogous role in the conversion of HNCO to HOCN. PMID:26290966

  14. Electrochemical detection of nucleic acids, proteins, small molecules and cells using a DNA-nanostructure-based universal biosensing platform.

    PubMed

    Lin, Meihua; Song, Ping; Zhou, Guobao; Zuo, Xiaolei; Aldalbahi, Ali; Lou, Xiaoding; Shi, Jiye; Fan, Chunhai

    2016-07-01

    The occurrence and prognosis of many complex diseases, such as cancers, is associated with the variation of various molecules, including DNA at the genetic level, RNA at the regulatory level, proteins at the functional level and small molecules at the metabolic level (defined collectively as multilevel molecules). Thus it is highly desirable to develop a single platform for detecting multilevel biomarkers for early-stage diagnosis. Here we report a protocol on DNA-nanostructure-based programmable engineering of the biomolecular recognition interface, which provides a universal electrochemical biosensing platform for the ultrasensitive detection of nucleic acids (DNA/RNA), proteins, small molecules and whole cells. The protocol starts with the synthesis of a series of differentially sized, self-assembled tetrahedral DNA nanostructures (TDNs) with site-specifically modified thiol groups that can be readily anchored on the surface of a gold electrode with high reproducibility. By exploiting the rigid structure, nanoscale addressability and versatile functionality of TDNs, one can tailor the type of biomolecular probes appended on individual TDNs for the detection of specific molecules of interest. Target binding occurring on the gold surface patterned with TDNs is quantitatively translated into electrochemical signals via a coupled enzyme-based catalytic process. This uses a sandwich assay strategy in which biotinylated reporter probes recognize TDN-bound target biomolecules, which then allow binding of horseradish-peroxidase-conjugated avidin (avidin-HRP). Hydrogen peroxide (H2O2) is then reduced by avidin-HRP in the presence of TMB (3,3',5,5'-tetramethylbenzidine) to generate a quantitative electrochemical signal. The time range for the entire protocol is ∼1 d, whereas the detection process takes ∼30 min to 3 h. PMID:27310264

  15. Enantioselective small molecule synthesis by carbon dioxide fixation using a dual Brønsted acid/base organocatalyst.

    PubMed

    Vara, Brandon A; Struble, Thomas J; Wang, Weiwei; Dobish, Mark C; Johnston, Jeffrey N

    2015-06-17

    Carbon dioxide exhibits many of the qualities of an ideal reagent: it is nontoxic, plentiful, and inexpensive. Unlike other gaseous reagents, however, it has found limited use in enantioselective synthesis. Moreover, unprecedented is a tool that merges one of the simplest biological approaches to catalysis-Brønsted acid/base activation-with this abundant reagent. We describe a metal-free small molecule catalyst that achieves the three component reaction between a homoallylic alcohol, carbon dioxide, and an electrophilic source of iodine. Cyclic carbonates are formed enantioselectively.

  16. Effect of Varying Magnetic Fields on Targeted Gene Delivery of Nucleic Acid-Based Molecules.

    PubMed

    Oral, Ozlem; Cıkım, Taha; Zuvin, Merve; Unal, Ozlem; Yagci-Acar, Havva; Gozuacik, Devrim; Koşar, Ali

    2015-11-01

    Several physical methods have been developed to introduce nucleic acid expression vectors into mammalian cells. Magnetic transfection (magnetofection) is one such transfection method, and it involves binding of nucleic acids such as DNA, RNA or siRNA to magnetic nanoparticles followed by subsequent exposure to external magnetic fields. However, the challenge between high efficiency of nucleic acid uptake by cells and toxicity was not totally resolved. Delivery of nucleic acids and their transport to the target cells require carefully designed and controlled systems. In this study, we introduced a novel magnetic system design providing varying magnet turn speeds and magnetic field directions. The system was tested in the magnetofection of human breast (MCF-7), prostate (DU-145, PC-3) and bladder (RT-4) cancer cell lines using green fluorescent protein DNA as a reporter. Polyethylenimine coated superparamagnetic iron oxide nanoparticles (SPIONs) were used as nucleic acid carriers. Adsorption of PEI on SPION improved the cytocompatibility dramatically. Application of external magnetic field increased intracellular uptake of nanoparticles and transfection efficiency without any additional cytotoxicity. We introduce our novel magnetism-based method as a promising tool for enhanced nucleic acid delivery into mammalian cells. PMID:25963582

  17. Deoxyribonucleic acid-protein and deoxyribonucleic acid interstrand cross-links induced in isolated chromatin by hydrogen peroxide and ferrous ethylenediaminetetraacetate chelates

    SciTech Connect

    Lesko, S.A.; Drocourt, J.; Yang, S.

    1982-01-01

    DNA-protein and DNA interstrand cross-links were induced in isolated chromatin after treatment with H/sub 2/O/sub 2/ and ferrous ethylenediaminetetraacetate (EDTA). Retention of DNA on membrane filters after heating of chromatin in a dissociating solvent indicated the presence of a stable linkage between DNA and protein. Treatment of protein-free DNA with H/sub 2/O/sub 2//Fe/sup 2 +/-EDTA did not result in enhanced filter retention. Incubation of cross-linked chromatin with proteinase K completely eliminated filter retention. Resistance to S/sub 1/ nuclease after a denaturation-renaturation cycle was used to detect DNA interstrand cross-links. Heating the treated chromatin at 45/sup 0/C for 16 h and NaBH/sub 4/ reduction enhanced the extent of interstrand cross-linking. The following data are consistent with, but do not totally prove, the hypothesis that cross-links are induced by hydroxyl radicals generated in Fenton-type reactions: (1) cross-linking was inhibited by hydroxyl radical scavengers; (2) the degree of inhibition of DNA interstrand cross-links correlated very closely with the rate constants of the scavengers for reaction with hydroxyl radicals; (3) cross-linking was eliminated or greatly reduced by catalase; (4) the extent of cross-linking was directly related to the concentration of Fe/sup 2 +/-EDTA. Partial inhibition of cross-linking by superoxide dismutase indicates that super-oxide-driven Fenton chemistry is involved. The data indicate that DNA cross-linking may play a role in the manifestation of the biological activity of agents of systems that generate reactive hydroxyl radicals.

  18. Anthramycin binding to deoxyribonucleic acid-mitomycin C complexes. Evidence for drug-induced deoxyribonucleic acid conformational change and cooperativity in mitomycin C binding.

    PubMed

    Kaplan, D J; Hurley, L H

    1981-12-22

    Anthramycin and mitomycin C (MC) are two DNA reactive drugs, which bind covalently to GC pairs producing different effects on DNA: anthramycin stiffening and MC distorsion. This paper describes experiments in which we have used anthramycin as a probe to sense quantitatively the effects on DNA of MC binding. Saturation binding experiments show that both anthramycin and MC partially inhibit the binding of the other drug to DNA (maximum inhibition by MC and anthramycin, 22.4% and 19.7%, respectively) but by a mechanism other than direct site exclusion. This suggests that MC binds in the major groove of DNA, since anthramycin is known to bind in the minor groove. An abrupt reduction in the binding of anthramycin to DNA-MC complexes occurs between MC binding ratios of 0.030 and 0.035, which parallels and probably results from sudden intensification of a MC-induced DNA conformational change occurring between these binding ratios. Dialysis measurements indicate that anthramycin is very possibly binding at sites distant from MC sites and suggest a clustering of closely bound MC chromophores resulting from possible cooperative binding. S1 nuclease digest experiments demonstrate an initial enhancement of nuclease activity in DNA-MC complexes, the magnitude of which correlates well with the reduction of anthramycin binding, relative to the degree of MC binding. The enhanced nuclease activity in these complexes indicates regions of exposed DNA or helix base distortion which is related to or is the result of conformational change. PMID:6798992

  19. Searching for new NO-donor aspirin-like molecules: Furoxanylacyl derivatives of salicylic acid and related furazans.

    PubMed

    Lazzarato, Loretta; Cena, Clara; Rolando, Barbara; Marini, Elisabetta; Lolli, Marco Lucio; Guglielmo, Stefano; Guaita, Elena; Morini, Giuseppina; Coruzzi, Gabriella; Fruttero, Roberta; Gasco, Alberto

    2011-10-01

    A new group of derivatives of salicylic acid containing NO-donor furoxans, and the related des-NO-furazans, were synthesized and evaluated as new aspirin-like molecules. Their stability was assessed in acid (pH 1) and physiological solutions (pH 7.4), and in human serum. No compound exhibited COX-inhibitory activity against COX-1 and COX-2 isoforms, when tested up to 100μM, respectively, on isolated platelets and on monocytes. Phenylsulfonyl- and cyano-substituted furoxans inhibited platelet aggregation induced by collagen in human platelet-rich plasma, through a cGMP dependent mechanism. Furoxan derivatives displayed cGMP-dependent vasodilator activities, tested on rat aorta strips precontracted with phenylephrine. All products showed anti-inflammatory activity similar to that of ASA, tested on rats by the carrageenan-induced paw edema assay. Unlike ASA, all products showed markedly reduced gastrotoxicity in a rat lesion model.

  20. The pharmacology and therapeutic potential of small molecule inhibitors of acid-sensing ion channels in stroke intervention

    PubMed Central

    Leng, Tian-dong; Xiong, Zhi-gang

    2013-01-01

    In the nervous system, a decrease in extracellular pH is a common feature of various physiological and pathological processes, including synaptic transmission, cerebral ischemia, epilepsy, brain trauma, and tissue inflammation. Acid-sensing ion channels (ASICs) are proton-gated cation channels that are distributed throughout the central and peripheral nervous systems. Following the recent identification of ASICs as critical acid-sensing extracellular proton receptors, growing evidence has suggested that the activation of ASICs plays important roles in physiological processes such as nociception, mechanosensation, synaptic plasticity, learning and memory. However, the over-activation of ASICs is also linked to adverse outcomes for certain pathological processes, such as brain ischemia and multiple sclerosis. Based on the well-demonstrated role of ASIC1a activation in acidosis-mediated brain injury, small molecule inhibitors of ASIC1a may represent novel therapeutic agents for the treatment of neurological disorders, such as stroke. PMID:22820909

  1. Peptide nucleic acids rather than RNA may have been the first genetic molecule

    NASA Technical Reports Server (NTRS)

    Nelson, K. E.; Levy, M.; Miller, S. L.

    2000-01-01

    Numerous problems exist with the current thinking of RNA as the first genetic material. No plausible prebiotic processes have yet been demonstrated to produce the nucleosides or nucleotides or for efficient two-way nonenzymatic replication. Peptide nucleic acid (PNA) is a promising precursor to RNA, consisting of N-(2-aminoethyl)glycine (AEG) and the adenine, uracil, guanine, and cytosine-N-acetic acids. However, PNA has not yet been demonstrated to be prebiotic. We show here that AEG is produced directly in electric discharge reactions from CH(4), N(2), NH(3), and H(2)O. Electric discharges also produce ethylenediamine, as do NH(4)CN polymerizations. AEG is produced from the robust Strecker synthesis with ethylenediamine. The NH(4)CN polymerization in the presence of glycine leads to the adenine and guanine-N(9)-acetic acids, and the cytosine and uracil-N(1)-acetic acids are produced in high yield from the reaction of cyanoacetaldehyde with hydantoic acid, rather than urea. Preliminary experiments suggest that AEG may polymerize rapidly at 100 degrees C to give the polypeptide backbone of PNA. The ease of synthesis of the components of PNA and possibility of polymerization of AEG reinforce the possibility that PNA may have been the first genetic material.

  2. Visualising single molecules of HIV-1 and miRNA nucleic acids

    PubMed Central

    2013-01-01

    Background The scarcity of certain nucleic acid species and the small size of target sequences such as miRNA, impose a significant barrier to subcellular visualization and present a major challenge to cell biologists. Here, we offer a generic and highly sensitive visualization approach (oligo fluorescent in situ hybridization, O-FISH) that can be used to detect such nucleic acids using a single-oligonucleotide probe of 19–26 nucleotides in length. Results We used O-FISH to visualize miR146a in human and avian cells. Furthermore, we reveal the sensitivity of O-FISH detection by using a HIV-1 model system to show that as little as 1–2 copies of nucleic acids can be detected in a single cell. We were able to discern newly synthesized viral cDNA and, moreover, observed that certain HIV RNA sequences are only transiently available for O-FISH detection. Conclusions Taken together, these results suggest that the O-FISH method can potentially be used for in situ probing of, as few as, 1–2 copies of nucleic acid and, additionally, to visualize small RNA such as miRNA. We further propose that the O-FISH method could be extended to understand viral function by probing newly transcribed viral intermediates; and discern the localisation of nucleic acids of interest. Additionally, interrogating the conformation and structure of a particular nucleic acid in situ might also be possible, based on the accessibility of a target sequence. PMID:23590669

  3. Lactoferrin Combined with Retinoic Acid Stimulates B1 Cells to Express IgA Isotype and Gut-homing Molecules.

    PubMed

    Kang, Seong-Ho; Jin, Bo-Ra; Kim, Hyeon-Jin; Seo, Goo-Young; Jang, Young-Saeng; Kim, Sun-Jin; An, Sun-Jin; Park, Seok-Rae; Kim, Woan-Sub; Kim, Pyeung-Hyeun

    2015-02-01

    It is well established that TGF-β1 and retinoic acid (RA) cause IgA isotype switching in mice. We recently found that lactoferrin (LF) also has an activity of IgA isotype switching in spleen B cells. The present study explored the effect of LF on the Ig production by mouse peritoneal B cells. LF, like TGF-β1, substantially increased IgA production in peritoneal B1 cells but little in peritoneal B2 cells. In contrast, LF increased IgG2b production in peritoneal B2 cells much more strongly than in peritoneal B1 cells. LF in combination with RA further enhanced the IgA production and, interestingly, this enhancement was restricted to IgA isotype and B1 cells. Similarly, the combination of the two molecules also led to expression of gut homing molecules α4β7 and CCR9 on peritoneal B1 cells, but not on peritoneal B2 cells. Thus, these results indicate that LF and RA can contribute to gut IgA response through stimulating IgA isotype switching and expression of gut-homing molecules in peritoneal B1 cells.

  4. Effects of marine n-3 fatty acids on circulating levels of soluble adhesion molecules in patients with chronic heart failure.

    PubMed

    Eschen, O; Christensen, J H; LA Rovere, M T; Romano, P; Sala, P; Schmidt, E B

    2010-01-01

    Inflammatory markers as circulating soluble cellular adhesion molecules (sCAMs) and high sensitive C-reactive protein (hsCRP) are elevated in patients with chronic heart failure (CHF), and may constitute an increased risk of adverse outcome. Marine n-3 polyunsaturated fatty acids ( n-3 PUFA) may have anti-inflammatory effect and reduce levels of sCAMs (soluble intercellular adhesion molecule-1 (sICAM-1), vascular adhesion molecule-1 (sVCAM-1), P-selectin) and hsCRP. In a randomized, controlled trial, 138 patients with NYHA class II-III CHF were allocated to receive a daily supplement of 0.9 g of n-3 PUFA or olive oil for 24 weeks. After supplementation, no significant changes occurred in sCAMs or hsCRP after adjusting for possible confounders. However, a significant reduction was observed in sP-selectin in patients receiving n-3 PUFA, but this result was only of borderline significance in a between-group analysis. In conclusion, a daily supplement with 0.9 g of n-3 PUFA does not significantly affect plasma levels of sCAMs or hs-CRP in patients with CHF. n-3 PUFA may reduce sP-selectin, indicating a possible effect on platelet (and endothelial) activation. The results also indicate that the low dose of n-3 PUFA used in many intervention trials does not have deleterious effects on sCAMs or hsCRP.

  5. Coupled Cluster Evaluation of the Stability of Atmospheric Acid-Base Clusters with up to 10 Molecules.

    PubMed

    Myllys, Nanna; Elm, Jonas; Halonen, Roope; Kurtén, Theo; Vehkamäki, Hanna

    2016-02-01

    We investigate the utilization of the domain local pair natural orbital coupled cluster (DLPNO-CCSD(T)) method for calculating binding energies of atmospherical molecular clusters. Applied to small complexes of atmospherical relevance we find that the DLPNO method significantly reduces the scatter in the binding energy, which is commonly present in DFT calculations. For medium sized clusters consisting of sulfuric acid and bases the DLPNO method yields a systematic underestimation of the binding energy compared to canonical coupled cluster results. The errors in the DFT binding energies appear to be more random, while the systematic nature of the DLPNO results allows the establishment of a scaling factor, to better mimic the canonical coupled cluster calculations. Based on the trends identified for the small and medium sized systems, we further extend the application of the DLPNO method to large acid - base clusters consisting of up to 10 molecules, which have previously been out of reach with accurate coupled cluster methods. Using the Atmospheric Cluster Dynamics Code (ACDC) we compare the sulfuric acid dimer formation based on the new DLPNO binding energies with previously published RI-CC2/aug-cc-pV(T+d)Z results. We also compare the simulated sulfuric acid dimer concentration as a function of the base concentration with measurement data from the CLOUD chamber and flow tube experiments. The DLPNO method, even after scaling, underpredicts the dimer concentration significantly. Reasons for this are discussed.

  6. Coupled Cluster Evaluation of the Stability of Atmospheric Acid-Base Clusters with up to 10 Molecules.

    PubMed

    Myllys, Nanna; Elm, Jonas; Halonen, Roope; Kurtén, Theo; Vehkamäki, Hanna

    2016-02-01

    We investigate the utilization of the domain local pair natural orbital coupled cluster (DLPNO-CCSD(T)) method for calculating binding energies of atmospherical molecular clusters. Applied to small complexes of atmospherical relevance we find that the DLPNO method significantly reduces the scatter in the binding energy, which is commonly present in DFT calculations. For medium sized clusters consisting of sulfuric acid and bases the DLPNO method yields a systematic underestimation of the binding energy compared to canonical coupled cluster results. The errors in the DFT binding energies appear to be more random, while the systematic nature of the DLPNO results allows the establishment of a scaling factor, to better mimic the canonical coupled cluster calculations. Based on the trends identified for the small and medium sized systems, we further extend the application of the DLPNO method to large acid - base clusters consisting of up to 10 molecules, which have previously been out of reach with accurate coupled cluster methods. Using the Atmospheric Cluster Dynamics Code (ACDC) we compare the sulfuric acid dimer formation based on the new DLPNO binding energies with previously published RI-CC2/aug-cc-pV(T+d)Z results. We also compare the simulated sulfuric acid dimer concentration as a function of the base concentration with measurement data from the CLOUD chamber and flow tube experiments. The DLPNO method, even after scaling, underpredicts the dimer concentration significantly. Reasons for this are discussed. PMID:26771121

  7. Development and characterization of structured lipids containing capric and conjugated linoleic acids as functional dietary lipid molecules.

    PubMed

    Vu, Phuong-Lan; Shin, Jung-Ah; Lee, Yun-Jeung; Nam, Ha-Young; Lee, Jeung-Hee; Akoh, Casimir C; Lee, Ki-Teak

    2008-03-01

    Recently, dietary oil with high diacylglycerol (DAG) contents, so called DAG-oil, was introduced in Japan and the USA. It was claimed that the oil mostly composed of DAG is metabolized differently from conventional triacylglycerol oil, reducing body weight and fat mass because DAG tends to be oxidized to provide energy rather than stored as fat in the body. Monoacylglcyerol and DAG could be prepared by lipase-catalyzed reactions including hydrolysis, esterification, and glycerolysis. In this study, modified lipid containing some DAG esterified with the health-beneficial medium-chain fatty acids and conjugated linoleic acid was produced by lipase-catalyzed reactions. Many health benefits of medium-chain fatty acids (C6:0-C12:0) and conjugated linoleic acid isomers have been reported, including anticarcinogenic and antiatherogenic activities, and being rapid energy sources for humans with little or no deposition as body fat. The produced lipid molecules in this study have potential applications as functional healthy dietary fats and oils.

  8. Direct Determination of a Small-Molecule Drug, Valproic Acid, by an Electrically-Detected Microcantilever Biosensor for Personalized Diagnostics

    PubMed Central

    Huang, Long-Sun; Gunawan, Christian; Yen, Yi-Kuang; Chang, Kai-Fung

    2015-01-01

    Direct, small-molecule determination of the antiepileptic drug, valproic acid, was investigated by a label-free, nanomechanical biosensor. Valproic acid has long been used as an antiepileptic medication, which is administered through therapeutic drug monitoring and has a narrow therapeutic dosage range of 50–100 μg·mL−1 in blood or serum. Unlike labeled and clinically-used measurement techniques, the label-free, electrical detection microcantilever biosensor can be miniaturized and simplified for use in portable or hand-held point-of-care platforms or personal diagnostic tools. A micromachined microcantilever sensor was packaged into the micro-channel of a fluidic system. The measurement of the antiepileptic drug, valproic acid, in phosphate-buffered saline and serum used a single free-standing, piezoresistive microcantilever biosensor in a thermally-controlled system. The measured surface stresses showed a profile over a concentration range of 50–500 μg·mL−1, which covered the clinically therapeutic range of 50–100 μg·mL−1. The estimated limit of detection (LOD) was calculated to be 45 μg·mL−1, and the binding affinity between the drug and the antibody was measured at around 90 ± 21 μg·mL−1. Lastly, the results of the proposed device showed a similar profile in valproic acid drug detection with those of the clinically-used fluorescence polarization immunoassay. PMID:25632826

  9. Adsorption of biomedical coating molecules, amino acids, and short peptides on magnetite (110)

    NASA Astrophysics Data System (ADS)

    Aschauer, Ulrich; Selloni, Annabella

    2015-07-01

    Superparamagnetic iron oxide nanoparticles for biomedical applications are usually coated with organic molecules to form a steric barrier against agglomeration. The stability of these coatings is well established in the synthesis medium but is more difficult to assess in physiological environment. To obtain a first theoretical estimate of their stability in such an environment, we perform density functional theory calculations of the adsorption of water, polyvinyl alcohol (PVA) and polyethylene glycol (PEG) coating molecules, as well as the monomer and dimer of glycine as a prototype short peptide, on the (110) surface of magnetite (Fe3O4) in vacuo. Our results show that PVA binds significantly stronger to the surface than both PEG and glycine, while the difference between the latter two is quite small. Depending on the coverage, the water adsorption strength is intermediate between PVA and glycine. Due to its strongly interacting OH side groups, PVA is likely to remain bound to the surface in the presence of short peptides. This stability will have to be further assessed by molecular dynamics in the solvated state for which the present work forms the basis.

  10. Adsorption of biomedical coating molecules, amino acids, and short peptides on magnetite (110).

    PubMed

    Aschauer, Ulrich; Selloni, Annabella

    2015-07-28

    Superparamagnetic iron oxide nanoparticles for biomedical applications are usually coated with organic molecules to form a steric barrier against agglomeration. The stability of these coatings is well established in the synthesis medium but is more difficult to assess in physiological environment. To obtain a first theoretical estimate of their stability in such an environment, we perform density functional theory calculations of the adsorption of water, polyvinyl alcohol (PVA) and polyethylene glycol (PEG) coating molecules, as well as the monomer and dimer of glycine as a prototype short peptide, on the (110) surface of magnetite (Fe3O4) in vacuo. Our results show that PVA binds significantly stronger to the surface than both PEG and glycine, while the difference between the latter two is quite small. Depending on the coverage, the water adsorption strength is intermediate between PVA and glycine. Due to its strongly interacting OH side groups, PVA is likely to remain bound to the surface in the presence of short peptides. This stability will have to be further assessed by molecular dynamics in the solvated state for which the present work forms the basis. PMID:26233155

  11. Fluorescence study on the aggregation of collagen molecules in acid solution influenced by hydroxypropyl methylcellulose.

    PubMed

    Ding, Cuicui; Zhang, Min; Li, Guoying

    2016-01-20

    The effect of hydroxypropyl methylcellulose (HPMC) on the aggregation of collagen molecules with collagen concentrations of 0.25, 0.5 and 1.0mg/mL was studied by fluorescence techniques. On one hand, both the synchronous fluorescence spectra and fluorescence emission spectra showed that there was no change in the fluorescence intensity of collagen intrinsic fluorescence when 30% HPMC was added, while it decreased obviously when HPMC content ≥ 50%. From the two-dimensional fluorescence correlation analysis, it was indicated that collagen molecules in 0.25 and 0.5mg/mL collagen solutions were more sensitive to HPMC than those in 1.0mg/mL collagen solution. On the other hand, the pyrene fluorescence and the fluorescence anisotropy measurements indicated that HPMC inhibited the collagen aggregation for 0.25 and 0.5mg/mL collagen, but promoted it for 1.0mg/mL collagen. The atomic force microscopy images further confirmed the effect of HPMC on collagen with different initial states.

  12. Cooperative effect of water molecules in the self-catalyzed neutral hydrolysis of isocyanic acid: a comprehensive theoretical study.

    PubMed

    Wei, Xi-Guang; Sun, Xiao-Ming; Wu, Xiao-Peng; Geng, Song; Ren, Yi; Wong, Ning-Bew; Li, Wai-Kee

    2011-08-01

    The detailed reaction mechanism for the water-assisted hydrolysis of isocyanic acid, HNCO + (n + 1) H(2)O → CO(2) + NH(3) + nH(2)O (n = 0-6), taking place in the gas phase, has been investigated. All structures were optimized and characterized at the MP2/6-31 + G level of theory, and then re-optimized at MP2/6-311++G. The seven explicit water molecules participating in the hydrolysis can be divided into two groups, one directly involved in the proton relay, and the other located in the vicinity of the substrate playing the cooperative role by engaging in hydrogen-bonding to HN = C = O. Two possible reaction pathways, the addition of water molecule across the C = N bond or across the C = O bond, are discussed, and the former is proved to be more favorable energetically. Our calculations suggest that, in the most kinetically favorable pathway for the titled hydrolysis, three water molecules are directly participating in the hydrogen transfer via an eight-membered cyclic transition state, while the other four water molecules catalyze the hydrolysis of HN = C = O by forming three eight-membered cooperative loops near the substrate. This strain-free hydrogen-bond network leads to the best estimated rate-determining activation energy of 24.9 kJ mol(-1) at 600 K, in excellent agreement with the gas-phase kinetic experimental result, 25.8 kJ mol(-1). PMID:21161555

  13. Effect of folic acid decorated magnetic fluorescent nanoparticles on the sedimentation of starch molecules

    NASA Astrophysics Data System (ADS)

    Palanikumar, S.; Kannammal, L.; Meenarathi, B.; Anbarasan, R.

    2014-04-01

    Ferrite-folic acid (FA) nanohybrids were synthesized and characterized by various analytical tools like Fourier transform infrared spectroscopy, UV-Visible spectroscopy, fluorescence spectroscopy, field emission scanning electron microscopy, X-ray diffraction analysis and vibrating sample measurement techniques. After the nanohybrid formation, both the crystallinity and the magnetization values of ferrite were disturbed due to the surface functionalization of ferrite by FA. The role of nanohybrid on the structure-property relationship of starch, particularly the sedimentation of starch under three different pHs, was evaluated. Again the magnetization value of Fe3O4-FA/starch nanocomposite system was reduced due to the encapsulation effect. The sedimentation velocity of starch under the influence of nanohybrid was enhanced in the acidic medium.

  14. Cooperative Aspects of Small Ion, Small Molecule Interactions with Nucleic Acids

    PubMed Central

    Hughes, Floyd

    1970-01-01

    Ionic conductivity measurements vs. temperature were made on KCl solutions of K-polyriboadenylic acid + K-polyribouridylic acid (K-poly-A + K-poly-U) in regions of temperature and composition where the helix-coil transition occurred. It was possible to relate the measurements to a differential helix-to-coil binding of K+ to nucleotide. The results were, within experimental error, the same as those obtained from a limited number of differential KCl activity coefficient measurements and from a theoretical interpretation of polymer free-boundary electrophoretic mobilities. It was concluded that the alkali ion-phosphate interaction in polynucleotides must be regarded as cooperative in nature and several criteria for recognition of such phenomena were given. A brief outline for a proposed statistical mechanical model for binding was presented. PMID:5475728

  15. Single molecule force spectroscopy study of γ-polyglutamic acid by using atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Ahamed, Parbhej; Kawakami, Masaru; Furukawa, Hidemitsu

    2016-04-01

    γ-PGA is a versatile multi-functional biopolymer possessing much useful biological functionality. Each biological function is associated with specific properties related to various forms of γ-PGA. However, to date, knowledge about the molecular mechanism to control specific structures of γ-PGA under a certain environmental conditions are unknown. In this study, we used single molecule force spectroscopy (SMFS) method to characterize the structure of γ-PGA in two environmental conditions. A water environment or 0.5 M MgCl2 salt solution was used to observe the effect of metal ion on γ-PGA structure at room temperature. The obtained results revealed that γ-PGA exists branched and/or cross-linked structure of γ-PGA in water or MgCl2 salt solution.

  16. Conformation-activity relationship of sweet molecules. Comparison of aspartame and naphthimidazolesulfonic acids.

    PubMed

    Castiglione-Morelli, M A; Lelj, F; Naider, F; Tallon, M; Tancredi, T; Temussi, P A

    1990-02-01

    The shape of the active site of the receptor for sweet molecules was previously defined on the basis of a combination of both rigid (saccharins) and flexible (aspartame) molds. In this paper, the sweetness receptor is refined with use of the shapes of 3-anilino-2-styryl-3H-naphtho[1,2-d]imidazolesulfonate (sweet) and of 3-anilino-2-phenyl-3H-naphtho[1,2-d]imidazolesulfonate (tasteless), two large and almost completely rigid tastants. The minimum-energy conformations of the flexible portions of these tastants have been determined by using a detailed conformational analysis based on ab initio calculations. The refined receptor site is still consistent with all previously examined sweet molecules. In order to unequivocally assign the prochiral beta-CH2 protons of the Phe moiety of aspartame, (2S,3S)-[2H]-alpha-L-Asp-L-PheOMe was synthesized and examined by 500-MHz 1H NMR spectroscopy. The results indicate that the minimum-energy conformation for aspartame in water, DMSO-d6, and CDCl3 (as a crown ether complex) is different from that originally proposed (FIIDII instead of FIDII, according to a notation referred to the side chains). Although this conformation is not directly consistent with the shape of the sweet receptor, the interconversion of FIIDII to FIDII was found to require only 1 kcal/mol. Furthermore, a 120-ps molecular dynamics simulation in vacuo confirms the high flexibility of aspartame and the accessibility of the FIDII conformer whose topology is fully consistent with our model. PMID:2299622

  17. Conformation-activity relationship of sweet molecules. Comparison of aspartame and naphthimidazolesulfonic acids.

    PubMed

    Castiglione-Morelli, M A; Lelj, F; Naider, F; Tallon, M; Tancredi, T; Temussi, P A

    1990-02-01

    The shape of the active site of the receptor for sweet molecules was previously defined on the basis of a combination of both rigid (saccharins) and flexible (aspartame) molds. In this paper, the sweetness receptor is refined with use of the shapes of 3-anilino-2-styryl-3H-naphtho[1,2-d]imidazolesulfonate (sweet) and of 3-anilino-2-phenyl-3H-naphtho[1,2-d]imidazolesulfonate (tasteless), two large and almost completely rigid tastants. The minimum-energy conformations of the flexible portions of these tastants have been determined by using a detailed conformational analysis based on ab initio calculations. The refined receptor site is still consistent with all previously examined sweet molecules. In order to unequivocally assign the prochiral beta-CH2 protons of the Phe moiety of aspartame, (2S,3S)-[2H]-alpha-L-Asp-L-PheOMe was synthesized and examined by 500-MHz 1H NMR spectroscopy. The results indicate that the minimum-energy conformation for aspartame in water, DMSO-d6, and CDCl3 (as a crown ether complex) is different from that originally proposed (FIIDII instead of FIDII, according to a notation referred to the side chains). Although this conformation is not directly consistent with the shape of the sweet receptor, the interconversion of FIIDII to FIDII was found to require only 1 kcal/mol. Furthermore, a 120-ps molecular dynamics simulation in vacuo confirms the high flexibility of aspartame and the accessibility of the FIDII conformer whose topology is fully consistent with our model.

  18. The Fatty Acid Signaling Molecule cis-2-Decenoic Acid Increases Metabolic Activity and Reverts Persister Cells to an Antimicrobial-Susceptible State

    PubMed Central

    Morozov, Aleksey; Planzos, Penny; Zelaya, Hector M.

    2014-01-01

    Persister cells, which are tolerant to antimicrobials, contribute to biofilm recalcitrance to therapeutic agents. In turn, the ability to kill persister cells is believed to significantly improve efforts in eradicating biofilm-related, chronic infections. While much research has focused on elucidating the mechanism(s) by which persister cells form, little is known about the mechanism or factors that enable persister cells to revert to an active and susceptible state. Here, we demonstrate that cis-2-decenoic acid (cis-DA), a fatty acid signaling molecule, is able to change the status of Pseudomonas aeruginosa and Escherichia coli persister cells from a dormant to a metabolically active state without an increase in cell number. This cell awakening is supported by an increase of the persister cells' respiratory activity together with changes in protein abundance and increases of the transcript expression levels of several metabolic markers, including acpP, 16S rRNA, atpH, and ppx. Given that most antimicrobials target actively growing cells, we also explored the effect of cis-DA on enhancing antibiotic efficacy in killing persister cells due to their inability to keep a persister cell state. Compared to antimicrobial treatment alone, combinational treatments of persister cell subpopulations with antimicrobials and cis-DA resulted in a significantly greater decrease in cell viability. In addition, the presence of cis-DA led to a decrease in the number of persister cells isolated. We thus demonstrate the ability of a fatty acid signaling molecule to revert bacterial cells from a tolerant phenotype to a metabolically active, antimicrobial-sensitive state. PMID:25192989

  19. Preparation and affinity identification of glutamic acid-urea small molecule analogs in prostate cancer

    PubMed Central

    Zhang, Zhiwei; Zhu, Zheng; Yang, Deyong; Fan, Weiwei; Wang, Jianbo; Li, Xiancheng; Chen, Xiaochi; Wang, Qifeng; Song, Xishuang

    2016-01-01

    In recent years, study concerning activity inhibitors of prostate-specific membrane antigen (PSMA) has been concentrated on the glutamic urea (Glu-urea-R) small molecule and its analogs. The present study aimed to synthesize 4 analogs of Glu-urea-R and identify the affinities of these compounds to PSMA. The compounds were synthesized from raw materials, and the experimental procedures of the present study were in accordance with standard techniques under anhydrous and anaerobic conditions. Glu-urea-Lysine (Glu-urea-Lys), Glu-urea-Ornithine (Glu-urea-Orn), Glu-urea-Glutamine (Glu-urea-Gln) and Glu-urea-Asparagine (Glu-urea-Asn) were successfully synthesized, and their structures were confirmed to be as desired using nuclear magnetic resonance spectroscopy and mass spectrometry. An affinity assay was performed to detect the affinity between the various compounds and PSMA expressed from the prostate cancer LNCap cell line. Glu-urea-Gln had the highest affinity to PSMA, followed by Glu-urea-Asn, Glu-urea-Orn and Glu-urea-Lys. In conclusion, the present study demonstrated that Glu-urea-R specifically binds PSMA expressed in the LNCap cell line and inhibits its activity. PMID:27446384

  20. Hyaluronic Acid-Based Clinical Biomaterials Derived for Cell and Molecule Delivery in Regenerative Medicine

    PubMed Central

    Prestwich, Glenn D.

    2013-01-01

    The development of injectable and biocompatible vehicles for delivery, retention, growth, and differentiation of stem cells is of paramount importance for regenerative medicine. For cell therapy and the development of clinical combination products, we created a hyaluronan (HA)-based synthetic extracellular matrix (sECM) that provides highly reproducible, manufacturable, approvable, and affordable biomaterials. The composition of the sECM can be customized for use with progenitor and mature cell populations obtained from skin, fat, liver, heart, muscle, bone, cartilage, nerves, and other tissues. This overview describes the design criteria for “living” HA derivatives, and the many uses of this in situ crosslinkable HA-based sECM hydrogel for three-dimensional (3-D) culture of cells in vitro and translational use in vivo. Recent advances allow rapid expansion and recovery of cells in 3-D, and the bioprinting of engineered tissue constructs. The uses of HA-derived sECMs for cell and molecule delivery in vivo will be reviewed, including applications in cancer biology and tumor imaging. PMID:21513749

  1. Self-assembly modes of glycyrrhetinic acid esters in view of the crystal packing of related triterpene molecules.

    PubMed

    Langer, Dominik; Wicher, Barbara; Szczołko, Wojciech; Gdaniec, Maria; Tykarska, Ewa

    2016-08-01

    The crystal structures of three ester derivatives of glycyrrhetinic acid (GE) are reported. X-ray crystallography revealed that despite differences in the size of the ester substituents (ethyl, isopropyl and 2-morpholinoethyl) the scheme of molecular self-assembly is similar in all three cases but differs significantly from that observed in other known GE esters. According to our analysis, the two basic patterns of self-assembly of GE esters observed in their unsolvated crystals correspond to two distinct orientations of the ester groups relative to the triterpene backbone. Moreover, comparison of the self-assembly modes of GE esters in their unsolvated forms with the supramolecular organization of GE and carbenoxolone in their solvated crystals revealed that ester substituents replace solvent molecules hydrogen bonded to the COOH group at the triterpene skeleton, resulting in similar packing arrangements of these compounds. PMID:27484379

  2. Acidic attack of perfluorinated alkyl ether lubricant molecules by metal oxide surfaces

    NASA Technical Reports Server (NTRS)

    Zehe, Michael J.; Faut, Owen D.

    1990-01-01

    The reactions of linear perfluoropolyalkylether (PFAE) lubricants with alpha-Fe203 and Fe203-based solid superacids were studied. The reaction with alpha-Fe203 proceeds in two stages. The first stage is an initial slow catalytic decomposition of the fluid. This reaction releases reactive gaseous products which attach the metal oxide and convert it to FeF3. The second stage is a more rapid decomposition of the fluid, effected by the surface FeF3. A study of the initial breakdown step was performed using alpha-Fe203, alpha-Fe203 preconverted to FeF3, and sulfate-promoted alpha-Fe203 superacids. The results indicate that the breakdown reaction involves acidic attack at fluorine atoms on acetal carbons in the linear PFAE. Possible approaches to combat the problem are outlined.

  3. Acidic attack of perfluorinated alkyl ether lubricant molecules by metal oxide surfaces

    NASA Technical Reports Server (NTRS)

    Zehe, Michael J.; Faut, Owen D.

    1989-01-01

    The reactions of linear perfluoropolyalkylether (PFAE) lubricants with alpha-Fe2O3 and Fe2O3-based solid superacids were studied. The reaction with alpha-Fe2O3 proceeds in two stages. The first stage is an initial slow catalytic decomposition of the fluid. This reaction releases reactive gaseous products which attach the metal oxide and convert it to FeF3. The second stage is a more rapid decomposition of the fluid, effected by the surface FeF3. A study of the inital breakdown step was performed using alpha-Fe2O3, alpha-Fe2O3 preconverted to FeF3, and sulfate-promoted alpha-Fe2O3 superacids. The results indicate that the breakdown reaction involves acidic attack at fluorine atoms on acetal carbons in the linear PFAE. Possible approaches to combat the problem are outlined.

  4. Nitrooxyacyl derivatives of salicylic acid: aspirin-like molecules that covalently inactivate cyclooxygenase-1.

    PubMed

    Cena, Clara; Tosco, Paolo; Marini, Elisabetta; Lazzarato, Loretta; Piccinini, Marco; Ramondetti, Cristina; Lupino, Elisa; Fruttero, Roberta; Gasco, Alberto

    2011-03-01

    A recently described series of nitrooxyacyl derivatives of salicylic acid, displaying aspirin-like anti-inflammatory and platelet anti-aggregatory properties, were evaluated for their abilities to inhibit cyclooxygenase (COX). A number of these compounds irreversibly inhibited both COX-1 and COX-2 isoforms when tested in isolated human platelets and monocytes. Further studies using COX-1 expressed in human HEK293T cells showed that this inhibition mechanism is similar to that of aspirin; namely, the products are able to covalently bind to the Ser 530 residue present in the active cleft of the enzyme. Molecular modeling enabled us to rationalize this behavior. Because these products were previously found to display NO-dependent properties in rat animal models, particularly as they decreased in vivo gastrotoxicity and induced in vitro vasodilation, they represent a new and interesting class of potential aspirin-like antithrombotic agents worthy of further study.

  5. An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket

    SciTech Connect

    Debler, Erik W.; Müller, Roger; Hilvert, Donald; Wilson, Ian A.

    2009-12-01

    Design of catalysts featuring multiple functional groups is a desirable, yet formidable goal. Antibody 13G5, which accelerates the cleavage of unactivated benzisoxazoles, is one of few artificial enzymes that harness an acid and a base to achieve efficient proton transfer. X-ray structures of the Fab-hapten complexes of wild-type 13G5 and active-site variants now afford detailed insights into its mechanism. The parent antibody preorganizes Asp{sup H35} and Glu{sup L34} to abstract a proton from substrate and to orient a water molecule for leaving group stabilization, respectively. Remodeling the environment of the hydrogen bond donor with a compensatory network of ordered waters, as seen in the Glu{sup L34} to alanine mutant, leads to an impressive 10{sup 9}-fold rate acceleration over the nonenzymatic reaction with acetate, illustrating the utility of buried water molecules in bifunctional catalysis. Generalization of these design principles may aid in creation of catalysts for other important chemical transformations.

  6. An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket.

    PubMed

    Debler, Erik W; Müller, Roger; Hilvert, Donald; Wilson, Ian A

    2009-11-01

    Design of catalysts featuring multiple functional groups is a desirable, yet formidable goal. Antibody 13G5, which accelerates the cleavage of unactivated benzisoxazoles, is one of few artificial enzymes that harness an acid and a base to achieve efficient proton transfer. X-ray structures of the Fab-hapten complexes of wild-type 13G5 and active-site variants now afford detailed insights into its mechanism. The parent antibody preorganizes Asp(H35) and Glu(L34) to abstract a proton from substrate and to orient a water molecule for leaving group stabilization, respectively. Remodeling the environment of the hydrogen bond donor with a compensatory network of ordered waters, as seen in the Glu(L34) to alanine mutant, leads to an impressive 10(9)-fold rate acceleration over the nonenzymatic reaction with acetate, illustrating the utility of buried water molecules in bifunctional catalysis. Generalization of these design principles may aid in creation of catalysts for other important chemical transformations.

  7. Amino Acid Polymorphisms in Hepatitis C Virus Core Affect Infectious Virus Production and Major Histocompatibility Complex Class I Molecule Expression

    PubMed Central

    Tasaka-Fujita, Megumi; Sugiyama, Nao; Kang, Wonseok; Masaski, Takahiro; Murayama, Asako; Yamada, Norie; Sugiyama, Ryuichi; Tsukuda, Senko; Watashi, Koichi; Asahina, Yasuhiro; Sakamoto, Naoya; Wakita, Takaji; Shin, Eui-Cheol; Kato, Takanobu

    2015-01-01

    Amino acid (aa) polymorphisms in the hepatitis C virus (HCV) genotype 1b core protein have been reported to be a potent predictor for poor response to interferon (IFN)-based therapy and a risk factor for hepatocarcinogenesis. We investigated the effects of these polymorphisms with genotype 1b/2a chimeric viruses that contained polymorphisms of Arg/Gln at aa 70 and Leu/Met at aa 91. We found that infectious virus production was reduced in cells transfected with chimeric virus RNA that had Gln at aa 70 (aa70Q) compared with RNA with Arg at aa 70 (aa70R). Using flow cytometry analysis, we confirmed that HCV core protein accumulated in aa70Q clone transfected cells, and it caused a reduction in cell-surface expression of major histocompatibility complex (MHC) class I molecules induced by IFN treatment through enhanced protein kinase R phosphorylation. We could not detect any effects due to the polymorphism at aa 91. In conclusion, the polymorphism at aa 70 was associated with efficiency of infectious virus production, and this deteriorated virus production in strains with aa70Q resulted in the intracellular accumulation of HCV proteins and attenuation of MHC class I molecule expression. These observations may explain the strain-associated resistance to IFN-based therapy and hepatocarcinogenesis of HCV. PMID:26365522

  8. Gamma-aminobutyric acid and related molecules in the sea fan Eunicella cavolini (Cnidaria: Octocorallia): a biochemical and immunohistochemical approach.

    PubMed

    Girosi, Laura; Ferrando, Sara; Beltrame, Francesco; Ciarcia, Gaetano; Diaspro, Alberto; Fato, Marco; Magnone, Mirko; Raiteri, Luca; Ramoino, Paola; Tagliafierro, Grazia

    2007-07-01

    The aim of this study has been the biochemical demonstration of the presence of gamma-aminobutyric acid (GABA) in the Mediterranean sea fan Eunicella cavolini by means of high-performance liquid chromatography, and the description of the distribution pattern of GABA and its related molecules, glutamic acid decarboxylase (GAD), vesicular GABA transporter (VGAT) and one of the GABA receptors (GABA(B) R) by immunohistochemical methods. The interrelationships of GABA, GAD and GABA receptor immunoreactivity have been established by using double-immunohistochemical methods and confocal microscopy. The immunodetection of monoclonal and/or polyclonal antibodies has revealed GABA immunoreactivity throughout the polyp tissue, both in neuronal and non-neuronal elements. GAD immunoreactivity has been mostly localized in the neuronal compartment, contacting epithelial and muscular elements. GABA(B) R immunoreactivity appears particularly intense in the nematocytes and in the oocyte envelope; its presence in GAD-immunoreactive neurons in the tentacles suggests an autocrine type of regulation. Western blot analysis has confirmed that a GABA(B) R, with a molecular weight of 142 kDa, similar to that of rat brain, is present in E. cavolini polyp tissue. The identification of the sites of the synthesis, vesicular transport, storage and reception of GABA strongly suggests the presence of an almost complete set of GABA-related molecules for the functioning of the GABAergic system in this simple nervous system. The distribution of these different immunoreactivities has allowed us to hypothesize GABA involvement in nematocyst discharge, in body wall and enteric muscular contraction, in neuronal integration and in male gametocyte differentiation.

  9. Nucleic acid molecules encoding isopentenyl monophosphate kinase, and methods of use

    DOEpatents

    Croteau, Rodney B.; Lange, Bernd M.

    2001-01-01

    A cDNA encoding isopentenyl monophosphate kinase (IPK) from peppermint (Mentha x piperita) has been isolated and sequenced, and the corresponding amino acid sequence has been determined. Accordingly, an isolated DNA sequence (SEQ ID NO:1) is provided which codes for the expression of isopentenyl monophosphate kinase (SEQ ID NO:2), from peppermint (Mentha x piperita). In other aspects, replicable recombinant cloning vehicles are provided which code for isopentenyl monophosphate kinase, or for a base sequence sufficiently complementary to at least a portion of isopentenyl monophosphate kinase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding isopentenyl monophosphate kinase. Thus, systems and methods are provided for the recombinant expression of the aforementioned recombinant isopentenyl monophosphate kinase that may be used to facilitate its production, isolation and purification in significant amounts. Recombinant isopentenyl monophosphate kinase may be used to obtain expression or enhanced expression of isopentenyl monophosphate kinase in plants in order to enhance the production of isopentenyl monophosphate kinase, or isoprenoids derived therefrom, or may be otherwise employed for the regulation or expression of isopentenyl monophosphate kinase, or the production of its products.

  10. Quinolinic Acid, an endogenous molecule combining excitotoxicity, oxidative stress and other toxic mechanisms.

    PubMed

    Pérez-De La Cruz, Verónica; Carrillo-Mora, Paul; Santamaría, Abel

    2012-01-01

    Quinolinic acid (QUIN), an endogenous metabolite of the kynurenine pathway, is involved in several neurological disorders, including Huntington's disease, Alzheimer's disease, schizophrenia, HIV associated dementia (HAD) etc. QUIN toxicity involves several mechanisms which trigger various metabolic pathways and transcription factors. The primary mechanism exerted by this excitotoxin in the central nervous system (CNS) has been largely related with the overactivation of N-methyl-D-aspartate receptors and increased cytosolic Ca(2+) concentrations, followed by mitochondrial dysfunction, cytochrome c release, ATP exhaustion, free radical formation and oxidative damage. As a result, this toxic pattern is responsible for selective loss of middle size striatal spiny GABAergic neurons and motor alterations in lesioned animals. This toxin has recently gained attention in biomedical research as, in addition to its proven excitotoxic profile, a considerable amount of evidence suggests that oxidative stress and energetic disturbances are major constituents of its toxic pattern in the CNS. Hence, this profile has changed our perception of how QUIN-related disorders combine different toxic mechanisms resulting in brain damage. This review will focus on the description and integration of recent evidence supporting old and suggesting new mechanisms to explain QUIN toxicity.

  11. Quinolinic Acid, an Endogenous Molecule Combining Excitotoxicity, Oxidative Stress and Other Toxic Mechanisms

    PubMed Central

    Pérez-De La Cruz, Verónica; Carrillo-Mora, Paul; Santamaría, Abel

    2012-01-01

    Quinolinic acid (QUIN), an endogenous metabolite of the kynurenine pathway, is involved in several neurological disorders, including Huntington’s disease, Alzheimer’s disease, schizophrenia, HIV associated dementia (HAD) etc. QUIN toxicity involves several mechanisms which trigger various metabolic pathways and transcription factors. The primary mechanism exerted by this excitotoxin in the central nervous system (CNS) has been largely related with the overactivation of N-methyl-D-aspartate receptors and increased cytosolic Ca2+ concentrations, followed by mitochondrial dysfunction, cytochrome c release, ATP exhaustion, free radical formation and oxidative damage. As a result, this toxic pattern is responsible for selective loss of middle size striatal spiny GABAergic neurons and motor alterations in lesioned animals. This toxin has recently gained attention in biomedical research as, in addition to its proven excitotoxic profile, a considerable amount of evidence suggests that oxidative stress and energetic disturbances are major constituents of its toxic pattern in the CNS. Hence, this profile has changed our perception of how QUIN-related disorders combine different toxic mechanisms resulting in brain damage. This review will focus on the description and integration of recent evidence supporting old and suggesting new mechanisms to explain QUIN toxicity. PMID:22408367

  12. Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli

    PubMed Central

    Howard, Thomas P.; Middelhaufe, Sabine; Moore, Karen; Edner, Christoph; Kolak, Dagmara M.; Taylor, George N.; Parker, David A.; Lee, Rob; Smirnoff, Nicholas; Aves, Stephen J.; Love, John

    2013-01-01

    Biofuels are the most immediate, practical solution for mitigating dependence on fossil hydrocarbons, but current biofuels (alcohols and biodiesels) require significant downstream processing and are not fully compatible with modern, mass-market internal combustion engines. Rather, the ideal biofuels are structurally and chemically identical to the fossil fuels they seek to replace (i.e., aliphatic n- and iso-alkanes and -alkenes of various chain lengths). Here we report on production of such petroleum-replica hydrocarbons in Escherichia coli. The activity of the fatty acid (FA) reductase complex from Photorhabdus luminescens was coupled with aldehyde decarbonylase from Nostoc punctiforme to use free FAs as substrates for alkane biosynthesis. This combination of genes enabled rational alterations to hydrocarbon chain length (Cn) and the production of branched alkanes through upstream genetic and exogenous manipulations of the FA pool. Genetic components for targeted manipulation of the FA pool included expression of a thioesterase from Cinnamomum camphora (camphor) to alter alkane Cn and expression of the branched-chain α-keto acid dehydrogenase complex and β-keto acyl-acyl carrier protein synthase III from Bacillus subtilis to synthesize branched (iso-) alkanes. Rather than simply reconstituting existing metabolic routes to alkane production found in nature, these results demonstrate the ability to design and implement artificial molecular pathways for the production of renewable, industrially relevant fuel molecules. PMID:23610415

  13. Structure and properties of Al-MIL-53-ADP, a breathing MOF based on the aliphatic linker molecule adipic acid.

    PubMed

    Reinsch, Helge; Pillai, Renjith S; Siegel, Renée; Senker, Jürgen; Lieb, Alexandra; Maurin, Guillaume; Stock, Norbert

    2016-03-14

    The new aluminium based metal-organic framework [Al(OH)(O2C-C4H8-CO2)]·H2O denoted as Al-MIL-53-ADP-lp (lp stands for large pore) was synthesised under solvothermal conditions. This solid is an analogue of the archetypical aluminium terephthalate Al-MIL-53 based on the aliphatic single-chain linker molecule adipic acid (H2ADP, hexanedioic acid). In contrast to its aromatic counterparts, Al-MIL-53-ADP exhibits a structural breathing behaviour solely upon dehydration/rehydration. The crystal structure of the anhydrous compound denoted as Al-MIL-53-ADP-np (np stands for narrow pore) was determined by a combination of forcefield-based computations and Rietveld refinement of the powder X-ray diffraction data while the structure of the hydrated form Al-MIL-53-ADP-lp was derived computationally by a combination of force field based methods and Density Functional Theory calculations. Both structures were further supported by (1)H, (13)C and (27)Al high-resolution NMR MAS 1D data coupled again with simulations. Al-MIL-53-ADP was further characterised by means of vibrational spectroscopy, elemental analysis, thermogravimetry and water vapour sorption. PMID:26498663

  14. Polysaccharide arabinogalactan from larch Larix sibirica as carrier for molecules of salicylic and acetylsalicylic acid: preparation, physicochemical and pharmacological study.

    PubMed

    Chistyachenko, Yulia S; Dushkin, Alexandr V; Polyakov, Nikolay E; Khvostov, Mikhail V; Tolstikova, Tatyana G; Tolstikov, Genrikh A; Lyakhov, Nikolay Z

    2015-05-01

    Inclusion complexes of salicylic acid (SA) and acetylsalicylic acid (aspirin, ASA) with polysaccharide arabinogalactan (AG) from larch wood Larix sibirica and Larix gmelinii were synthesized using mechanochemical technology. In the present study, we have investigated physicochemical properties of the synthesized complexes in solid state and in aqueous solutions as well as their anti-aggregation and ulcerogenic activity. The evidence of the complexes formation was obtained by nuclear magnetic resonance (NMR) relaxation technique. It was shown that in aqueous solution the molecules of SA and ASA are in fast exchange between the complex with AG macromolecules and solution. The stability constant of aspirin complex was calculated. It was shown that mechanochemically synthesized complexes are more stable when compared to the complex obtained by mixing solutions of the components. Complexes of ASA show two-fold increase of anti-platelet effect. It allows to reduce the dose of the antithrombotic drug and its ulcerogenic activity. These results substantiate the possibility to design new preparations on the basis of ASA with increased activity and safety.

  15. Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli.

    PubMed

    Howard, Thomas P; Middelhaufe, Sabine; Moore, Karen; Edner, Christoph; Kolak, Dagmara M; Taylor, George N; Parker, David A; Lee, Rob; Smirnoff, Nicholas; Aves, Stephen J; Love, John

    2013-05-01

    Biofuels are the most immediate, practical solution for mitigating dependence on fossil hydrocarbons, but current biofuels (alcohols and biodiesels) require significant downstream processing and are not fully compatible with modern, mass-market internal combustion engines. Rather, the ideal biofuels are structurally and chemically identical to the fossil fuels they seek to replace (i.e., aliphatic n- and iso-alkanes and -alkenes of various chain lengths). Here we report on production of such petroleum-replica hydrocarbons in Escherichia coli. The activity of the fatty acid (FA) reductase complex from Photorhabdus luminescens was coupled with aldehyde decarbonylase from Nostoc punctiforme to use free FAs as substrates for alkane biosynthesis. This combination of genes enabled rational alterations to hydrocarbon chain length (Cn) and the production of branched alkanes through upstream genetic and exogenous manipulations of the FA pool. Genetic components for targeted manipulation of the FA pool included expression of a thioesterase from Cinnamomum camphora (camphor) to alter alkane Cn and expression of the branched-chain α-keto acid dehydrogenase complex and β-keto acyl-acyl carrier protein synthase III from Bacillus subtilis to synthesize branched (iso-) alkanes. Rather than simply reconstituting existing metabolic routes to alkane production found in nature, these results demonstrate the ability to design and implement artificial molecular pathways for the production of renewable, industrially relevant fuel molecules.

  16. Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli.

    PubMed

    Howard, Thomas P; Middelhaufe, Sabine; Moore, Karen; Edner, Christoph; Kolak, Dagmara M; Taylor, George N; Parker, David A; Lee, Rob; Smirnoff, Nicholas; Aves, Stephen J; Love, John

    2013-05-01

    Biofuels are the most immediate, practical solution for mitigating dependence on fossil hydrocarbons, but current biofuels (alcohols and biodiesels) require significant downstream processing and are not fully compatible with modern, mass-market internal combustion engines. Rather, the ideal biofuels are structurally and chemically identical to the fossil fuels they seek to replace (i.e., aliphatic n- and iso-alkanes and -alkenes of various chain lengths). Here we report on production of such petroleum-replica hydrocarbons in Escherichia coli. The activity of the fatty acid (FA) reductase complex from Photorhabdus luminescens was coupled with aldehyde decarbonylase from Nostoc punctiforme to use free FAs as substrates for alkane biosynthesis. This combination of genes enabled rational alterations to hydrocarbon chain length (Cn) and the production of branched alkanes through upstream genetic and exogenous manipulations of the FA pool. Genetic components for targeted manipulation of the FA pool included expression of a thioesterase from Cinnamomum camphora (camphor) to alter alkane Cn and expression of the branched-chain α-keto acid dehydrogenase complex and β-keto acyl-acyl carrier protein synthase III from Bacillus subtilis to synthesize branched (iso-) alkanes. Rather than simply reconstituting existing metabolic routes to alkane production found in nature, these results demonstrate the ability to design and implement artificial molecular pathways for the production of renewable, industrially relevant fuel molecules. PMID:23610415

  17. Polysaccharide arabinogalactan from larch Larix sibirica as carrier for molecules of salicylic and acetylsalicylic acid: preparation, physicochemical and pharmacological study.

    PubMed

    Chistyachenko, Yulia S; Dushkin, Alexandr V; Polyakov, Nikolay E; Khvostov, Mikhail V; Tolstikova, Tatyana G; Tolstikov, Genrikh A; Lyakhov, Nikolay Z

    2015-05-01

    Inclusion complexes of salicylic acid (SA) and acetylsalicylic acid (aspirin, ASA) with polysaccharide arabinogalactan (AG) from larch wood Larix sibirica and Larix gmelinii were synthesized using mechanochemical technology. In the present study, we have investigated physicochemical properties of the synthesized complexes in solid state and in aqueous solutions as well as their anti-aggregation and ulcerogenic activity. The evidence of the complexes formation was obtained by nuclear magnetic resonance (NMR) relaxation technique. It was shown that in aqueous solution the molecules of SA and ASA are in fast exchange between the complex with AG macromolecules and solution. The stability constant of aspirin complex was calculated. It was shown that mechanochemically synthesized complexes are more stable when compared to the complex obtained by mixing solutions of the components. Complexes of ASA show two-fold increase of anti-platelet effect. It allows to reduce the dose of the antithrombotic drug and its ulcerogenic activity. These results substantiate the possibility to design new preparations on the basis of ASA with increased activity and safety. PMID:24517849

  18. Synthesis and biological evaluation of boswellic acid-NSAID hybrid molecules as anti-inflammatory and anti-arthritic agents.

    PubMed

    Shenvi, Suvarna; Kiran, K R; Kumar, Krishna; Diwakar, Latha; Reddy, G Chandrasekara

    2015-06-15

    Methyl esters of the β-boswellic acid (BA) and 11-keto-β-boswellic acid (KBA) obtained from Boswellia serrata resin were subjected to Steglich esterification with the different non-steroidal anti-inflammatory drugs (NSAID) viz., ibuprofen, naproxen, diclophenac and indomethacin. The novel hybrids of methyl boswellate (5-8) and that of methyl 11-keto boswellate (9-12) were evaluated for anti-inflammatory activity by carrageenan-induced rat hind paw edema model and anti-arthritic activity by Complete Freund's Adjuvant (CFA) induced arthritis in Wister albino rat. Significant inhibition on carrageenan-induced paw edema has been observed with 5, 6 and 10 where as in CFA induced rats, hybrids 5, 8, 9 and 12 exhibited pronounced antiarthritic activity. Hybrid molecules 5 and 9 have been found to be more effective in inhibiting in-vivo COX-2 than ibuprofen by itself, thus showing the synergistic effect. Hybrid 5 and 9 tested for in-vitro lipoxygenase and cyclooxygenase-2 (LOX/COX-2) inhibitory activity. The studies revealed that both 5 and 9 inhibited COX-2 relatively better than LOX enzyme. PMID:26010018

  19. Single-molecule surface studies of fibrinogen and DNA on semiconductors

    NASA Astrophysics Data System (ADS)

    Kong, Xianhua

    Understanding of protein adsorption onto non-biological substrates is of fundamental interest in science, but also has great potential technological applications in medical devices and biosensors. This study explores the non-specific interaction, at the single molecule level, of a blood protein and DNA with semiconductor surfaces through the use of a custom built, non rastering electron emission microscope and a scanning probe microscope. The specifics and history of electron emission are described as well as the equipment used in this study. The protein examined in this study is human plasma fibrinogen, which plays an important role in haemostatis and thrombosis, and deoxyribonucleic acid (DNA) is also studied. A novel technique for determining the photothreshold of biomolecules on single molecule level is developed and applied to fibrinogen molecules adsorbed on oxidized silicon surfaces, using photo-electron emission microscopy (PEEM). Three theoretical models are employed and compared to analyze the experimental photothreshold data. The non-specific adsorption of human plasma fibrinogen on oxidized p- and n- type silicon (100) surfaces is investigated to characterize both hydrophobic interactions and electrostatic forces. The experimental results indicate that hydrophobic interactions are one of the driving forces for protein adsorption and the electrostatic interactions also play a role in the height of the fibrinogen molecules adsorbed on the surface. PEEM images establish a photo threshold of 5.0 +/- 0.2 eV for fibrinogen on both n-type and p-type Si (100) surfaces. We suggest that the photothreshold results from surface state associated Fermi level (EF) pinning and there exists negative charge transfer from the adsorbed fibrinogen onto the p-type silicon substrates, while on n-type silicon substrates negative charge is transferred in the opposite direction. The adsorption of deoxyribonucleic acid (DNA) on mica and silicon is studied in liquid and ambient

  20. The First Detections of the Key Prebiotic Molecule PO in Star-forming Regions

    NASA Astrophysics Data System (ADS)

    Rivilla, V. M.; Fontani, F.; Beltrán, M. T.; Vasyunin, A.; Caselli, P.; Martín-Pintado, J.; Cesaroni, R.

    2016-08-01

    Phosphorus is a crucial element in biochemistry, in particular the P‑O bond, which is key in the formation of the backbone of deoxyribonucleic acid. So far, PO has only been detected toward the envelope of evolved stars, but never toward star-forming regions. We report the first detection of PO toward two massive star-forming regions, W51 e1/e2 and W3(OH), using data from the IRAM 30 m telescope. PN has also been detected toward the two regions. The abundance ratio PO/PN is 1.8 and 3 for W51 and W3(OH), respectively. Our chemical model indicates that the two molecules are chemically related and are formed via gas-phase ion–molecule and neutral–neutral reactions during cold collapse. The molecules freeze out onto grains at the end of the collapse and desorb during the warm-up phase once the temperature reaches ˜35 K. Similar abundances of the two species are expected during a period of ˜5 × 104 yr at the early stages of the warm-up phase, when the temperature is in the range 35–90 K. The observed molecular abundances of 10‑10 are predicted by the model if a relatively high initial abundance of 5 × 10‑9 of depleted phosphorus is assumed.

  1. Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

    NASA Astrophysics Data System (ADS)

    Zavadlav, J.; Podgornik, R.; Melo, M. N.; Marrink, S. J.; Praprotnik, M.

    2016-07-01

    We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MARTINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell surrounding the DNA molecule, whereas the solvent in the outer shell is modeled by the coarse-grained model. The solvent entities can exchange between the two domains and adapt their resolution accordingly. We critically asses the performance of our multiscale model in adaptive resolution simulations of an infinitely long DNA molecule, focusing on the structural characteristics of the solvent around DNA. Our analysis shows that the adaptive resolution scheme does not produce any noticeable artifacts in comparison to a reference system simulated in full detail. The effect of using a bundled-SPC model, required for multiscaling, compared to the standard free SPC model is also evaluated. Our multiscale approach opens the way for large scale applications of DNA and other biomolecules which require a large solvent reservoir to avoid boundary effects.

  2. The First Detections of the Key Prebiotic Molecule PO in Star-forming Regions

    NASA Astrophysics Data System (ADS)

    Rivilla, V. M.; Fontani, F.; Beltrán, M. T.; Vasyunin, A.; Caselli, P.; Martín-Pintado, J.; Cesaroni, R.

    2016-08-01

    Phosphorus is a crucial element in biochemistry, in particular the P-O bond, which is key in the formation of the backbone of deoxyribonucleic acid. So far, PO has only been detected toward the envelope of evolved stars, but never toward star-forming regions. We report the first detection of PO toward two massive star-forming regions, W51 e1/e2 and W3(OH), using data from the IRAM 30 m telescope. PN has also been detected toward the two regions. The abundance ratio PO/PN is 1.8 and 3 for W51 and W3(OH), respectively. Our chemical model indicates that the two molecules are chemically related and are formed via gas-phase ion-molecule and neutral-neutral reactions during cold collapse. The molecules freeze out onto grains at the end of the collapse and desorb during the warm-up phase once the temperature reaches ˜35 K. Similar abundances of the two species are expected during a period of ˜5 × 104 yr at the early stages of the warm-up phase, when the temperature is in the range 35-90 K. The observed molecular abundances of 10-10 are predicted by the model if a relatively high initial abundance of 5 × 10-9 of depleted phosphorus is assumed.

  3. Analytical continuation in coupling constant method; application to the calculation of resonance energies and widths for organic molecules: Glycine, alanine and valine and dimer of formic acid

    NASA Astrophysics Data System (ADS)

    Papp, P.; Matejčík, Š.; Mach, P.; Urban, J.; Paidarová, I.; Horáček, J.

    2013-06-01

    The method of analytic continuation in the coupling constant (ACCC) in combination with use of the statistical Padé approximation is applied to the determination of resonance energy and width of some amino acids and formic acid dimer. Standard quantum chemistry codes provide accurate data which can be used for analytic continuation in the coupling constant to obtain the resonance energy and width of organic molecules with a good accuracy. The obtained results are compared with the existing experimental ones.

  4. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 155-92 site in a specific hemizygous diploid line of dairy breeds of domestic goats (Capra aegagrus... of humans) in the mammary gland of goats derived from lineage progenitor 155-92. (b) Sponsor. See No. 042976 in § 510.600 of this chapter. (c) Limitations. Food or feed from GTC-155-92 goats is not...

  5. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 155-92 site in a specific hemizygous diploid line of dairy breeds of domestic goats (Capra aegagrus... of humans) in the mammary gland of goats derived from lineage progenitor 155-92. (b) Sponsor. See No. 042976 in § 510.600 of this chapter. (c) Limitations. Food or feed from GTC-155-92 goats is not...

  6. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 155-92 site in a specific hemizygous diploid line of dairy breeds of domestic goats (Capra aegagrus... of humans) in the mammary gland of goats derived from lineage progenitor 155-92. (b) Sponsor. See No. 042976 in § 510.600 of this chapter. (c) Limitations. Food or feed from GTC-155-92 goats is not...

  7. Purification of influenza deoxyribonucleic acid-based vaccine using agmatine monolith.

    PubMed

    Bicho, D; Caramelo-Nunes, C; Sousa, A; Sousa, F; Queiroz, J A; Tomaz, C T

    2016-02-15

    Lately, researchers have made several efforts to improve vaccine production to fight highly contagious respiratory diseases like influenza. One of the most promising options for reducing the impact of this virus is DNA vaccination. However, a large quantity of highly pure plasmid DNA (pDNA) is necessary to attain this goal. The present work describes the production and purification of the plasmid NTC7482-41H-VA2HA expressing influenza virus hemagglutinin using an agmatine monolith. This ligand was chosen to purify supercoiled (sc) pDNA from complex lysates because of its versatile multimodal character. Its natural intervention in several biological systems together with its similarity with the highly studied arginine ligand allowed the development of a simpler and more specific purification process. Agmatine works under two strategies: descending ammonium sulfate gradient and ascending sodium chloride gradient. Furthermore, pH manipulation revealed an important role in pDNA isoforms selectivity. Dynamic binding capacity (DBC) experiments were performed varying different parameters and showed an increase with pDNA concentration, while high flow rate and high pH had the opposite effect. Sc pDNA was purified with high yield and was efficient with respect to cell transfection and cell viability. This monolith showed to be appropriate to purify the plasmid NTC7482-41H-VA2HA, providing a valuable tool for pDNA influenza vaccines preparation. PMID:26827278

  8. [Epigenetic heredity (deoxyribonucleic acid methylation): Clinical context in neurodegenerative disorders and ATXN2 gene].

    PubMed

    Laffita-Mesa, José Miguel; Bauer, Peter

    2014-10-21

    Epigenetics is the group of changes in the phenotype which are related with the process independently of the primary DNA sequence. These changes are intimately related with changes in the gene expression level and its profile across the body. These are mediated by histone tail modifications, DNA methylation, micro-RNAs, with chromatin remodeling remaining as the foundation of epigenetic changes. DNA methylation involves the covalent addition of methyl group to cytosine of the DNA, which is mediated by methyltransferases enzymes. DNA methylation regulates gene expression by repressing transcription, while de-methylation activates gene transcription. Several human diseases are related with the epigenetic process: cancer, Alzheimer disease, stroke, Parkinson disease, and diabetes. We present here the basis of epigenetic inheritance and show the pathogenic mechanisms relating epigenetics in human diseases, specifically with regard to neurodegeneration. We discuss current concepts aimed at understanding the contribution of epigenetics to human neurodegenerative diseases. We also discuss recent findings obtained in our and other centers regarding the ATXN2 gene that causes spinocerebellar ataxia 2 and amyotrophic lateral sclerosis. Epigenetics play a pivotal role in the pathogenesis of human diseases and in several neurodegenerative disorders, and this knowledge will illuminate the pathways in the diagnostic and therapeutic field, which ultimately will be translated into the clinic context of neurodegenerative diseases.

  9. Development of a small gantry robotic workcell for deoxyribonucleic acid (DNA) filter array construction

    SciTech Connect

    Beugelsdijk, T.J.; Hollen, R.M.; Snider, K.T.

    1990-01-01

    At Los Alamos National Laboratory, we have constructed a primary cosmid library of human chromosome 16. This library consists of an 11-fold representation of the chromosome and is arrayed in microtiter plate format. A need has arisen in the large scale physical mapping of this chromosome, to array spots of DNA from each of these colonies onto filter media for hybridization studies. We are currently developing a small gantry robot-based workcell to array small spots of DNA in an interleaved format. This allows for the construction of a high spot density format filter array. This paper will discuss the features incorporated into this workcell for the handling of thousands of colonies and their automatic tracking and positioning onto the filter. 7 refs., 3 figs., 1 tab.

  10. Relationship between pregnancy, embryo development, and sperm deoxyribonucleic acid fragmentation dynamics.

    PubMed

    Wdowiak, Artur; Bojar, Iwona

    2016-09-01

    The way the dynamics of DNA fragmentation affects the growth of embryos in real time, and effectiveness of infertility treatment using the ICSI procedure were determined in 148 couples treated with the ICSI technique. The percentage of sperm with fragmented DNA (known as the DNA fragmentation index [DFI]) in semen samples was determined at 3, 6 and 12 h. Embryo culture was assessed continuously during 12 h of observation monitoring. Statistically significant difference was found in DFI at 12 h and outcome of treatment. For the remaining time intervals, no statistically significant differences were noted. An analysis of relationship between the DFI dynamics over time at individual measurements and achievement of pregnancy, confirmed a statistically significant relationship between the rate measured at 6-12 h of observations of DFI changes (DFI 12 h%/h), and achieving pregnancy. Correlation was observed between DFI (during 0, 3, 6 and 12 h), the growth rate in DFI, and time of embryo development. A statistically significant relationship was found between the rate from the start to the end of observations of the DFI, and outcome of treatment. Intensity level regarding fragmentation of sperm DNA and its growth rate affected the time of embryo development in the ICSI procedure. The most significant prognostic factor for achieving pregnancy was intensification of sperm DNA fragmentation after 12 h. PMID:27579009

  11. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 155-92 site in a specific hemizygous diploid line of dairy breeds of domestic goats (Capra aegagrus... of humans) in the mammary gland of goats derived from lineage progenitor 155-92. (b) Sponsor. See No. 042976 in § 510.600 of this chapter. (c) Limitations. Food or feed from GTC-155-92 goats is not...

  12. Transcription of rat liver deoxyribonucleic acid in vitro at low ionic strength.

    PubMed Central

    Pays, E

    1978-01-01

    1. When RNA polymerase is in excess over DNA, the single-stranded breaks of DNA can be recognized as initiation sites for the ezyme. On the other hand stabel initiation complexes (resistant to inhibition by heparin) are the most abundant under these conditions. The formation of these complexes needs double-stranded DNA. It seems that RNA sequences rich in cytidine are preferentially synthesized; since rat liver DNA is A + T-rich, the transcription thus appears not to be random with respect to the base composition of DNA. 2. When the template is in excess over the polymerase, the single-stranded gaps of DNA are preferentially transcribed by rat liver RNA polymerase B and native DNA regions by Escherichia coli RNA polymerase. 3. With a large excess of DNA over the polymerase, the enzyme activity is markedly inhibited. This inhibition is proportional to the concentration of double-stranded DNA ends, but it also depends on the presence of a contaminant of DNA, removed when DNA is banded in a CsCl gradient. This contaminant could be polyphosphates. Low concentrations of spermine completely reverse this inhibition, by enhancing the rate of RNA chain elongation. 4. Double-stranded RNA is synthesized in great abundance when RNA polymerase is in excess over native DNA. Besides a majority of symmetrical sequences, stable 'hairpins' can be found. Whereas the synthesis of symmetrical sequences is more prevalent in polymerase excess, it seems that the proportion of stable 'hairpins' in RNA is independent of the polymerase/DNA ratio. PMID:32873

  13. Estimation of gene reiteration from hybridization kinetics in moderate deoxyribonucleic acid excess.

    PubMed Central

    Muto, M

    1977-01-01

    Theoretical calculations were carried out to clarify how the DNA/RNA or the DNA/cDNA (complementary DNA) ratio in the hybridization reaction mixture affects the kinetics of DNA-RNA or DNA-cDNA reassociation, and theoretical formulae were derived as a function of these ratios. From these formulae, it was found that the DNA/RNA of the DNA/cDNA ratio did not much affect the initial reaction rates of hybridization, but greatly affected the terminal value for the extent of hybrid formation. Therefore the results obtained when one normalizes the experimental data for hydridization and derives the reiteration frequency from a number called the 'half Cot' (Cot 1/2) are not accurate, especially in the presence of a moderate excess of DNA. A simple method for the estimation of gene reiteration was demonstrated that did not use the half Cot value in the determination. This simple method is useful even if DNA-RNA or DNA/cDNA hybridization are done with a moderate excess of DNA. With mouse myeloma cells as a model system, the gene reiteration of the 28S rRNA cristron was determined. PMID:889572

  14. Formation of rings from segments of HeLa-cell nuclear deoxyribonucleic acid

    PubMed Central

    Hardman, Norman

    1974-01-01

    Duplex segments of HeLa-cell nuclear DNA were generated by cleavage with DNA restriction endonuclease from Haemophilus influenzae. About 20–25% of the DNA segments produced, when partly degraded with exonuclease III and annealed, were found to form rings visible in the electron microscope. A further 5% of the DNA segments formed structures that were branched in configuration. Similar structures were generated from HeLa-cell DNA, without prior treatment with restriction endonuclease, when the complementary polynucleotide chains were exposed by exonuclease III action at single-chain nicks. After exposure of an average single-chain length of 1400 nucleotides per terminus at nicks in HeLa-cell DNA by exonuclease III, followed by annealing, the physical length of ring closures was estimated and found to be 0.02–0.1μm, or 50–300 base pairs. An almost identical distribution of lengths was recorded for the regions of complementary base sequence responsible for branch formation. It is proposed that most of the rings and branches are formed from classes of reiterated base sequence with an average length of 180 base pairs arranged intermittenly in HeLa-cell DNA. From the rate of formation of branched structures when HeLa-cell DNA segments were heat-denatured and annealed, it is estimated that the reiterated sequences are in families containing approximately 2400–24000 copies. ImagesPLATE 2PLATE 1 PMID:4462738

  15. Purification of influenza deoxyribonucleic acid-based vaccine using agmatine monolith.

    PubMed

    Bicho, D; Caramelo-Nunes, C; Sousa, A; Sousa, F; Queiroz, J A; Tomaz, C T

    2016-02-15

    Lately, researchers have made several efforts to improve vaccine production to fight highly contagious respiratory diseases like influenza. One of the most promising options for reducing the impact of this virus is DNA vaccination. However, a large quantity of highly pure plasmid DNA (pDNA) is necessary to attain this goal. The present work describes the production and purification of the plasmid NTC7482-41H-VA2HA expressing influenza virus hemagglutinin using an agmatine monolith. This ligand was chosen to purify supercoiled (sc) pDNA from complex lysates because of its versatile multimodal character. Its natural intervention in several biological systems together with its similarity with the highly studied arginine ligand allowed the development of a simpler and more specific purification process. Agmatine works under two strategies: descending ammonium sulfate gradient and ascending sodium chloride gradient. Furthermore, pH manipulation revealed an important role in pDNA isoforms selectivity. Dynamic binding capacity (DBC) experiments were performed varying different parameters and showed an increase with pDNA concentration, while high flow rate and high pH had the opposite effect. Sc pDNA was purified with high yield and was efficient with respect to cell transfection and cell viability. This monolith showed to be appropriate to purify the plasmid NTC7482-41H-VA2HA, providing a valuable tool for pDNA influenza vaccines preparation.

  16. Characterization of deoxyribonucleic acid from cells infected with Aleutian disease virus

    SciTech Connect

    Hahn, E.C.; Ramos, L.; Kenyon, A.J.

    1983-07-01

    Viral DNA was extracted from Crandell feline kidney (CRFK) cells infected with Aleutian disease virus (ADV) and labeled with (/sup 3/H)thymidine. The sedimentation coefficient in alkaline sucrose gradients was 16S corresponding to a molecular weight of 1.5 X 10(6). The buoyant densities of DNA from infected and control cells were determined by isopyknic sedimentation in CsCl and NaI gradients. Two additional peaks of (/sup 3/H)DNA were found in infected cells, but not in control cell extracts. Fractionation of this DNA on hydroxylapatite indicated that the new peaks represented a single-stranded component, density 1.728 g/cm3, and a double-stranded component, presumed to be a viral replicative intermediate, density 1.718 g/cm3. The target antigen formation in CRFK cells was measured by gamma-irradiation of ADV and assayed for focus formation. The calculated size of ADV based on these measurements was 1.1 X 10(6). The H-1 parvovirus also was shown to have a size of 1.5 X 10(6) daltons for both antigen and plaque formation. The data indicated similarities existed between ADV and other autonomously replicating parvoviruses in most properties, except that less-than-unit length genome of ADV may be transcribed.

  17. Plasma Epstein–Barr Viral Deoxyribonucleic Acid Predicts Worse Outcomes in Pediatric Nonmetastatic Nasopharyngeal Carcinoma Patients

    PubMed Central

    Shen, Ting; Tang, Lin-Quan; Gu, Wei-Guang; Luo, Dong-Hua; Chen, Qiu-Yan; Li, Pei-Jing; Mai, Dong-Mei; Mai, Hai-Qiang; Mo, Hao-Yuan

    2015-01-01

    Abstract To evaluate the clinical significance of pretreatment levels of plasma Epstein–Barr virus DNA (pEBV DNA) on prognoses in pediatric nasopharyngeal carcinoma (NPC) patients. Eighty-nine patients aged 21 years old or younger with nonmetastatic NPC were evaluated to determine the effect of pEBV DNA levels on progression-free survival (PFS), distant metastasis-free survival (DMFS), and overall survival (OS). Survival probabilities in patient groups that were segregated by clinical stage or pEBV DNA load (low or high) were compared. The median pretreatment concentrations of pEBV DNA were 3440 copies/mL in 35 patients with stage III disease and 14,900 copies/mL in 50 patients with stage IV disease (P = 0.059). The median concentration of pEBV DNA was 34,500 copies/mL in 17 patients with relapse, which was higher than the concentration in 72 patients without relapse, who had a median level of 4985 copies/mL (P = 0.057). Further study showed that pretreatment pEBV DNA load was an independent prognostic indicator in pediatric NPC patients. High pEBV DNA was associated with adverse clinical outcomes, including PFS [3-year PFS rate = 80.5% versus 95.8%, hazard ratio (HR) = 5.00, 95% confidence interval (CI) = 1.00–25.00; P = 0.050], DMFS (3-year DMFS rate = 80.5% versus 95.8%, HR = 5.20, 95% CI = 1.04–26.00; P = 0.045), and OS (3-year OS rate = 82.9% versus 95.8%, HR = 5.41, 95% CI = 1.08–27.22; P = 0.040). Pretreatment pEBV DNA load was an independent prognostic indicator for PFS, DMFS, and OS in pediatric patients with NPC. Prospective studies, however, are needed to validate these results. PMID:26683909

  18. Dysembryoplastic neuroepithelial tumor: morphological, immunocytochemical, and deoxyribonucleic acid analyses in a pediatric series.

    PubMed

    Taratuto, A L; Pomata, H; Sevlever, G; Gallo, G; Monges, J

    1995-03-01

    Overtreatment by radiotherapy and/or chemotherapy for central nervous system tumors in infancy and childhood may be deleterious, so the recognition of surgically curable clinicopathological entities is mandatory. The dysembryoplastic neuroepithelial tumor is a complex multinodular lesion consisting of glial nodules, associated with a specific glioneuronal element and/or with focal cortical dysplasia, and occurring in young patients presenting with intractable, mostly complex partial, seizures without neurological deterioration. We report on 14 patients; 9 were from a series of 600 pediatric patients with intracranial central nervous system tumors studied at a single institution from 1988 to 1993, and 5 were referred from other pediatric hospitals. Six tumors were frontal, six were temporal, one was parietal, and one was occipitoparietal. Computed tomographic scans disclosed hypodense lesions with cystic appearances in 4 patients and slight focal postcontrast enhancements in only 2 patients, whereas magnetic resonance imaging, available for 7 of 14 patients, showed hypointense lesions in T1-weighted images and hyperintense lesions in T2-weighted images. Deformities of the overlying cranium were also observed in five patients. The age range at the time of surgery (excluding a 20-year-old male patient who underwent surgery at the main pediatric hospital) was 2.6 to 13 years, with a mean of 6.68 years. The male to female patient ratio was 10:4, and the duration of symptoms was 0.2 to 6 years.(ABSTRACT TRUNCATED AT 250 WORDS)

  19. DNA (deoxyribonucleic acid) synthesis following microinjection of heterologous sperm and somatic cell nuclei into hamster oocytes

    SciTech Connect

    Naish, S.J.; Perreault, S.D.; Zirkin, B.R.

    1987-01-01

    The authors investigated the ability of the hamster oocyte to initiate DNA synthesis in nuclei differing in basic protein content. DNA synthesis was studied by autoradiography in oocytes that had been incubated in /sup 3/H-thymidine after being parthenogenetically activated by sham microinjection, or microinjected with hamster, mouse, rabbit, or fish sperm nuclei, or hamster hepatocyte nuclei. Within 6 hr of sham or nucleus microinjection, nuclei of each type underwent transformation into pronuclei and synthesized DNA. These results demonstrated that the hamster egg can access and utilize its own and each type of template provided, whether homologous or heterologous. However, pronuclei derived from hamster sperm nuclei were more likely to be synthesizing DNA at 6 hr than pronuclei derived from sperm nuclei of other species. The authors conclude that the mechanisms employed by the hamster oocyte to transform hamster sperm nuclei into pronuclei and to effect DNA synthesis in these nuclei are not specific for the hamster sperm nucleus. Nevertheless, these mechanisms apparently operate more efficiently when the hamster sperm nucleus, rather than a heterologous sperm nucleus, is present.

  20. Detection of human papillomavirus deoxyribonucleic acid in the female genital tract.

    PubMed

    Czeglédy, J; Gergely, L; Hernádi, Z; Póka, R

    1989-01-01

    A total of 336 biopsies, scrapes and exfoliated cells from the cervix and from the lower genital tract were screened for human papilloma (HP) viral sequences of types 6, 11, 16 and 18 by Southern blot, dot blot and filter in situ (FISH) hybridizations with cloned 32P-radiolabeled HPV DNA probes. The specimens included cervical intraepithelial neoplasias (CIN I-III), carcinoma in situ and invasive carcinoma of the cervix and vagina, adenocarcinomas, vulvar and vaginal condylomata acuminata and healthy epithelial samples. The oncogenic HPV 16 was found in 46% of the cervical carcinomas. Most of the type 16 occurrences (75%) represented the third stage of inoperable cases. Similarly, HPV 18 was also most frequently present in this stage as well as in carcinoma in situ and in CIN III (25%, 18%). At the same time, in condylomata acuminata, types 6 and 11 were detectable in 88.7% of cares. In all, 13.5% of the normal samples harboured HPV DNA. PMID:2559306

  1. Characterization of a cardiac complementary deoxyribonucleic acid library from the Turkey (Meleagris gallopavo).

    PubMed

    Mendoza, K M; Chiang, W; Strasburg, G M; Reed, K M

    2008-06-01

    Although the domestic turkey (Meleagris gallopavo) is a valuable agricultural commodity, genetic studies on this species lag behind those of other agricultural species. In this study, we examined expressed sequence tags (EST) from a turkey cardiac cDNA library constructed from 4 birds representing 2 developmental stages. A collection of 3,937 EST sequences were sequenced and analyzed for gene annotation and sequence variation. Clustering of sequences resulted in 353 contigs and 874 singletons (1,227 putative transcripts). All EST sequences were compared by BLASTN to the chicken whole genome sequence and to Ensembl and National Center for Biotechnology Information databases. The majority of significant matches correspond to genes found in the chicken. Sequence polymorphisms were identified in 310 contigs, 64 where the minor allele was observed to be present in more than 1 sequence. This study gives species-specific insight into the cardiac transcriptome of turkeys and provides resources for future studies of cardiac function.

  2. Relatedness among coagulase-negative staphylococci: deoxyribonucleic acid reassociation and comparative immunological studies.

    PubMed

    Schleifer, K H; Meyer, S A; Rupprecht, M

    1979-07-01

    DNA-DNA-homology values were determined under restrictive to relaxed reassociation conditions with type strains and some additional strains of coagulase-negative staphylococci belonging to ten different species. The immunological relationship of the catalases present in the type strains of these species was also determined by applying double immunodiffusion and microcomplement fixation. The results of these studies support the previous proposal to subdivide the coagulase-negative staphylococci into at least ten separate species. However, it is evident that some of the species are more closely realted than others and can form species groups. According to the results presented in this study, the coagulase-negative staphylococci can be combined into five species groups: The Staphylococcus saprophyticus group is composed of S. saprophyticus, S. xylosus and S. cohnii. The S. epidermidis group comprises S. epidermis, S. capitis and S. warneri. The S. hominis group which exhibits a significant relationship to S. epidermidis includes S. hominis and S. haemolyticus. The species group S. sciuri consists of S. sciuri ssp. sciuri and S. sciuri ssp. lentus and the species group S. simulans is presently represented by the corresponding single species. PMID:92972

  3. A self-assembled deoxyribonucleic acid concatemer for sensitive detection of single nucleotide polymorphism.

    PubMed

    Wu, Wei; Chen, Junhua; Fang, Zhiyuan; Ge, Chenchen; Xiang, Zhicheng; Ouyang, Chuanyan; Lie, Puchang; Xiao, Zhuo; Yu, Luxin; Wang, Lin; Zeng, Lingwen

    2013-12-01

    Polymerase-free and label-free strategies for DNA detection have shown excellent sensitivity and specificity in various biological samples. Herein, we propose a method for single nucleotide polymorphism (SNP) detection by using self-assembled DNA concatemers. Capture probes, bound to magnetic beads, can joint mediator probes by T4 DNA ligase in the presence of target DNA that is complementary to the capture probe and mediator probe. The mediator probes trigger self-assembly of two auxiliary probes on magnetic beads to form DNA concatemers. Separated by a magnetic rack, the double-stranded concatemers on beads can recruit a great amount of SYBR Green I and eventually result in amplified fluorescent signals. In comparison with reported methods for SNP detection, the concatemer-based approach has significant advantages of low background, simplicity, and ultrasensitivity, making it as a convenient platform for clinical applications. As a proof of concept, BRAF(T1799A) oncogene mutation, a SNP involved in diverse human cancers, was used as a model target. The developed approach using a fluorescent intercalator can detect as low as 0.1 fM target BRAF(T1799A) DNA, which is better than those previously published methods for SNP detection. This method is robust and can be used directly to measure the BRAF(T1799A) DNA in complex human serum with excellent recovery (94-103%). It is expected that this assay principle can be directed toward other SNP genes by simply changing the mediator probe and auxiliary probes. PMID:24267087

  4. A Complex Deoxyribonucleic Acid Looping Configuration Associated with the Silencing of the Maternal Igf2 Allele

    PubMed Central

    Qiu, Xinwen; Vu, Thanh H.; Lu, Qiucheng; Ling, Jian Qun; Li, Tao; Hou, Aiju; Wang, Shu Kui; Chen, Hui Ling; Hu, Ji Fan; Hoffman, Andrew R.

    2008-01-01

    Alternate interactions between the H19 imprinting control region (ICR) and one of the two Igf2 differentially methylated regions has been proposed as a model regulating the reciprocal imprinting of Igf2 and H19. To study the conformation of this imprint switch, we performed a systematic structural analysis across the 140 kb of the mouse Igf2-H19 region, which includes enhancers located both between the two genes as well as downstream of H19, by using a scanning chromosome conformation capture (3C) technique. Our results suggest that on the active paternal Igf2 allele, the various enhancers have direct access to the Igf2 promoters, whereas the imprinted silent maternal Igf2 allele assumes a complex three-dimensional knotted loop that keeps the enhancers away from the Igf2 promoters and allows them to interact with the H19 promoter. This complex DNA looping of the maternal allele is formed by interactions involving differentially methylated region 1, the ICR, and enhancers. Binding of CTC-binding factor to the maternal, unmethylated ICR in conjunction with the presence of multicomplex components including interchromosomal interactions, create a barrier blocking the access of all enhancers to Igf2, thereby silencing the maternal Igf2. This silencing configuration exists in newborn liver, mouse embryonic fibroblast, and embryonic stem cells and persists during mitosis, conferring a mechanism for epigenetic memory. PMID:18356289

  5. Intracellular localization and effects on cell division of a plasmid blocked in deoxyribonucleic acid replication.

    PubMed Central

    MacQueen, H A; Donachie, W D

    1977-01-01

    Cell division in a uvr mutant of Escherichia coli is suppressed by introdcution into the cell of an ultraviolet-irradiated plasmid. Autoradiography was used to determine the localization of the incoming plasmid and the segregation pattern of the host chromosomes. PMID:334739

  6. Quantifying the ion atmosphere of unfolded, single-stranded nucleic acids using equilibrium dialysis and single-molecule methods

    PubMed Central

    Jacobson, David R.; Saleh, Omar A.

    2016-01-01

    To form secondary structure, nucleic acids (NAs) must overcome electrostatic strand–strand repulsion, which is moderated by the surrounding atmosphere of screening ions. The free energy of NA folding therefore depends on the interactions of this ion atmosphere with both the folded and unfolded states. We quantify such interactions using the preferential ion interaction coefficient or ion excess: the number of ions present near the NA in excess of the bulk concentration. The ion excess of the folded, double-helical state has been extensively studied; however, much less is known about the salt-dependent ion excess of the unfolded, single-stranded state. We measure this quantity using three complementary approaches: a direct approach of Donnan equilibrium dialysis read out by atomic emission spectroscopy and two indirect approaches involving either single-molecule force spectroscopy or existing thermal denaturation data. The results of these three approaches, each involving an independent experimental technique, are in good agreement. Even though the single-stranded NAs are flexible polymers that are expected to adopt random-coil configurations, we find that their ion atmosphere is quantitatively described by rod-like models that neglect large-scale conformational freedom, an effect that we explain in terms of the competition between the relevant structural and electrostatic length scales. PMID:27036864

  7. Enhancement of a Lewis acid-base interaction via solvation: ammonia molecules and the benzene radical cation.

    PubMed

    Chiang, Chi-Tung; Freindorf, Marek; Furlani, Thomas; DeLeon, Robert L; Richard, John P; Garvey, James F

    2007-07-12

    The interaction between ammonia and the benzene radical cation has been investigated by gas-phase studies of mass selected ion clusters {C(6)H(6)-(NH(3))(n=0-8)}(+) via tandem quadrupole mass spectrometry and through calculations. Experiments show a special stability for the cluster ion that contains four ammonias: {C(6)H(6)(NH(3))(4)}(+). Calculations provide evidence that the first ammonia forms a weak dative bond to the cyclohexadienyl radical cation, {C(6)H(6)-NH(3)}(+), where there is a transfer of electrons from ammonia to benzene. Additional solvating ammonia molecules form stabilizing hydrogen bonds to the ring-bound ammonia {C(6)H(6)-NH(3)}(+).(NH(3))(n), which cause cooperative changes in the structure of the cluster complex. Free ammonia is a weak hydrogen bond donor, but electron transfer from NH(3) to the benzene ring that strengthens the dative bond will increase the hydrogen acidity and the strength of the cluster hydrogen bonds to the added ammonia. A progressive "tightening" of this dative bond is observed upon addition of the first, second, and third ammonia to give a cluster stabilized by three N-(+)H x N hydrogen bonds. This shows that the energetic cost of tightening the dative bond is recovered with dividends in the formation of stable cluster hydrogen bonds.

  8. Structure and Mutagenesis of Neural Cell Adhesion Molecule Domains Evidence for Flexibility in the Placement of Polysialic Acid Attachment Sites

    SciTech Connect

    Foley, Deirdre A.; Swartzentruber, Kristin G.; Lavie, Arnon; Colley, Karen J.

    2010-11-09

    The addition of {alpha}2,8-polysialic acid to the N-glycans of the neural cell adhesion molecule, NCAM, is critical for brain development and plays roles in synaptic plasticity, learning and memory, neuronal regeneration, and the growth and invasiveness of cancer cells. Our previous work indicates that the polysialylation of two N-glycans located on the fifth immunoglobulin domain (Ig5) of NCAM requires the presence of specific sequences in the adjacent fibronectin type III repeat (FN1). To understand the relationship of these two domains, we have solved the crystal structure of the NCAM Ig5-FN1 tandem. Unexpectedly, the structure reveals that the sites of Ig5 polysialylation are on the opposite face from the FN1 residues previously found to be critical for N-glycan polysialylation, suggesting that the Ig5-FN1 domain relationship may be flexible and/or that there is flexibility in the placement of Ig5 glycosylation sites for polysialylation. To test the latter possibility, new Ig5 glycosylation sites were engineered and their polysialylation tested. We observed some flexibility in glycosylation site location for polysialylation and demonstrate that the lack of polysialylation of a glycan attached to Asn-423 may be in part related to a lack of terminal processing. The data also suggest that, although the polysialyltransferases do not require the Ig5 domain for NCAM recognition, their ability to engage with this domain is necessary for polysialylation to occur on Ig5 N-glycans.

  9. Microfluidic study of the chemotactic response of Escherichia coli to amino acids, signaling molecules and secondary metabolites.

    PubMed

    Nagy, Krisztina; Sipos, Orsolya; Valkai, Sándor; Gombai, Éva; Hodula, Orsolya; Kerényi, Ádám; Ormos, Pál; Galajda, Péter

    2015-07-01

    Quorum sensing and chemotaxis both affect bacterial behavior on the population level. Chemotaxis shapes the spatial distribution of cells, while quorum sensing realizes a cell-density dependent gene regulation. An interesting question is if these mechanisms interact on some level: Does quorum sensing, a density dependent process, affect cell density itself via chemotaxis? Since quorum sensing often spans across species, such a feedback mechanism may also exist between multiple species. We constructed a microfluidic platform to study these questions. A flow-free, stable linear chemical gradient is formed in our device within a few minutes that makes it suitable for sensitive testing of chemoeffectors: we showed that the amino acid lysine is a weak chemoattractant for Escherichia coli, while arginine is neutral. We studied the effect of quorum sensing signal molecules of Pseudomonas aeruginosa on E. coli chemotaxis. Our results show that N-(3-oxododecanoyl)-homoserine lactone (oxo-C12-HSL) and N-(butryl)-homoserine lactone (C4-HSL) are attractants. Furthermore, we tested the chemoeffector potential of pyocyanin and pyoverdine, secondary metabolites under a quorum sensing control. Pyocyanin is proved to be a weak attractant while pyoverdine are repellent. We demonstrated the usability of the device in co-culturing experiments, where we showed that various factors released by P. aeruginosa affect the dynamic spatial rearrangement of a neighboring E. coli population, while surface adhesion of the cells is also modulated. PMID:26339306

  10. Cyanobacteria produce N-(2-aminoethyl)glycine, a backbone for peptide nucleic acids which may have been the first genetic molecules for life on Earth.

    PubMed

    Banack, Sandra Anne; Metcalf, James S; Jiang, Liying; Craighead, Derek; Ilag, Leopold L; Cox, Paul Alan

    2012-01-01

    Prior to the evolution of DNA-based organisms on earth over 3.5 billion years ago it is hypothesized that RNA was the primary genetic molecule. Before RNA-based organisms arose, peptide nucleic acids may have been used to transmit genetic information by the earliest forms of life on earth. We discovered that cyanobacteria produce N-(2-aminoethyl)glycine (AEG), a backbone for peptide nucleic acids. We detected AEG in axenic strains of cyanobacteria with an average concentration of 1 µg/g. We also detected AEG in environmental samples of cyanobacteria as both a free or weakly bound molecule and a tightly bound form released by acid hydrolysis, at concentrations ranging from not detected to 34 µg/g. The production of AEG by diverse taxa of cyanobacteria suggests that AEG may be a primitive feature which arose early in the evolution of life on earth.

  11. Cyanobacteria Produce N-(2-Aminoethyl)Glycine, a Backbone for Peptide Nucleic Acids Which May Have Been the First Genetic Molecules for Life on Earth

    PubMed Central

    Banack, Sandra Anne; Metcalf, James S.; Jiang, Liying; Craighead, Derek; Ilag, Leopold L.; Cox, Paul Alan

    2012-01-01

    Prior to the evolution of DNA-based organisms on earth over 3.5 billion years ago it is hypothesized that RNA was the primary genetic molecule. Before RNA-based organisms arose, peptide nucleic acids may have been used to transmit genetic information by the earliest forms of life on earth. We discovered that cyanobacteria produce N-(2-aminoethyl)glycine (AEG), a backbone for peptide nucleic acids. We detected AEG in axenic strains of cyanobacteria with an average concentration of 1 µg/g. We also detected AEG in environmental samples of cyanobacteria as both a free or weakly bound molecule and a tightly bound form released by acid hydrolysis, at concentrations ranging from not detected to 34 µg/g. The production of AEG by diverse taxa of cyanobacteria suggests that AEG may be a primitive feature which arose early in the evolution of life on earth. PMID:23145061

  12. Chemical interaction of water molecules with framework Al in acid zeolites: a periodic ab initio study on H-clinoptilolite.

    PubMed

    Valdiviés-Cruz, Karell; Lam, Anabel; Zicovich-Wilson, Claudio M

    2015-09-28

    Periodic quantum-chemistry methods as implemented in the CRYSTAL14 code were considered to analyse the interaction of acid clinoptilolite with water. Initially adsorbed molecules hydrolyse the Al-O bonds, giving rise to defective dealuminated materials. A suitable and representative periodic model of the partially disordered hydrated H-zeolite is the primitive cell (18 T sites) of a decahydrated trialuminated structure of HEU topology. The water distribution inside the material cavities was initially investigated. The model considered for further dealumination was the most stable one from those generated through a combined force field Monte Carlo and ab initio optimization strategy. Optimizations and energy estimations were made at the hybrid DFT level of theory (PBE0 functional) with an atomic basis set of VDZP quality. The energetics of the different pathways involved in the dealumination process was addressed by considering the Gibbs free energy with thermal and zero-point corrections through phonon analysis. It arises that hydrated models exhibit protonated water clusters stabilized by different kinds of H-bonds. The first Al extraction is slightly more energetically favourable from T3 than T2 sites, but at the same time the latter is more probable owing to its larger Al population. However, concerning the second dealumination step, it is more favourable removing the Al atom from both remaining sites after a starting abstraction from T2 rather than T3. These facts determine that the most probable overall pathways go through a first Al removal from T2. The agreement with experimental results is discussed. PMID:26299763

  13. Mitigation of the Hematopoietic and Gastrointestinal Acute Radiation Syndrome by Octadecenyl Thiophosphate, a Small Molecule Mimic of Lysophosphatidic Acid

    PubMed Central

    Deng, Wenlin; Kimura, Yasuhiro; Gududuru, Veeresh; Wu, Wenjie; Balogh, Andrea; Szabo, Erzsebet; Thompson, Karin Emmons; Yates, C. Ryan; Balazs, Louisa; Johnson, Leonard R.; Miller, Duane D.; Strobos, Jur; McCool, W. Shannon; Tigyi, Gabor J.

    2015-01-01

    We have previously demonstrated that the small molecule octadecenyl thiophosphate (OTP), a synthetic mimic of the growth factor-like mediator lysophosphatidic acid (LPA), showed radioprotective activity in a mouse model of total-body irradiation (TBI) when given orally or intraperitoneally 30 min before exposure to 9 Gy γ radiation. In the current study, we evaluated the effects of OTP, delivered subcutaneously, for radioprotection or radiomitigation from −24 h before to up to +72 h postirradiation using a mouse TBI model with therapeutic doses at around 1 mg/kg. OTP was injected at 10 mg/kg without observable toxic side effects in mice, providing a comfortable safety margin. Treatment of C57BL/6 mice with a single dose of OTP over the time period from −12 h before to +26 h after a lethal dose of TBI reduced mortality by 50%. When administered at +48 h to +72 h postirradiation (LD50/30 to LD100/30), OTP reduced mortality by ≥34%. OTP administered at +24 h postirradiation significantly elevated peripheral white blood cell and platelet counts, increased crypt survival in the jejunum, enhanced intestinal glucose absorption and reduced endotoxin seepage into the blood. In the 6.4–8.6 Gy TBI range using LD50/10 as the end point, OTP yielded a dose modification factor of 1.2. The current data indicate that OTP is a potent radioprotector and radiomitigator ameliorating the mortality and tissue injury of acute hematopoietic as well as acute gastrointestinal radiation syndrome. PMID:25807318

  14. Chemical interaction of water molecules with framework Al in acid zeolites: a periodic ab initio study on H-clinoptilolite.

    PubMed

    Valdiviés-Cruz, Karell; Lam, Anabel; Zicovich-Wilson, Claudio M

    2015-09-28

    Periodic quantum-chemistry methods as implemented in the CRYSTAL14 code were considered to analyse the interaction of acid clinoptilolite with water. Initially adsorbed molecules hydrolyse the Al-O bonds, giving rise to defective dealuminated materials. A suitable and representative periodic model of the partially disordered hydrated H-zeolite is the primitive cell (18 T sites) of a decahydrated trialuminated structure of HEU topology. The water distribution inside the material cavities was initially investigated. The model considered for further dealumination was the most stable one from those generated through a combined force field Monte Carlo and ab initio optimization strategy. Optimizations and energy estimations were made at the hybrid DFT level of theory (PBE0 functional) with an atomic basis set of VDZP quality. The energetics of the different pathways involved in the dealumination process was addressed by considering the Gibbs free energy with thermal and zero-point corrections through phonon analysis. It arises that hydrated models exhibit protonated water clusters stabilized by different kinds of H-bonds. The first Al extraction is slightly more energetically favourable from T3 than T2 sites, but at the same time the latter is more probable owing to its larger Al population. However, concerning the second dealumination step, it is more favourable removing the Al atom from both remaining sites after a starting abstraction from T2 rather than T3. These facts determine that the most probable overall pathways go through a first Al removal from T2. The agreement with experimental results is discussed.

  15. Small-Molecule Inhibitors of the Pseudaminic Acid Biosynthetic Pathway: Targeting Motility as a Key Bacterial Virulence Factor

    PubMed Central

    Ménard, Robert; Schoenhofen, Ian C.; Tao, Limei; Aubry, Annie; Bouchard, Patrice; Reid, Christopher W.; Lachance, Paule; Twine, Susan M.; Fulton, Kelly M.; Cui, Qizhi; Hogues, Hervé; Purisima, Enrico O.

    2014-01-01

    Helicobacter pylori is motile by means of polar flagella, and this motility has been shown to play a critical role in pathogenicity. The major structural flagellin proteins have been shown to be glycosylated with the nonulosonate sugar, pseudaminic acid (Pse). This glycan is unique to microorganisms, and the process of flagellin glycosylation is required for H. pylori flagellar assembly and consequent motility. As such, the Pse biosynthetic pathway offers considerable potential as an antivirulence drug target, especially since motility is required for H. pylori colonization and persistence in the host. This report describes screening the five Pse biosynthetic enzymes for small-molecule inhibitors using both high-throughput screening (HTS) and in silico (virtual screening [VS]) approaches. Using a 100,000-compound library, 1,773 hits that exhibited a 40% threshold inhibition at a 10 μM concentration were identified by HTS. In addition, VS efforts using a 1.6-million compound library directed at two pathway enzymes identified 80 hits, 4 of which exhibited reasonable inhibition at a 10 μM concentration in vitro. Further secondary screening which identified 320 unique molecular structures or validated hits was performed. Following kinetic studies and structure-activity relationship (SAR) analysis of selected inhibitors from our refined list of 320 compounds, we demonstrated that three inhibitors with 50% inhibitory concentrations (IC50s) of approximately 14 μM, which belonged to a distinct chemical cluster, were able to penetrate the Gram-negative cell membrane and prevent formation of flagella. PMID:25267679

  16. A computational study of ultrafast acid dissociation and acid-base neutralization reactions. II. The relationship between the coordination state of solvent molecules and concerted versus sequential acid dissociation.

    PubMed

    Maurer, Patrick; Thomas, Vibin; Iftimie, Radu

    2011-03-01

    We investigate the role played by the coordination state of pre-existing water wires during the dissociation of moderately strong acids by means of first-principles molecular dynamics calculations. By preparing 2,4,6-tricyanophenol (calc. pKa∼0.5) in two different initial states, we are able to observe sequential as well as concerted trajectories of dissociation: On one hand, equilibrium dissociation takes place on a ∼50 ps timescale; proton conduction occurs through three-coordinated water wires in this case, by means of sequential Grotthus hopping. On the other hand, by preparing 2,4,6-tricyanophenol in a hydration state inherited from that of equilibrated phenol (calc. pKa=7.6), the moderately strong acid finds itself in a presolvated state from which dissociation can take place on a ∼1 ps timescale. In this case, concerted dissociation trajectories are observed, which consist of proton translocation through two intervening, four-coordinated, water molecules in 0.1-1.0 ps. The present results suggest that, in general, the mechanism of proton translocation depends on how the excess proton is injected into a hydrogen bond network. In particular, if the initial conditions favour proton release to a fourfold H-bonded water molecule, proton translocation by as much as 6-8 Å can take place on a sub-picosecond timescale.

  17. A computational study of ultrafast acid dissociation and acid-base neutralization reactions. II. The relationship between the coordination state of solvent molecules and concerted versus sequential acid dissociation

    NASA Astrophysics Data System (ADS)

    Maurer, Patrick; Thomas, Vibin; Iftimie, Radu

    2011-03-01

    We investigate the role played by the coordination state of pre-existing water wires during the dissociation of moderately strong acids by means of first-principles molecular dynamics calculations. By preparing 2,4,6-tricyanophenol (calc. pKa˜0.5) in two different initial states, we are able to observe sequential as well as concerted trajectories of dissociation: On one hand, equilibrium dissociation takes place on a ˜50 ps timescale; proton conduction occurs through three-coordinated water wires in this case, by means of sequential Grotthus hopping. On the other hand, by preparing 2,4,6-tricyanophenol in a hydration state inherited from that of equilibrated phenol (calc. pKa = 7.6), the moderately strong acid finds itself in a presolvated state from which dissociation can take place on a ˜1 ps timescale. In this case, concerted dissociation trajectories are observed, which consist of proton translocation through two intervening, four-coordinated, water molecules in 0.1-1.0 ps. The present results suggest that, in general, the mechanism of proton translocation depends on how the excess proton is injected into a hydrogen bond network. In particular, if the initial conditions favour proton release to a fourfold H-bonded water molecule, proton translocation by as much as 6-8 Å can take place on a sub-picosecond timescale.

  18. Iridium-catalyzed ortho-selective C-H silylation of aromatic compounds directed toward the synthesis of π-conjugated molecules with Lewis acid-base interaction.

    PubMed

    Wakaki, Takayuki; Kanai, Motomu; Kuninobu, Yoichiro

    2015-04-01

    We successfully developed an iridium-catalyzed ortho-selective C-H silylation of aromatic compounds. The reaction exhibited a wide substrate scope, and a variety of π-conjugated molecules were synthesized in good to excellent yields, even in gram scale. Several silyl groups could also be introduced into the products. The experimental results indicated that the regioselectivity could be controlled by a Lewis acid-base interaction between the Lewis acidic silicon atoms of fluorinated hydrosilanes and the Lewis basic nitrogen atoms of aromatic compounds.

  19. Selective Enrichment and MALDI-TOF MS Analysis of Small Molecule Compounds with Vicinal Diols by Boric Acid-Functionalized Graphene Oxide.

    PubMed

    Zhang, Jing; Zheng, Xiaoling; Ni, Yanli

    2015-08-01

    In this study, a 4-vinylphenylboronic acid-functionalized graphene oxide (GO) material was prepared via atom-transfer radical polymerization (ATRP) method and applied for the first time as a novel matrix for the selective enrichment and analysis of small-molecule compounds with vicinal diols, which have been the focus of intense research in the field of life science, by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in positive-ion mode. There are two main factors playing a decisive role in assisting laser D/I process comparing to some traditional matrices: (1) GO provides π-conjugated system by itself for laser absorption and energy transfer; (2) the modified 4-vinylphenylboronic acid can selectively capture small-molecule compounds with vicinal diols. The results demonstrate that the novel material has distinct advantages over previously reported matrices in enriching and assisting the highly efficient ionization of target molecules for mass spectrometry analysis. This work indicates a new application branch for graphene-based matrices and provides an alternative solution for small-molecules analysis.

  20. Selective Enrichment and MALDI-TOF MS Analysis of Small Molecule Compounds with Vicinal Diols by Boric Acid-Functionalized Graphene Oxide

    NASA Astrophysics Data System (ADS)

    Zhang, Jing; Zheng, Xiaoling; Ni, Yanli

    2015-08-01

    In this study, a 4-vinylphenylboronic acid-functionalized graphene oxide (GO) material was prepared via atom-transfer radical polymerization (ATRP) method and applied for the first time as a novel matrix for the selective enrichment and analysis of small-molecule compounds with vicinal diols, which have been the focus of intense research in the field of life science, by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in positive-ion mode. There are two main factors playing a decisive role in assisting laser D/I process comparing to some traditional matrices: (1) GO provides π-conjugated system by itself for laser absorption and energy transfer; (2) the modified 4-vinylphenylboronic acid can selectively capture small-molecule compounds with vicinal diols. The results demonstrate that the novel material has distinct advantages over previously reported matrices in enriching and assisting the highly efficient ionization of target molecules for mass spectrometry analysis. This work indicates a new application branch for graphene-based matrices and provides an alternative solution for small-molecules analysis.

  1. FORMATION OF CARBONIC ACID (H{sub 2}CO{sub 3}) BY SURFACE REACTIONS OF NON-ENERGETIC OH RADICALS WITH CO MOLECULES AT LOW TEMPERATURES

    SciTech Connect

    Oba, Yasuhiro; Watanabe, Naoki; Kouchi, Akira; Hama, Tetsuya; Pirronello, Valerio

    2010-10-20

    We present the experimental results of carbonic acid (H{sub 2}CO{sub 3}) formation through surface reactions of CO molecules with non-energetic hydroxyl (OH) radicals at 10-40 K. The formation of H{sub 2}CO{sub 3} was clearly identified both in the IR spectra and in the thermally programmed desorption mass spectra. The H{sub 2}CO{sub 3} yield was rather high, amounting to approximately 40%-70% relative to that of CO{sub 2} formed by the reaction of CO with OH. The structure of H{sub 2}CO{sub 3} formed by reactions of CO with OH may differ from that formed by energetic processes such as UV irradiation, ion irradiation, and electron irradiation of H{sub 2}O/CO{sub 2} binary ices. In this paper, we envisage some of the possible roles H{sub 2}CO{sub 3} may have in the interstellar medium, such as enriching grain mantles of new molecules via acid-base reactions with basic species and contributing to the formation of the unidentified band at 6.8 {mu}m; we suggest possible reasons for its non-detection yet and discuss the restoration of carbonic acid molecules in the gas phase.

  2. Detection of Gold Nanoparticles Aggregation Growth Induced by Nucleic Acid through Laser Scanning Confocal Microscopy.

    PubMed

    Gary, Ramla; Carbone, Giovani; Petriashvili, Gia; De Santo, Maria Penelope; Barberi, Riccardo

    2016-01-01

    The gold nanoparticle (GNP) aggregation growth induced by deoxyribonucleic acid (DNA) is studied by laser scanning confocal and environmental scanning electron microscopies. As in the investigated case the direct light scattering analysis is not suitable, we observe the behavior of the fluorescence produced by a dye and we detect the aggregation by the shift and the broadening of the fluorescence peak. Results of laser scanning confocal microscopy images and the fluorescence emission spectra from lambda scan mode suggest, in fact, that the intruding of the hydrophobic moiety of the probe within the cationic surfactants bilayer film coating GNPs results in a Förster resonance energy transfer. The environmental scanning electron microscopy images show that DNA molecules act as template to assemble GNPs into three-dimensional structures which are reminiscent of the DNA helix. This study is useful to design better nanobiotechnological devices using GNPs and DNA. PMID:26907286

  3. Detection of Gold Nanoparticles Aggregation Growth Induced by Nucleic Acid through Laser Scanning Confocal Microscopy

    PubMed Central

    Gary, Ramla; Carbone, Giovani; Petriashvili, Gia; De Santo, Maria Penelope; Barberi, Riccardo

    2016-01-01

    The gold nanoparticle (GNP) aggregation growth induced by deoxyribonucleic acid (DNA) is studied by laser scanning confocal and environmental scanning electron microscopies. As in the investigated case the direct light scattering analysis is not suitable, we observe the behavior of the fluorescence produced by a dye and we detect the aggregation by the shift and the broadening of the fluorescence peak. Results of laser scanning confocal microscopy images and the fluorescence emission spectra from lambda scan mode suggest, in fact, that the intruding of the hydrophobic moiety of the probe within the cationic surfactants bilayer film coating GNPs results in a Förster resonance energy transfer. The environmental scanning electron microscopy images show that DNA molecules act as template to assemble GNPs into three-dimensional structures which are reminiscent of the DNA helix. This study is useful to design better nanobiotechnological devices using GNPs and DNA. PMID:26907286

  4. DFT study of adsorption of picric acid molecule on the surface of single-walled ZnO nanotube; as potential new chemical sensor

    NASA Astrophysics Data System (ADS)

    Farmanzadeh, Davood; Tabari, Leila

    2015-01-01

    Using density functional theory (DFT), we have investigated the adsorption of picric acid (PA) molecule on the surface of (8,0) single-walled ZnO nanotube (ZnONT). The results show that the PA molecule can be chemisorbed on the surface of ZnONT with adsorption energies of -82.01 and -75.26 kJ/mol in gas and aqueous phase, respectively. Frontier molecular orbital analysis show that HOMO/LUMO gap of ZnONT reduces from 1.66 and 1.75 eV in the pristine nanotube to 0.83 and 0.72 eV in PA-adsorbed form in gas and aqueous phase, respectively. It suggests that the process can affect the electronic properties of the studied nanotube which would lead to its conductance change upon the adsorption of PA molecule. The modifying effect on the electrical conductance of ZnONT underlies the working mechanism of gas sensors for detecting the PA molecules. Analyses of the adsorption behavior of the electrically charged ZnONT toward PA molecule in the gas phase show that the PA molecule can be strongly adsorbed on the negatively charged ZnONT surface with significant adsorption energy (-135.1 kJ/mol). However, from the HOMO/LUMO gap changes, it can be concluded that the positive ZnONT might sensitively detect the PA molecule in comparison to the negative tube. These results can provide helpful information for experimental investigation to develop novel nanotube-based sensors.

  5. A highly processive topoisomerase I: studies at the single-molecule level.

    PubMed

    Szafran, Marcin Jan; Strick, Terence; Strzałka, Agnieszka; Zakrzewska-Czerwińska, Jolanta; Jakimowicz, Dagmara

    2014-07-01

    Amongst enzymes which relieve torsional strain and maintain chromosome supercoiling, type IA topoisomerases share a strand-passage mechanism that involves transient nicking and re-joining of a single deoxyribonucleic acid (DNA) strand. In contrast to many bacterial species that possess two type IA topoisomerases (TopA and TopB), Actinobacteria possess only TopA, and unlike its homologues this topoisomerase has a unique C-terminal domain that lacks the Zn-finger motifs characteristic of type IA enzymes. To better understand how this unique C-terminal domain affects the enzyme's activity, we have examined DNA relaxation by actinobacterial TopA from Streptomyces coelicolor (ScTopA) using real-time single-molecule experiments. These studies reveal extremely high processivity of ScTopA not described previously for any other topoisomerase of type I. Moreover, we also demonstrate that enzyme processivity varies in a torque-dependent manner. Based on the analysis of the C-terminally truncated ScTopA mutants, we propose that high processivity of the enzyme is associated with the presence of a stretch of positively charged amino acids in its C-terminal region.

  6. A split G-quadruplex-based DNA nano-tweezers structure as a signal-transducing molecule for the homogeneous detection of specific nucleic acids.

    PubMed

    Nakatsuka, Keisuke; Shigeto, Hajime; Kuroda, Akio; Funabashi, Hisakage

    2015-12-15

    A portable method of specific nucleic acid detection would be very useful for monitoring public health in a variety of settings for point-of-care and point-of-need testing. However, conventional methods for the detection of nucleic acids are not ideal for use in the field, as they require skilled operators and complex equipment. Here, we constructed a method for specific nucleic acid detection using a split G-quadruplex (Gq) structure that can recognize target nucleic acids without competitive reactions in a bimolecular reaction and directly produce a detectable signal based on peroxidase activity. We developed a single signal-transducing molecule with a split Gq-based DNA-nano tweezers (NT) structure that self-assembles from three single-stranded DNAs through simple mixing, and detects its target without requiring any washing steps. A model target, a partial norovirus mRNA (NV-RNA), was specifically recognized by the split Gq-based DNA-NT, causing it to undergo a structural change that restored its peroxidase activity. The peroxidase activity was measured by following the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), which gave a greenish colorimetric response, and was proportional to the NV-RNA concentration. The lower detection limit was 4 nM. Our results demonstrated the feasibility of detecting specific nucleic acids with a split Gq-based DNA-NT structure as a nucleic acid signal-transducing molecule in a homogenous assay format. Also the target recognition sites of split Gq-based DNA-NT can easily be designed without delicate optimization of tweezers structure. Thus a split Gq-based DNA-NT technique is readily applicable to a basic platform for the development of a portable device.

  7. A comparative study of the vibrational spectra of the anticancer drug melphalan and its fundamental molecules 3-phenylpropionic acid and L-phenylalanine

    NASA Astrophysics Data System (ADS)

    Badawi, Hassan M.; Khan, Ibrahim

    2016-04-01

    The structural stability and the vibrational spectra of the anticancer drug melphalan and its parent compounds 3-phenylpropionic acid and L-phenylalanine were investigated by the DFT B3LYP/6-311G** calculations. Melphalan and its fundamental compounds were predicted to exist predominantly in non-planar structures. The vibrational frequencies of the low energy structures of melphalan, 3-phenylpropionic acid, and phenylalanine were computed at the DFT B3LYP level of theory. Complete vibrational assignments of the normal modes of melphalan, 3-phenylpropionic acid, and phenylalanine were provided by combined theoretical and experimental data of the molecules. The experimental infrared spectra of phenylalanine and melphalan show a significantly different pattern of the Cdbnd O stretching mode as compared to those of normal carboxylic acids. A comparison of the 3700-2000 cm-1 infrared spectral region of the three molecules suggests the presence of similar intermolecular H-bonding in their condensed phases. The observed infrared and Raman spectra are consistent with the presence of one predominant melphalan conformation at room temperature.

  8. The role of outer surface/inner bulk Brønsted acidic sites in the adsorption of a large basic molecule (simazine) on H-Y zeolite.

    PubMed

    Sannino, Filomena; Pansini, Michele; Marocco, Antonello; Bonelli, Barbara; Garrone, Edoardo; Esposito, Serena

    2015-11-21

    The simple means adopted for investigating H-Y zeolite acidity in water is the pH-dependence of the amount of a basic molecule adsorbed under isochoric conditions, a technique capable of yielding, under equilibrium conditions, an estimate of the pKa value of the involved acidic centres: the behaviour with temperature of adsorbed amounts yields instead some information on thermodynamics. Simazine (Sim, 2-chloro-4,6-bis(ethylamino)-s-triazine) was chosen as an adsorbate because its transverse dimension (7.5 Å) is close to the opening of the supercage in the faujasite structure of H-Y (7.4 Å). In short term measurements, Sim adsorption at 25 °C occurs only at the outer surface of H-Y particles. Two types of mildly acidic centres are present (with pKaca. 7 and ca. 8, respectively) and no strong one is observed. Previous adsorption of ammonia from the gas phase discriminates between the two. The former survives, and shows features common with the silanols of amorphous silica. The latter is suppressed: because of this and other features distinguishing this site from silanol species (e.g. the formation of dimeric Sim2H(+) species, favoured by coverage and unfavoured by temperatures of adsorption higher than ambient temperature) a candidate is an Al based site. We propose a Lewis centre coordinating a water molecule, exhibiting acidic properties. This acidic water molecule can be replaced by the stronger base ammonia, also depleting inner strong Brønsted sites. A mechanism for the generation of the two sites from surface Brønsted species is proposed. Long term adsorption measurements at 25 °C already show the onset of the interaction with inner strongly acidic Brønsted sites: because of its size, activation is required for Sim to pass the supercage openings and reach inner acidic sites. When adsorption is run at 40-50 °C, uptake is much larger and increases with temperature. Isochoric measurements suggest a pKa value of ca. 3 compatible with its marked acidic

  9. Single-molecule tracing on a fluidic microchip for quantitative detection of low-abundance nucleic acids.

    PubMed

    Wang, Tza-Huei; Peng, Yahui; Zhang, Chunyang; Wong, Pak Kin; Ho, Chih-Ming

    2005-04-20

    Here, we report a method capable of quantitative detection of low-abundance DNA/RNA molecules by incorporating confocal fluorescence spectroscopy, molecular beacons, and a molecular-confinement microfluidic reactor. By using a combination of ac and dc fields via a trio of 3-D electrodes in the microreactor, we are able to precisely direct the transport of individual molecules to a minuscule laser-focused detection volume ( approximately 1 fL). A burst of fluorescence photons is detected whenever a molecular beacon-target hybrid flows through the detection region, and the amount of targets can be directly quantified according to the number of recorded single-molecule flow-through events. This assay consumes only attomoles of molecular probes and is able to quantitatively detect subpicomolar DNA targets. A measurement time of less than 2 min is sufficient to complete the detection.

  10. Effect of propane-2-sulfonic acid octadec-9-enyl-amide on the expression of adhesion molecules in human umbilical vein endothelial cells.

    PubMed

    Chen, Cai-Xia; Yang, Li-Chao; Xu, Xu-Dong; Wei, Xiao; Gai, Ya-Ting; Peng, Lu; Guo, Han; Hao-Zhou; Wang, Yi-Qing; Jin, Xin

    2015-06-01

    Oleoylethanolamide (OEA), an endogenous agonist of PPARα, has been reported to have anti-atherosclerotic properties. However, OEA can be enzymatically hydrolyzed to oleic acid and ethanolamine and, thus, is not expected to be orally active. In the present study, we designed and synthesized an OEA analog, propane-2-sulfonic acid octadec-9-enyl-amide (N15), which is resistant to enzymatic hydrolysis. The purpose of this study was to investigate the effects of N15 on the expression of adhesion molecules in human umbilical vein endothelial cells (HUVECs). The results showed that N15 inhibited TNFα-induced production of vascular cell adhesion molecule-1 and intercellular adhesion molecule-1 and the adhesion of monocytes to TNFα-induced HUVECs. Furthermore, the protective effect of N15 on inflammation is dependent upon a PPAR-α/γ-mediated mechanism. In conclusion, N15 protects against TNFα-induced vascular endothelial inflammation. This anti-inflammatory effect of N15 is dependent on PPAR-α/γ dual targets.

  11. Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids.

    PubMed

    Aramesh, M; Shimoni, O; Fox, K; Karle, T J; Lohrmann, A; Ostrikov, K; Prawer, S; Cervenka, J

    2015-04-14

    Extracellular nucleic acids freely circulating in blood and other physiologic fluids are important biomarkers for non-invasive diagnostics and early detection of cancer and other diseases, yet difficult to detect because they exist in very low concentrations and large volumes. Here we demonstrate a new broad-range sensor platform for ultrasensitive and selective detection of circulating DNA down to the single-molecule level. The biosensor is based on a chemically functionalized nanoporous diamond-like carbon (DLC) coated alumina membrane. The few nanometer-thick, yet perfect and continuous DLC-coating confers the chemical stability and biocompatibility of the sensor, allowing its direct application in biological conditions. The selective detection is based on complementary hybridization of a fluorescently-tagged circulating cancer oncomarker (a 21-mer nucleic acid) with covalently immobilized DNA on the surface of the membrane. The captured DNAs are detected in the nanoporous structure of the sensor using confocal scanning laser microscopy. The flow-through membrane sensor demonstrates broad-range sensitivity, spanning from 10(15) molecules per cm(2) down to single molecules, which is several orders of magnitude improvement compared to the flat DNA microarrays. Our study suggests that these flow-through type nanoporous sensors represent a new powerful platform for large volume sampling and ultrasensitive detection of different chemical biomarkers. PMID:25744416

  12. Towards an understanding of the molecular mechanism of solvation of drug molecules: a thermodynamic approach by crystal lattice energy, sublimation, and solubility exemplified by hydroxybenzoic acids.

    PubMed

    Perlovich, German L; Volkova, Tatyana V; Bauer-Brandl, Annette

    2006-07-01

    Temperature dependencies of saturated vapor pressure and heat capacities for the 2-, 3-, and 4-hydroxybenzoic acids were measured and thermodynamic functions of sublimation calculated (2-hydroxybenzoic acid: DeltaG(sub) (298) = 38.5 kJ/mol; DeltaH(sub) (298) = 96.6 +/- 0.8 kJ/mol; DeltaS(sub) (298) = 191 +/- 3 J/mol . K; 3-hydroxybenzoic acid: DeltaG(sub) (298) = 50.6 kJ/mol; DeltaH(sub) (298) = 105.2 +/- 0.8 kJ/mol; DeltaS(sub) (298) = 180 +/- 2 J/mol . K; 4-hydroxybenzoic acid: DeltaG(sub) (298) = 55.0 kJ/mol; DeltaH(sub) (298) = 113.3 +/- 0.7 kJ/mol; DeltaS(sub) (298) = 193 +/- 2 J/mol . K). Analysis of crystal lattice packing energies based on geometry optimization of the molecules in the crystal using diffraction data and the program Dmol(3) was carried out. The energetic contributions of van der Waals, Coulombic, and hydrogen bond terms to the total packing energy were analyzed. The fraction of hydrogen bond energy in the packing energy increases as: 3-hydroxybenzoic (29.7%) < 2-hydroxybenzoic (34.7%) < 4-hydroxybenzoic acid (42.0%). Enthalpies of evaporation were estimated from enthalpies of sublimation and fusion. Temperature dependencies of the solubility in n-octanol and n-hexane were measured. The thermodynamic functions of solubility and solvation processes were deduced. Specific and nonspecific solvation terms were distinguished using the transfer from the "inert" n-hexane to the other solvents. The transfer of the molecules from water to n-octanol is enthalpy driven process.

  13. Flow-through Capture and in Situ Amplification Can Enable Rapid Detection of a Few Single Molecules of Nucleic Acids from Several Milliliters of Solution.

    PubMed

    Schlappi, Travis S; McCalla, Stephanie E; Schoepp, Nathan G; Ismagilov, Rustem F

    2016-08-01

    Detecting nucleic acids (NAs) at zeptomolar concentrations (few molecules per milliliter) currently requires expensive equipment and lengthy processing times to isolate and concentrate the NAs into a volume that is amenable to amplification processes, such as PCR or LAMP. Shortening the time required to concentrate NAs and integrating this procedure with amplification on-device would be invaluable to a number of analytical fields, including environmental monitoring and clinical diagnostics. Microfluidic point-of-care (POC) devices have been designed to address these needs, but they are not able to detect NAs present in zeptomolar concentrations in short time frames because they require slow flow rates and/or they are unable to handle milliliter-scale volumes. In this paper, we theoretically and experimentally investigate a flow-through capture membrane that solves this problem by capturing NAs with high sensitivity in a short time period, followed by direct detection via amplification. Theoretical predictions guided the choice of physical parameters for a chitosan-coated nylon membrane; these predictions can also be applied generally to other capture situations with different requirements. The membrane is also compatible with in situ amplification, which, by eliminating an elution step enables high sensitivity and will facilitate integration of this method into sample-to-answer detection devices. We tested a wide range of combinations of sample volumes and concentrations of DNA molecules using a capture membrane with a 2 mm radius. We show that for nucleic acid detection, this approach can concentrate and detect as few as ∼10 molecules of DNA with flow rates as high as 1 mL/min, handling samples as large as 50 mL. In a specific example, this method reliably concentrated and detected ∼25 molecules of DNA from 50 mL of sample. PMID:27429181

  14. SALDI-TOF-MS analyses of small molecules (citric acid, dexasone, vitamins E and A) using TiO2 nanocrystals as substrates.

    PubMed

    Popović, Iva A; Nešić, Maja; Vranješ, Mila; Šaponjić, Zoran; Petković, Marijana

    2016-10-01

    Surface-assisted laser desorption/ionisation time-of-flight mass spectrometry (SALDI-TOF-MS) might be the method of choice for the analysis of low mass molecules (less than m/z 500). Titanium dioxide (TiO2) nanocrystals as a substrate for SALDI-TOF-MS improve the reproducibility of the signal intensities and prevent the fragmentation of some molecules upon laser irradiation, as we have previously shown. In addition, variously shaped and sized TiO2 nanocrystals/substrates for SALDI-MS could be used for quantification of small molecules, which are otherwise difficult to detect with the assistance of organic matrices. TiO2-assisted LDI-MS spectra could be acquired with excellent reproducibility and repeatability and with low detection limit. In the current study, we analysed the spectra of dexasone, citric acid, vitamin E and vitamin A acquired with TiO2 nanocrystals of various shapes and dimensions, i.e. the colloidal TiO2 nanoparticles (TiO2 NPs), TiO2 prolate nanospheroids (TiO2 PNSs) and TiO2 nanotubes (TiO2 NTs). Various shapes and dimensions of substrates were used since these factors determine desorption and ionisation processes. The homogeneity on the target plate was compared based on signal-to-noise values of peaks of interest of analysed molecules as well as the within-day and day-to-day repeatability. In summary, the obtained results show that the applicability of individual TiO2 nanocrystals depends on the analyte. Signals which are acquired with the assistance of TiO2 PNSs have the highest sensitivity and reproducibility (the smallest standard deviation), even compared with those in the LDI mode. This implies that TiO2 PNSs could also be suitable for quantitative analyses of small molecules. PMID:27510281

  15. Single Qdot-labeled glycosylase molecules use a wedge amino acid to probe for lesions while scanning along DNA.

    PubMed

    Dunn, Andrew R; Kad, Neil M; Nelson, Shane R; Warshaw, David M; Wallace, Susan S

    2011-09-01

    Within the base excision repair (BER) pathway, the DNA N-glycosylases are responsible for locating and removing the majority of oxidative base damages. Endonuclease III (Nth), formamidopyrimidine DNA glycosylase (Fpg) and endonuclease VIII (Nei) are members of two glycosylase families: the helix-hairpin-helix (HhH) superfamily and the Fpg/Nei family. The search mechanisms employed by these two families of glycosylases were examined using a single molecule assay to image quantum dot (Qdot)-labeled glycosylases interacting with YOYO-1 stained λ-DNA molecules suspended between 5 µm silica beads. The HhH and Fpg/Nei families were found to have a similar diffusive search mechanism described as a continuum of motion, in keeping with rotational diffusion along the DNA molecule ranging from slow, sub-diffusive to faster, unrestricted diffusion. The search mechanism for an Fpg variant, F111A, lacking a phenylalanine wedge residue no longer displayed slow, sub-diffusive motion compared to wild type, suggesting that Fpg base interrogation may be accomplished by Phe(111) insertion.

  16. Single Qdot-labeled glycosylase molecules use a wedge amino acid to probe for lesions while scanning along DNA.

    PubMed

    Dunn, Andrew R; Kad, Neil M; Nelson, Shane R; Warshaw, David M; Wallace, Susan S

    2011-09-01

    Within the base excision repair (BER) pathway, the DNA N-glycosylases are responsible for locating and removing the majority of oxidative base damages. Endonuclease III (Nth), formamidopyrimidine DNA glycosylase (Fpg) and endonuclease VIII (Nei) are members of two glycosylase families: the helix-hairpin-helix (HhH) superfamily and the Fpg/Nei family. The search mechanisms employed by these two families of glycosylases were examined using a single molecule assay to image quantum dot (Qdot)-labeled glycosylases interacting with YOYO-1 stained λ-DNA molecules suspended between 5 µm silica beads. The HhH and Fpg/Nei families were found to have a similar diffusive search mechanism described as a continuum of motion, in keeping with rotational diffusion along the DNA molecule ranging from slow, sub-diffusive to faster, unrestricted diffusion. The search mechanism for an Fpg variant, F111A, lacking a phenylalanine wedge residue no longer displayed slow, sub-diffusive motion compared to wild type, suggesting that Fpg base interrogation may be accomplished by Phe(111) insertion. PMID:21666255

  17. The sequence of rat leukosialin (W3/13 antigen) reveals a molecule with O-linked glycosylation of one third of its extracellular amino acids.

    PubMed Central

    Killeen, N; Barclay, A N; Willis, A C; Williams, A F

    1987-01-01

    Leukosialin is one of the major glycoproteins of thymocytes and T lymphocytes and is notable for a very high content of O-linked carbohydrate structures. The full protein sequence for rat leukosialin as translated from cDNA clones is now reported. The molecule contains 371 amino acids with 224 residues outside the cell, one transmembrane sequence and 124 cytoplasmic residues. Data from the peptide sequence and carbohydrate composition suggest that one in three of the extracellular amino acids may be O-glycosylated with no N-linked glycosylation sites. The cDNA sequence contained a CpG rich region in the 3' coding sequence and a large 3' non-coding region which included tandem repeats of the sequence GGAT. Images Fig. 4. PMID:2965006

  18. Nanopore integrated with Au clusters formed under electron beam irradiation for single molecule analysis

    NASA Astrophysics Data System (ADS)

    Choi, Seong Soo; Park, Myoung Jin; Han, Chul Hee; Kim, Sung In; Yoo, Jung Ho; Park, Kyung Jin; Park, Nam Kyou; Kim, Yong-Sang

    2016-02-01

    Recently the single molecules such as protein and deoxyribonucleic acid (DNA) have been successfully characterized using a solidstate nanopore with an electrical detection technique. However, the optical plasmonic nanopore has yet to be fabricated. The optical detection technique can be better utilized as next generation ultrafast geneome sequencing devices due to the possible utilization of the current optical technique for genome sequencing. In this report, we have investigated the Au nanopore formation under the electron beam irradiation on an Au aperture. The circular-type nanoopening with ~ 5 nm diameter on the diffused membrane is fabricated by using 2 keV electron beam irradiation by using field emission scanning electron microscopy (FESEM). We found the Au cluster on the periphery of the drilled aperture under a 2 keV electron beam irradiation. Immediately right after electron beam irradiation, no Au cluster and no Au crystal lattice structure on the diffused plane are observed. However, after the sample was kept for ~ 6 months under a room environment, the Au clusters are found on the diffused membrane and the Au crystal lattice structures on the diffused membrane are also found using high resolution transmission electron microscopy. These phenomena can be attributed to Ostwald ripening. In addition, the Au nano-hole on the 40 nm thick Au membrane was also drilled by using 200 keV scanning transmission electron microscopy.

  19. A Broad Anti-influenza Hybrid Small Molecule That Potently Disrupts the Interaction of Polymerase Acidic Protein-Basic Protein 1 (PA-PB1) Subunits.

    PubMed

    Massari, Serena; Nannetti, Giulio; Desantis, Jenny; Muratore, Giulia; Sabatini, Stefano; Manfroni, Giuseppe; Mercorelli, Beatrice; Cecchetti, Violetta; Palù, Giorgio; Cruciani, Gabriele; Loregian, Arianna; Goracci, Laura; Tabarrini, Oriana

    2015-05-14

    In continuing our efforts to identify small molecules able to disrupt the interaction of the polymerase acidic protein-basic protein 1 (PA-PB1) subunits of influenza virus (Flu) RNA-dependent RNA polymerase, this paper is devoted to the optimization of a dihydrotriazolopyrimidine derivative, previously identified through structure-based drug discovery. The structure modifications performed around the bicyclic core led to the identification of compounds endowed with both the ability to disrupt PA-PB1 subunits interaction and anti-Flu activity with no cytotoxicity. Very interesting results were obtained with the hybrid molecules 36 and 37, designed by merging some peculiar structural features known to impart PA-PB1 interaction inhibition, with compound 36 that emerged as the most potent PA-PB1 interaction inhibitor (IC50 = 1.1 μM) among all the small molecules reported so far. Calculations showed a very favored H-bonding between the 2-amidic carbonyl of 36 and Q408, which seems to justify its potent ability to interfere with the interaction of the polymerase subunits.

  20. A pliable electroporation patch (ep-Patch) for efficient delivery of nucleic acid molecules into animal tissues with irregular surface shapes.

    PubMed

    Wei, Zewen; Huang, Yuanyu; Zhao, Deyao; Hu, Zhiyuan; Li, Zhihong; Liang, Zicai

    2015-01-05

    Delivery of nucleic acids into animal tissues by electroporation is an appealing approach for various types of gene therapy, but efficiency of existing methodsis not satisfactory. Here we present the validation of novel electroporation patch (ep-Patch) for efficient delivery of DNA and siRNA into mouse tissues. Using micromachining technology, closely spaced gold electrodes were made on the pliable parylene substrate to form a patch-like electroporation metrics. It enabled large coverage of the target tissues and close surface contact between the tissues and electrodes, thus providing a uniform electric field to deliver nucleic acids into tissues, even beneath intact skin. Using this ep-Patch for efficiently delivery of both DNA and siRNA, non-invasive electroporation of healthy mouse muscle tissue was successfully achieved. Delivery of these nucleic acids was performed to intact tumors with satisfactory results. Silencing of tumor genes using the ep-Patch was also demonstrated on mice. This pliable electroporation patch method constitutes a novel way of in vivo delivery of siRNA and DNA to certain tissues or organs to circumvent the disadvantages of existing methodologies for in vivo delivery of nucleic acid molecules.

  1. Just three water molecules can trigger the undesired nonenzymatic reactions of aspartic acid residues: new insight from a quantum-chemical study

    NASA Astrophysics Data System (ADS)

    Takahashi, O.

    2014-03-01

    Aspartic acid (Asp) residues in peptides and proteins (L-Asp) can undergo spontaneous, nonenzymatic reactions under physiological conditions by which abnormal L-β-Asp, D-Asp, and/or D-β-Asp residues are formed. These altered Asp residues may affect the three-dimensional structures of the peptides and proteins and hence their properties and functions. In fact, the altered Asp residues are relevant to age-related diseases such as cataract and Alzheimer's disease. Most of the above reactions of the L-Asp residue proceed via a cyclic succinimide intermediate. In this paper, I propose a detailed mechanism of cyclization of an Asp residue (forming a precursor of the succinimide) by the B3LYP/6-31+G(d,p) density functional theory calculations carried out for a small Asp-containing model compound complexed with three water molecules which act as general acid-base catalysts in proton transfers. In the proposed mechanism, the amide group on the C-terminal side of the Asp residue is first converted to the tautomeric iminol form. Then, successive reorientation of a water molecule and conformational change occur followed by the nucleophilic attack of the iminol nitrogen atom on the carboxyl carbon atom of the Asp side chain to form a five-membered ring. A satisfactory agreement was obtained between the calculated and experimental energetics.

  2. Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids

    NASA Astrophysics Data System (ADS)

    Aramesh, M.; Shimoni, O.; Fox, K.; Karle, T. J.; Lohrmann, A.; Ostrikov, K.; Prawer, S.; Cervenka, J.

    2015-03-01

    Extracellular nucleic acids freely circulating in blood and other physiologic fluids are important biomarkers for non-invasive diagnostics and early detection of cancer and other diseases, yet difficult to detect because they exist in very low concentrations and large volumes. Here we demonstrate a new broad-range sensor platform for ultrasensitive and selective detection of circulating DNA down to the single-molecule level. The biosensor is based on a chemically functionalized nanoporous diamond-like carbon (DLC) coated alumina membrane. The few nanometer-thick, yet perfect and continuous DLC-coating confers the chemical stability and biocompatibility of the sensor, allowing its direct application in biological conditions. The selective detection is based on complementary hybridization of a fluorescently-tagged circulating cancer oncomarker (a 21-mer nucleic acid) with covalently immobilized DNA on the surface of the membrane. The captured DNAs are detected in the nanoporous structure of the sensor using confocal scanning laser microscopy. The flow-through membrane sensor demonstrates broad-range sensitivity, spanning from 1015 molecules per cm2 down to single molecules, which is several orders of magnitude improvement compared to the flat DNA microarrays. Our study suggests that these flow-through type nanoporous sensors represent a new powerful platform for large volume sampling and ultrasensitive detection of different chemical biomarkers.Extracellular nucleic acids freely circulating in blood and other physiologic fluids are important biomarkers for non-invasive diagnostics and early detection of cancer and other diseases, yet difficult to detect because they exist in very low concentrations and large volumes. Here we demonstrate a new broad-range sensor platform for ultrasensitive and selective detection of circulating DNA down to the single-molecule level. The biosensor is based on a chemically functionalized nanoporous diamond-like carbon (DLC) coated

  3. Self-assembly of folic acid: a chiral-aligning medium for enantiodiscrimination of organic molecules in an aqueous environment.

    PubMed

    Lokesh; Suryaprakash, N

    2012-09-10

    Weak orienting medium: Self-assembly of alkaline salt of folic acid yielded a weak liquid-crystalline phase in an aqueous environment. This medium has the ability to discriminate enantiomers. The mesophase exists over a broad range and has the physical parameter dependent tunability of degree of alignment (see scheme).

  4. A study of functionally active amino acids involved in the interaction of HLA-A2 or HLA-A3 molecules with cytolytic T lymphocytes.

    PubMed

    Healy, F; Sire, J; Gomard, E; Yssel, H; Jordan, B; Levy, J P

    1988-10-01

    A large series of HLA-A2/HLA-A3 recombinant genes were generated by using the in vivo recombination technique. These genes have each been modified in the last two-thirds of the third exon such that one or several HLA-A2-specific substitutions have been made in the HLA-A3 gene and vice versa. The recombinant genes were transfected into the murine cell line P815 and the transfectants were used as targets for a series of 20 human CTL lines or clones specific for HLA-A2 or HLA-A3, or restricted by HLA-A2 and specific for influenza A. Several patterns of anti-HLA-A2, anti-HLA-A3, and HLA-A2-restricted anti-influenza CTL activity were observed and when uncloned cell lines were studied, a progressive selection of some clones with a similar pattern of activity was regularly found. From the comparison of these different patterns the following conclusions can be drawn: 1) In most but not all cases both domains of the class I molecule were essential for CTL recognition, but residue 152 was critically important for the majority of CTL tested; 2) amino acids 114/116 were also critical in most cases, and their position close to amino acid 152 in the tertiary structure of the molecule may have some functional significance; and 3) amino acid 161, although highly conserved, plays an unexpected but very important role in CTL function. PMID:2459213

  5. Bile acid signaling through FXR induces intracellular adhesion molecule-1 expression in mouse liver and human hepatocytes.

    PubMed

    Qin, Pu; Borges-Marcucci, Lisa A; Evans, Mark J; Harnish, Douglas C

    2005-08-01

    Previous studies have demonstrated a dramatic induction of inflammatory gene expression in livers from mice fed a high-fat, high-cholesterol diet containing cholate after 3-5 wk. To determine the contribution of cholate in mediating these inductions, C57BL/6 mice were fed a chow diet supplemented with increasing concentrations of cholic acid (CA) for 5 days. A dose-dependent induction in the hepatic levels of TNF-alpha, VCAM-1, ICAM-1, and SAA-2 mRNA were observed. As positive controls, a dose-dependent repression of cholesterol 7alpha-hydroxylase and a dose-dependent induction of small heterodimer partner (SHP) expression were also observed, suggesting that farnesoid X receptor (FXR) was activated. In addition, ICAM-1 and SHP mRNA levels were also induced in primary human hepatocytes when treated with chenodeoxycholic acid or GW4064, a FXR-selective agonist. The involvement of FXR in CA-induced inflammatory gene expression was further investigated in the human hepatic cell line HepG2. Both ICAM-1 and SHP expression were induced in a dose- and time-dependent manner by treatment with the FXR-selective agonist GW4064. Moreover, the induction of ICAM-1 by GW4064 was inhibited by the FXR antagonist guggulsterone or with transfection of FXR siRNA. Finally, the activity of FXR was mapped to a retinoic acid response element (RARE) site containing an imbedded farnesoid X response element (FXRE) on the human ICAM-1 promoter and FXR and retinoid X receptor were demonstrated to bind to this site. Finally, FXR-mediated activation of ICAM-1 could be further enhanced by TNF-alpha cotreatment in hepatocytes, suggesting a potential cooperation between cytokine and bile acid-signaling pathways during hepatic inflammatory events.

  6. Observation of new particle formation and measurement of sulfuric acid, ammonia, amines and highly oxidized organic molecules at a rural site in central Germany

    NASA Astrophysics Data System (ADS)

    Kürten, Andreas; Bergen, Anton; Heinritzi, Martin; Leiminger, Markus; Lorenz, Verena; Piel, Felix; Simon, Mario; Sitals, Robert; Wagner, Andrea C.; Curtius, Joachim

    2016-10-01

    The exact mechanisms for new particle formation (NPF) under different boundary layer conditions are not known yet. One important question is whether amines and sulfuric acid lead to efficient NPF in the atmosphere. Furthermore, it is not clear to what extent highly oxidized organic molecules (HOMs) are involved in NPF. We conducted field measurements at a rural site in central Germany in the proximity of three larger dairy farms to investigate whether there is a connection between NPF and the presence of amines and/or ammonia due to the local emissions from the farms. Comprehensive measurements using a nitrate chemical ionization-atmospheric pressure interface time-of-flight (CI-APi-TOF) mass spectrometer, a proton-transfer-reaction mass spectrometer (PTR-MS), particle counters and differential mobility analyzers (DMAs), as well as measurements of trace gases and meteorological parameters, were performed. We demonstrate here that the nitrate CI-APi-TOF is suitable for sensitive measurements of sulfuric acid, amines, a nitrosamine, ammonia, iodic acid and HOMs. NPF was found to correlate with sulfuric acid, while an anti-correlation with RH, amines and ammonia is observed. The anti-correlation between NPF and amines could be due to the efficient uptake of these compounds by nucleating clusters and small particles. Much higher HOM dimer (C19/C20 compounds) concentrations during the night than during the day indicate that these HOMs do not efficiently self-nucleate as no nighttime NPF is observed. Observed iodic acid probably originates from an iodine-containing reservoir substance, but the iodine signals are very likely too low to have a significant effect on NPF.

  7. The influence of chemisorbed molecules on mass transfer in H-ZSM-5-type zeolites and the location of Broensted acid sites

    SciTech Connect

    Caro, J.; Buelow, M. ); Kaerger, J.; Pfeifer, H. )

    1988-11-01

    Heterogeneous catalysis is one of the most important applications of zeolites. Therefore, various methods have been developed to determine the strength and concentration of Bronsted acid sites in zeolites. Among them, in the last few years, {sup 1}H MAS NMR has become a powerful tool. In addition to the accessibility of the acid sites probed by chemisorption of N-bases, the steric environment of these catalytically active sites is of importance since it imposes constraints on the geometry of the transition state. However, only a few studies have been reported on this topic. Information was obtained from quantum chemical calculations, catalytic experiments, I.R. spectroscopy, and the arrangement of guest molecules. From these investigations it has been concluded that in H-ZSM-5 the channel intersections should be preferential location centers for the Bronsted acid sites. In adsorption technology, in the use of zeolites as shape-selective adsorbents, modification of the molecular sieve properties by chemisorption of nitrogen-containing bases (N-compounds) has become a common technique. The authors have applied the NMR pulsed field gradient technique to study the influence of chemisorbed N-compounds on transport properties of molecular sieves, considering the chemisorbed compounds as transport obstacles.

  8. Alpha2,6-sialic acid on platelet endothelial cell adhesion molecule (PECAM) regulates its homophilic interactions and downstream antiapoptotic signaling.

    PubMed

    Kitazume, Shinobu; Imamaki, Rie; Ogawa, Kazuko; Komi, Yusuke; Futakawa, Satoshi; Kojima, Soichi; Hashimoto, Yasuhiro; Marth, Jamey D; Paulson, James C; Taniguchi, Naoyuki

    2010-02-26

    Antiangiogenesis therapies are now part of the standard repertoire of cancer therapies, but the mechanisms for the proliferation and survival of endothelial cells are not fully understood. Although endothelial cells are covered with a glycocalyx, little is known about how endothelial glycosylation regulates endothelial functions. Here, we show that alpha2,6-sialic acid is necessary for the cell-surface residency of platelet endothelial cell adhesion molecule (PECAM), a member of the immunoglobulin superfamily that plays multiple roles in cell adhesion, mechanical stress sensing, antiapoptosis, and angiogenesis. As a possible underlying mechanism, we found that the homophilic interactions of PECAM in endothelial cells were dependent on alpha2,6-sialic acid. We also found that the absence of alpha2,6-sialic acid down-regulated the tyrosine phosphorylation of PECAM and recruitment of Src homology 2 domain-containing protein-tyrosine phosphatase 2 and rendered the cells more prone to mitochondrion-dependent apoptosis, as evaluated using PECAM- deficient endothelial cells. The present findings open up a new possibility that modulation of glycosylation could be one of the promising strategies for regulating angiogenesis. PMID:20048157

  9. Oligonucleotide-conjugated thiazole orange probes as "light-up" probes for messenger ribonucleic acid molecules in living cells.

    PubMed

    Privat, E; Melvin, T; Asseline, U; Vigny, P

    2001-10-01

    "Light-up" probes, icosa-alpha-thymidylate-thiazole orange conjugates, for the in situ time-resolved detection of messenger ribonucleic acid (mRNA) in living cells are evaluated. Upon annealing with polyA in aqueous solutions, the icosa-alpha-thymidylate-thiazole orange conjugates were shown to be up to 15 times more fluorescent. Microinjection of these probes into adherent fibroblasts resulted in high yields of hybridization and fluorescent signals. Incubation of cells in the presence of these probes resulted in facile internalization of the probe and similar painting of the messenger RNA in the nuclear and cytosolic regions.

  10. Synthesis of structured lipids and etherlipids with antioxidants: combination of a selena fatty acid and a selena fatty alcohol with a carotenoic acid in glyceride molecules.

    PubMed

    Houte, H; Partali, V; Sliwka, H R; Quartey, E G

    2000-03-01

    Selenium and carotenoids show similar and complementary properties and protect against a variety of pathological processes. Mixtures of both compounds are found in nutritional supplements and are used to prevent several diseases. The synthetic connection of carotenoids with selenium in glycerols may increase the chemopreventive activity of the individual compounds. Beta-apo-8'-carotenoic acid and 7-selenacapryloic acid were esterified with glycerol to highly unsaturated stable di- and triglycerides. Intramolecular selenium:carotenoid ratios of 1:1, 2:1 and 1:2 were obtained for 1-(7-selenaoctanoyl)-3-(3beta-apo-8 -carotenoyl)-glycerol, 1,3-di-(beta-apo-8'-carotenoyl)-2-(7-selenaoctanoyl)-glycero l and 1,2-di-(7-selenaoctanoyl)-3-(beta-apo-8'-carotenoyl)-glycero l, respectively. The carotenoic acid was likewise connected to the pharmacologically interesting 11-selenalaurylglycerolether forming an alkyl-acylglyceride: 1-(11-selenadodecyl)-3-(beta-apo-8'-carotenoyl)-glycerol.

  11. The Cell Adhesion Molecule “CAR” and Sialic Acid on Human Erythrocytes Influence Adenovirus In Vivo Biodistribution

    PubMed Central

    Wodrich, Harald; Billet, Olivier; Perreau, Matthieu; Hippert, Claire; Mennechet, Franck; Schoehn, Guy; Lortat-Jacob, Hugues; Dreja, Hanna; Ibanes, Sandy; Kalatzis, Vasiliki; Wang, Jennifer P.; Finberg, Robert W.; Cusack, Stephen; Kremer, Eric J.

    2009-01-01

    Although it has been known for 50 years that adenoviruses (Ads) interact with erythrocytes ex vivo, the molecular and structural basis for this interaction, which has been serendipitously exploited for diagnostic tests, is unknown. In this study, we characterized the interaction between erythrocytes and unrelated Ad serotypes, human 5 (HAd5) and 37 (HAd37), and canine 2 (CAV-2). While these serotypes agglutinate human erythrocytes, they use different receptors, have different tropisms and/or infect different species. Using molecular, biochemical, structural and transgenic animal-based analyses, we found that the primary erythrocyte interaction domain for HAd37 is its sialic acid binding site, while CAV-2 binding depends on at least three factors: electrostatic interactions, sialic acid binding and, unexpectedly, binding to the coxsackievirus and adenovirus receptor (CAR) on human erythrocytes. We show that the presence of CAR on erythrocytes leads to prolonged in vivo blood half-life and significantly reduced liver infection when a CAR-tropic Ad is injected intravenously. This study provides i) a molecular and structural rationale for Ad–erythrocyte interactions, ii) a basis to improve vector-mediated gene transfer and iii) a mechanism that may explain the biodistribution and pathogenic inconsistencies found between human and animal models. PMID:19119424

  12. Gold Nanorods as Colorful Chromogenic Substrates for Semiquantitative Detection of Nucleic Acids, Proteins, and Small Molecules with the Naked Eye.

    PubMed

    Ma, Xiaoming; Chen, Zhitao; Kannan, Palanisamy; Lin, Zhenyu; Qiu, Bin; Guo, Longhua

    2016-03-15

    Herein, we report for the first time a colorful chromogenic substrate, which displays vivid color responses in the presence of different concentration of analytes. Our investigation reveals that the selective shortening of gold nanorods (AuNRs) could generate a series of distinct colors that covers nearly the whole visible range from 400 to 760 nm. These vivid colors can be easily distinguished by the naked eye; as a result, the accuracy of visual inspection could be greatly improved. Next, we demonstrate the utility of AuNRs as multicolor chromogenic substrate to develop a number of colorimetric immunoassay methods, e.g., multicolor enzyme-linked immunosorbent assay (ELISA), multicolor competitive ELISA, and multicolor magnetic immunoassay (MIA). These methods allow us to visually quantify the concentration of a broad range of target molecules with the naked eye, and the obtained results are highly consistent with those state-of-the-art techniques that are tested by the sophisticated apparatus. These multicolor portable and cost-effective immunoassay approaches could be potentially useful for a number of applications, for example, in-home personal healthcare, on-site environmental monitoring, and food inspection in the field.

  13. Hypothesis of Lithocoding: Origin of the Genetic Code as a "Double Jigsaw Puzzle" of Nucleobase-Containing Molecules and Amino Acids Assembled by Sequential Filling of Apatite Mineral Cellules.

    PubMed

    Skoblikow, Nikolai E; Zimin, Andrei A

    2016-05-01

    The hypothesis of direct coding, assuming the direct contact of pairs of coding molecules with amino acid side chains in hollow unit cells (cellules) of a regular crystal-structure mineral is proposed. The coding nucleobase-containing molecules in each cellule (named "lithocodon") partially shield each other; the remaining free space determines the stereochemical character of the filling side chain. Apatite-group minerals are considered as the most preferable for this type of coding (named "lithocoding"). A scheme of the cellule with certain stereometric parameters, providing for the isomeric selection of contacting molecules is proposed. We modelled the filling of cellules with molecules involved in direct coding, with the possibility of coding by their single combination for a group of stereochemically similar amino acids. The regular ordered arrangement of cellules enables the polymerization of amino acids and nucleobase-containing molecules in the same direction (named "lithotranslation") preventing the shift of coding. A table of the presumed "LithoCode" (possible and optimal lithocodon assignments for abiogenically synthesized α-amino acids involved in lithocoding and lithotranslation) is proposed. The magmatic nature of the mineral, abiogenic synthesis of organic molecules and polymerization events are considered within the framework of the proposed "volcanic scenario". PMID:27048216

  14. Order of amino acids in C-terminal cysteine-containing peptide-based chelators influences cellular processing and biodistribution of 99mTc-labeled recombinant Affibody molecules.

    PubMed

    Altai, Mohamed; Wållberg, Helena; Orlova, Anna; Rosestedt, Maria; Hosseinimehr, Seyed Jalal; Tolmachev, Vladimir; Ståhl, Stefan

    2012-05-01

    Affibody molecules constitute a novel class of molecular display selected affinity proteins based on non-immunoglobulin scaffold. Preclinical investigations and pilot clinical data have demonstrated that Affibody molecules provide high contrast imaging of tumor-associated molecular targets shortly after injection. The use of cysteine-containing peptide-based chelators at the C-terminus of recombinant Affibody molecules enabled site-specific labeling with the radionuclide 99mTc. Earlier studies have demonstrated that position, composition and the order of amino acids in peptide-based chelators influence labeling stability, cellular processing and biodistribution of Affibody molecules. To investigate the influence of the amino acid order, a series of anti-HER2 Affibody molecules, containing GSGC, GEGC and GKGC chelators have been prepared and characterized. The affinity to HER2, cellular processing of 99mTc-labeled Affibody molecules and their biodistribution were investigated. These properties were compared with that of the previously studied 99mTc-labeled Affibody molecules containing GGSC, GGEC and GGKC chelators. All variants displayed picomolar affinities to HER2. The substitution of a single amino acid in the chelator had an appreciable influence on the cellular processing of 99mTc. The biodistribution of all 99mTc-labeled Affibody molecules was in general comparable, with the main difference in uptake and retention of radioactivity in excretory organs. The hepatic accumulation of radioactivity was higher for the lysine-containing chelators and the renal retention of 99mTc was significantly affected by the amino acid composition of chelators. The order of amino acids influenced renal uptake of some conjugates at 1 h after injection, but the difference decreased at later time points. Such information can be helpful for the development of other scaffold protein-based imaging and therapeutic radiolabeled conjugates.

  15. Inclusion complexation behavior of dyestuff guest molecules by a bridged bis(cyclomaltoheptaose)[bis(beta-cyclodextrin)] with a pyromellitic acid diamide tether.

    PubMed

    Liu, Yu; Li, Li; Zhang, Heng-Yi; Liang, Peng; Wang, Hao

    2003-08-12

    A novel bridged bis(beta-cyclodextrin) with a pyromellitic acid 2,5-diamide tether (2) has been synthesized by reaction of 6(I)-(2-aminoethyleneamino)-6-deoxycyclomaltoheptaose [mono 6-(2-aminoethyleneamino)-6-deoxy-beta-cyclodextrin] with 1,2,4,5-benzenetetracarboxylic dianhydride. Its inclusion complexation behavior with some representative dyestuffs, i.e., Acridine Red (AR), Rhodamine B (RhB), Neutral Red (NR), Brilliant Green (BG), was studied by using UV-absorption, fluorescence, and 2D NMR spectroscopy. Fluorescence titrations have been performed at 25 degrees C in pH 7.2 buffer solution to calculate the binding constants of resulting complexes. These results obtained indicated that bis(beta-cyclodextrin) 2 exhibits the strongly enhanced binding ability with all dye molecules examined compared with natural cyclodextrins. The binding modes of 2 with dye molecules have been deduced by 2D NMR experiments to establish the correlations between molecular conformations and binding constants of inclusion complexation. It is found that the improved binding ability and molecular selectivity of 2 could be attributed to double-cavity cooperative inclusion interaction and the size/shape matching between the host and guest.

  16. Exogenous adenosine 5'-phosphoramidate behaves as a signal molecule in plants; it augments metabolism of phenylpropanoids and salicylic acid in Arabidopsis thaliana seedlings.

    PubMed

    Pietrowska-Borek, Małgorzata; Nuc, Katarzyna; Guranowski, Andrzej

    2015-09-01

    Cells contain various congeners of the canonical nucleotides. Some of these accumulate in cells under stress and may function as signal molecules. Their cellular levels are enzymatically controlled. Previously, we demonstrated a signaling function for diadenosine polyphosphates and cyclic nucleotides in Arabidopsis thaliana and grape, Vitis vinifera. These compounds increased the expression of genes for and the specific activity of enzymes of phenylpropanoid pathways resulting in the accumulation of certain products of these pathways. Here, we show that adenosine 5'-phosphoramidate, whose level can be controlled by HIT-family proteins, induced similar effects. This natural nucleotide, when added to A. thaliana seedlings, activated the genes for phenylalanine:ammonia lyase, 4-coumarate:coenzyme A ligase, cinnamate-4-hydroxylase, chalcone synthase, cinnamoyl-coenzyme A:NADP oxidoreductase and isochorismate synthase, which encode proteins catalyzing key reactions of phenylpropanoid pathways, and caused accumulation of lignins, anthocyanins and salicylic acid. Adenosine 5'-phosphofluoridate, a synthetic congener of adenosine 5'-phosphoramidate, behaved similarly. The results allow us to postulate that adenosine 5'-phosphoramidate should be considered as a novel signaling molecule.

  17. Hydrogen sulfide acts as a downstream signal molecule in salicylic acid-induced heat tolerance in maize (Zea mays L.) seedlings.

    PubMed

    Li, Zhong-Guang; Xie, Lin-Run; Li, Xiao-Juan

    2015-04-01

    Salicylic acid (SA), 2-hydroxy benzoic acid, is a small phenolic compound with multifunction that is involved in plant growth, development, and the acquisition of stress tolerance. In recent years, hydrogen sulfide (H2S) has been found to have similar functions, but cross talk between SA and H2S in the acquisition of heat tolerance is not clear. In this study, pretreatment of maize seedlings with SA improved the survival percentage of seedlings under heat stress, indicating that SA pretreatment could improve the heat tolerance of maize seedlings. In addition, treatment with SA enhanced the activity of L-cysteine desulfhydrase (L-DES), a key enzyme in H2S biosynthesis, which in turn induced accumulation of endogenous H2S. Interestingly, SA-induced heat tolerance was enhanced by addition of NaHS, a H2S donor, but weakened by specific inhibitors of H2S biosynthesis DL-propargylglycine (PAG) and its scavenger hydroxylamine (HT). Furthermore, pretreatment with paclobutrazol (PAC) and 2-aminoindan-2-phosphonic acid (AIP), inhibitors of SA biosynthesis, had no significant effect on NaHS-induced heat tolerance of maize seedlings. Similarly, significant change in the activities of phenylalanine ammonia lyase (PAL) and benzoic-acid-2-hydroxylase (BA2H), the key enzymes in SA biosynthesis, and the content of endogenous SA, was not observed in maize seedlings by NaHS treatment. All of the above-mentioned results suggest that SA pretreatment could improve the heat tolerance of maize seedlings, and H2S might be a novel downstream signal molecule in SA-induced heat tolerance.

  18. Folic acid deficiency increases delayed neuronal death, DNA damage, platelet endothelial cell adhesion molecule-1 immunoreactivity, and gliosis in the hippocampus after transient cerebral ischemia.

    PubMed

    Hwang, In Koo; Yoo, Ki-Yeon; Suh, Hong-Won; Kim, Young Sup; Kwon, Dae Young; Kwon, Young-Guen; Yoo, Jun-Hyun; Won, Moo-Ho

    2008-07-01

    Folic acid deficiency increases stroke risk. In the present study, we examined whether folic acid deficiency enhances neuronal damage and gliosis via oxidative stress in the gerbil hippocampus after transient forebrain ischemia. Animals were exposed to a folic acid-deficient diet (FAD) for 3 months and then subjected to occlusion of both common carotid arteries for 5 min. Exposure to an FAD increased plasma homocysteine levels by five- to eightfold compared with those of animals fed with a control diet (CD). In CD-treated animals, most neurons were dead in the hippocampal CA1 region 4 days after ischemia/reperfusion, whereas, in FAD-treated animals, this occurred 3 days after ischemia/reperfusion. Immunostaining for 8-hydroxy-2'-deoxyguanosine (8-OHdG) was performed to examine DNA damage in CA1 neurons in both groups after ischemia, and it was found that 8-OHdG immunoreactivity in both FAD and CD groups peaked at 12 hr after reperfusion, although the immunoreactivity in the FAD group was much greater than that in the CD group. Platelet endothelial cell adhesion molecule-1 (PECAM-1; a final mediator of neutrophil transendothelial migration) immunoreactivity in both groups increased with time after ischemia/reperfusion: Its immunoreactivity in the FAD group was much higher than that in the CD group 3 days after ischemia/reperfusion. In addition, reactive gliosis in the ischemic CA1 region increased with time after ischemia in both groups, but astrocytosis and microgliosis in the FAD group were more severe than in the CD group at all times after ischemia. Our results suggest that folic acid deficiency enhances neuronal damage induced by ischemia.

  19. Effects of caffeic acid phenethyl ester on matrix molecules and angiogenetic and anti-angiogenetic factors in gastric cancer cells cultured on different substrates.

    PubMed

    Kosova, F; Kurt, F O; Olmez, E; Tuğlu, I; Arı, Z

    2016-01-01

    Migration, invasion, metastasis and angiogenesis associated with cancer depend on the surrounding microenvironment. Angiogenesis, the growth of new capillaries, is a regulator of cancer growth and a useful target for cancer therapy. We examined matrix protein interactions in a gastric cancer cell culture that was treated with different doses of caffeic acid (3,4-dihydroxycinnamic acid) phenethyl ester (CAPE). We also investigated the relations among the levels of vascular endothelial growth factor (VEGF), matrix metalloproteinase-9 (MMP-9), endostatin (ES) and trombospondin-1 (TSP-1). Cytotoxity of CAPE was measured using the 3-(4,5-dmethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay. We examined the behavior of cells on laminin and collagen I coated surfaces in response to the angiogenic effect of these matrix molecules. We examined the protein alterations of these matrix molecules immunohistochemically and measured the levels of VEGF, MMP-9, ES and TSP-1 using the ELISA test. We showed that application of CAPE to the gastric cancer cell line on tissue culture plastic, laminin and collagen I significantly decreased the VEGF and MMP-9 protein levels. We found that TSP-1 levels were increased significantly in the gastric cancer cells after application of CAPE. The protein levels of gastric cancer cells also were increased significantly when tissue was cultured on laminin and collagen I. Application of CAPE to cells on laminin or collagen I coated surfaces significantly increased all of the proteins except ES. ES levels were increased on the collagen I covered surfaces, but the laminin surface decreased the levels of ES significantly. We demonstrated the beneficial effect of CAPE on a gastric cancer cell line including inhibition of proliferation and induction of some proteins that might be related to decreased angiogenesis. PMID:26523612

  20. Molecule nanoweaver

    DOEpatents

    Gerald, II; Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2009-03-10

    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  1. Effects of sub-lethal concentrations of thyme and oregano essential oils, carvacrol, thymol, citral and trans-2-hexenal on membrane fatty acid composition and volatile molecule profile of Listeria monocytogenes, Escherichia coli and Salmonella enteritidis.

    PubMed

    Siroli, Lorenzo; Patrignani, Francesca; Gardini, Fausto; Lanciotti, Rosalba

    2015-09-01

    The aim of this work was to investigate the modifications of cell membrane fatty acid composition and volatile molecule profiles of Listeria monocytogenes, Salmonella enteritidis, Escherichia coli, during growth in the presence of different sub-lethal concentrations of thyme and oregano essential oils as well as carvacrol, thymol, trans-2-hexenal and citral. The results evidenced that the tested molecules induced noticeable modifications of membrane fatty acid profiles and volatile compounds produced during the growth. Although specific differences in relation to the species considered were identified, the tested compounds induced a marked increase of some membrane associated fatty acids, particularly unsaturated fatty acids, trans-isomers, and specific released free fatty acids. These findings can contribute to the comprehension of the stress response mechanisms used by different pathogenic microorganisms often involved in food-borne diseases in relation to the exposure to sub-lethal concentrations of natural antimicrobials. PMID:25842326

  2. Effects of sub-lethal concentrations of thyme and oregano essential oils, carvacrol, thymol, citral and trans-2-hexenal on membrane fatty acid composition and volatile molecule profile of Listeria monocytogenes, Escherichia coli and Salmonella enteritidis.

    PubMed

    Siroli, Lorenzo; Patrignani, Francesca; Gardini, Fausto; Lanciotti, Rosalba

    2015-09-01

    The aim of this work was to investigate the modifications of cell membrane fatty acid composition and volatile molecule profiles of Listeria monocytogenes, Salmonella enteritidis, Escherichia coli, during growth in the presence of different sub-lethal concentrations of thyme and oregano essential oils as well as carvacrol, thymol, trans-2-hexenal and citral. The results evidenced that the tested molecules induced noticeable modifications of membrane fatty acid profiles and volatile compounds produced during the growth. Although specific differences in relation to the species considered were identified, the tested compounds induced a marked increase of some membrane associated fatty acids, particularly unsaturated fatty acids, trans-isomers, and specific released free fatty acids. These findings can contribute to the comprehension of the stress response mechanisms used by different pathogenic microorganisms often involved in food-borne diseases in relation to the exposure to sub-lethal concentrations of natural antimicrobials.

  3. Oleic and docosahexaenoic acid differentially phase separate from lipid raft molecules: a comparative NMR, DSC, AFM, and detergent extraction study.

    PubMed

    Shaikh, Saame Raza; Dumaual, Alfred C; Castillo, Alicia; LoCascio, Daniel; Siddiqui, Rafat A; Stillwell, William; Wassall, Stephen R

    2004-09-01

    We have previously suggested that the omega-3 polyunsaturated fatty acid, docosahexaenoic acid (DHA) may in part function by enhancing membrane lipid phase separation into lipid rafts. Here we further tested for differences in the molecular interactions of an oleic (OA) versus DHA-containing phospholipid with sphingomyelin (SM) and cholesterol (CHOL) utilizing (2)H NMR spectroscopy, differential scanning calorimetry, atomic force microscopy, and detergent extractions in model bilayer membranes. (2)H NMR and DSC (differential scanning calorimetry) established the phase behavior of the OA-containing 1-[(2)H(31)]palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (16:0-18:1PE-d(31))/SM (1:1) and the DHA-containing 1-[(2)H(31)]palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine (16:0-22:6PE-d(31))/SM (1:1) in the absence and presence of equimolar CHOL. CHOL was observed to affect the OA-containing phosphatidylethanolamine (PE) more than the DHA-containing PE, as exemplified by >2 x greater increase in order measured for the perdeuterated palmitic chain in 16:0-18:1PE-d(31)/SM (1:1) compared to 16:0-22:6PE-d(31)/SM (1:1) bilayers in the liquid crystalline phase. Atomic force microscopy (AFM) experiments showed less lateral phase separation between 16:0-18:1PE-rich and SM/CHOL-rich raft domains in 16:0-18:1PE/SM/CHOL (1:1:1) bilayers than was observed when 16:0-22:6PE replaced 16:0-18:1PE. Differences in the molecular interaction of 16:0-18:1PE and 16:0-22:6PE with SM/CHOL were also found using biochemical detergent extractions. In the presence of equimolar SM/CHOL, 16:0-18:1PE showed decreased solubilization in comparison to 16:0-22:6PE, indicating greater phase separation with the DHA-PE. Detergent experiments were also conducted with cardiomyocytes fed radiolabeled OA or DHA. Although both OA and DHA were found to be largely detergent solubilized, the amount of OA that was found to be associated with raft-rich detergent-resistant membranes exceeded DHA by

  4. IGF-I regulates redox status in breast cancer cells by activating the amino acid transport molecule xC-.

    PubMed

    Yang, Yuzhe; Yee, Douglas

    2014-04-15

    Insulin-like growth factors (IGF) stimulate cell growth in part by increasing amino acid uptake. xCT (SLC7A11) encodes the functional subunit of the cell surface transport system xC(-), which mediates cystine uptake, a pivotal step in glutathione synthesis and cellular redox control. In this study, we show that IGF-I regulates cystine uptake and cellular redox status by activating the expression and function of xCT in estrogen receptor-positive (ER(+)) breast cancer cells by a mechanism that relies on the IGF receptor substrate-1 (IRS-1). Breast cancer cell proliferation mediated by IGF-I was suppressed by attenuating xCT expression or blocking xCT activity with the pharmacologic inhibitor sulfasalazine (SASP). Notably, SASP sensitized breast cancer cells to inhibitors of the type I IGF receptor (IGF-IR) in a manner reversed by the reactive oxygen species (ROS) scavenger N-acetyl-L-cysteine. Thus, IGF-I promoted the proliferation of ER(+) breast cancer cells by regulating xC(-) transporter function to protect cancer cells from ROS in an IRS-1-dependent manner. Our findings suggest that inhibiting xC(-) transporter function may synergize with modalities that target the IGF-IR to heighten their therapeutic effects.

  5. Nanoparticles that deliver triplex-forming peptide nucleic acid molecules correct F508del CFTR in airway epithelium.

    PubMed

    McNeer, Nicole Ali; Anandalingam, Kavitha; Fields, Rachel J; Caputo, Christina; Kopic, Sascha; Gupta, Anisha; Quijano, Elias; Polikoff, Lee; Kong, Yong; Bahal, Raman; Geibel, John P; Glazer, Peter M; Saltzman, W Mark; Egan, Marie E

    2015-04-27

    Cystic fibrosis (CF) is a lethal genetic disorder most commonly caused by the F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. It is not readily amenable to gene therapy because of its systemic nature and challenges including in vivo gene delivery and transient gene expression. Here we use triplex-forming peptide nucleic acids and donor DNA in biodegradable polymer nanoparticles to correct F508del. We confirm modification with sequencing and a functional chloride efflux assay. In vitro correction of chloride efflux occurs in up to 25% of human cells. Deep-sequencing reveals negligible off-target effects in partially homologous sites. Intranasal delivery of nanoparticles in CF mice produces changes in the nasal epithelium potential difference assay, consistent with corrected CFTR function. Also, gene correction is detected in the nasal and lung tissue. This work represents facile genome engineering in vivo with oligonucleotides using a nanoparticle system to achieve clinically relevant levels of gene editing without off-target effects.

  6. Effect of perfluoroalkyl chain length on monolayer behavior of partially fluorinated oleic acid molecules at the air-water interface.

    PubMed

    Baba, Teruhiko; Takai, Katsuki; Takagi, Toshiyuki; Kanamori, Toshiyuki

    2013-01-01

    A series of oleic acid (OA) analogs containing terminal perfluoroalkyl groups (CF3, C2F5, n-C3F7, n-C4F9 or n-C8F17) was synthesized to clarify how the fluorinated chain length affects the stability and molecular packing of liquid-expanded OA monolayers at the air-water interface. Although the substitution of terminal CF3 group for CH3 in OA had no effect on monolayer stability, further fluorination led to a gradual increase in monolayer stability at 25 °C. Surface pressure-area isotherm revealed that partially fluorinated OA analogs form more expanded monolayers than OA at low surface pressures, and that the monolayer behavior of OA analogs with the even-carbon numbered fluorinated chain is almost the same as that of OA upon monolayer compression, whereas the behavior of OA analogs with the odd-carbon numbered fluorinated chain significantly differs from that of OA. These results indicate: (i) the terminal short part (at least C2 residue) in OA predominantly determines the liquid-expanded monolayer stability; (ii) the molecular packing state of OA may be perturbed by the substitution of a short odd-carbon numbered fluorinated chain; (iii) hence, OA analogs with even-carbon numbered chain are considered to be preferable as hydrophobic building blocks for the synthesis of fluorinated phospholipids.

  7. Effects of Hypoxanthine Substitution in Peptide Nucleic Acids Targeting KRAS2 Oncogenic mRNA Molecules: Theory and Experiment

    PubMed Central

    Sanders, Jeffrey M.; Wampole, Matthew E.; Chen, Chang-Po; Sethi, Dalip; Singh, Amrita; Dupradeau, François-Yves; Wang, Fan; Gray, Brian D.; Thakur, Mathew L.; Wickstrom, Eric

    2013-01-01

    Genetic disorders can arise from single base substitutions in a single gene. A single base substitution for wild type guanine in the twelfth codon of KRAS2 mRNA occurs frequently to initiate lung, pancreatic, and colon cancer. We have observed single base mismatch specificity in radioimaging of mutant KRAS2 mRNA in tumors in mice by in vivo hybridization with radiolabeled peptide nucleic acid (PNA) dodecamers. We hypothesized that multi-mutant specificity could be achieved with a PNA dodecamer incorporating hypoxanthine, which can form Watson-Crick basepairs with adenine, cytosine, thymine, and uracil. Using molecular dynamics simulations and free energy calculations, we show that hypoxanthine substitutions in PNAs are tolerated in KRAS2 RNA-PNA duplexes where wild type guanine is replaced by mutant uracil or adenine in RNA. To validate our predictions, we synthesized PNA dodecamers with hypoxanthine, and then measured the thermal stability of RNA-PNA duplexes. Circular dichroism thermal melting results showed that hypoxanthine-containing PNAs are more stable in duplexes where hypoxanthine-adenine and hypoxanthine-uracil base pairs are formed than single mismatch duplexes or duplexes containing hypoxanthine-guanine opposition. PMID:23972113

  8. Salicylic Acid Based Small Molecule Inhibitor for the Oncogenic Src Homology-2 Domain Containing Protein Tyrosine Phosphatase-2 (SHP2)

    SciTech Connect

    Zhang, Xian; He, Yantao; Liu, Sijiu; Yu, Zhihong; Jiang, Zhong-Xing; Yang, Zhenyun; Dong, Yuanshu; Nabinger, Sarah C.; Wu, Li; Gunawan, Andrea M.; Wang, Lina; Chan, Rebecca J.; Zhang, Zhong-Yin

    2010-08-13

    The Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2) plays a pivotal role in growth factor and cytokine signaling. Gain-of-function SHP2 mutations are associated with Noonan syndrome, various kinds of leukemias, and solid tumors. Thus, there is considerable interest in SHP2 as a potential target for anticancer and antileukemia therapy. We report a salicylic acid based combinatorial library approach aimed at binding both active site and unique nearby subpockets for enhanced affinity and selectivity. Screening of the library led to the identification of a SHP2 inhibitor II-B08 (compound 9) with highly efficacious cellular activity. Compound 9 blocks growth factor stimulated ERK1/2 activation and hematopoietic progenitor proliferation, providing supporting evidence that chemical inhibition of SHP2 may be therapeutically useful for anticancer and antileukemia treatment. X-ray crystallographic analysis of the structure of SHP2 in complex with 9 reveals molecular determinants that can be exploited for the acquisition of more potent and selective SHP2 inhibitors.

  9. A single amino acid change in the cytoplasmic domain of the simian immunodeficiency virus transmembrane molecule increases envelope glycoprotein expression on infected cells.

    PubMed Central

    LaBranche, C C; Sauter, M M; Haggarty, B S; Vance, P J; Romano, J; Hart, T K; Bugelski, P J; Marsh, M; Hoxie, J A

    1995-01-01

    We have described a virus termed CP-MAC, derived from the BK28 molecular clone of simian immunodeficiency virus, that was remarkable for its ability to infect Sup-T1 cells with rapid kinetics, cell fusion, and CD4 down-modulation (C. C. LaBranche, M. M. Sauter, B. S. Haggarty, P. J. Vance, J. Romano, T. K. Hart, P. J. Bugelski, and J. A. Hoxie, J. Virol. 68:5509-5522, 1994 [Erratum 68:7665-7667]). Compared with BK28, CP-MAC exhibited a number of changes in its envelope glycoproteins, including a highly stable association between the external (SU) and transmembrane (TM) molecules, a more rapid electrophoretic mobility of TM, and, of particular interest, a marked increase in the level of envelope protein expression on the surface of infected cells. These changes were shown to be associated with 11 coding mutations in the env gene (5 in SU and 6 in TM). In this report, we demonstrate that a single amino acid mutation of a Tyr to a Cys at position 723 (Y723C) in the TM cytoplasmic domain of CP-MAC is the principal determinant for the increased expression of envelope glycoproteins on the cell surface. When introduced into the env gene of BK28, the Y723C mutation produced up to a 25-fold increase in the levels of SU and TM on chronically infected cells, as determined by fluorescence-activated cell sorter analysis with monoclonal and polyclonal antibodies. A similar effect was observed when a Tyr-to-Cys change was introduced at the analogous position (amino acid 721) in the SIVmac239 molecular clone, which, unlike BK28 does not contain a premature stop codon in its TM cytoplasmic tail. Substituting other amino acids, including Ala, Ile, and Ser, at this position produced increases in surface envelope glycoproteins that were similar to that observed for the Cys substitution, while a Tyr-to-Phe mutation produced a smaller increase. These results could not be accounted for by differences in the kinetics or efficiency of envelope glycoprotein processing or by shedding of SU

  10. Equilibrium 2H/ 1H fractionations in organic molecules. II: Linear alkanes, alkenes, ketones, carboxylic acids, esters, alcohols and ethers

    NASA Astrophysics Data System (ADS)

    Wang, Ying; Sessions, Alex L.; Nielsen, Robert J.; Goddard, William A., III

    2009-12-01

    Equilibrium 2H/ 1H fractionation factors (α eq) for various H positions in alkanes, alkenes, ketones, carboxylic acids, esters, alcohols, and ethers were calculated between 0 and 100 °C using vibrational frequencies from ab initio QM calculations (B3LYP/6-311G**). Results were then corrected using a temperature-dependent linear calibration curve based on experimental data for H α in ketones ( Wang et al., 2009). The total uncertainty in reported α eq values is estimated at 10-20‰. The effects of functional groups were found to increase the value of α eq for H next to electron-donating groups, e.g. sbnd OR, sbnd OH or sbnd O(C dbnd O)R, and to decrease the value of α eq for H next to electron-withdrawing groups, e.g. sbnd (C dbnd O)R or sbnd (C dbnd O)OR. Smaller but significant functional group effects are also observed for H β and sometimes H γ. By summing over individual H positions, we estimate the equilibrium fractionation relative to water to be -90‰ to -70‰ for n-alkanes and around -100‰ for pristane and phytane. The temperature dependence of these fractionations is very weak between 0 and 100 °C. Our estimates of α eq agree well with field data for thermally mature hydrocarbons (δ 2H values between -80‰ and -110‰ relative to water). Therefore the observed δ 2H increase of individual hydrocarbons and the disappearance of the biosynthetic δ 2H offset between n-alkyl and linear isoprenoid lipids during maturation of organic matter can be confidently attributed to H exchange towards an equilibrium state. Our results also indicate that many n-alkyl lipids are biosynthesized with δ 2H values that are close to equilibrium with water. In these cases, constant down-core δ 2H values for n-alkyl lipids cannot be reliably used to infer a lack of isotopic exchange.

  11. Fluorescence detection in Lab-on-a-chip systems using ultrafast nucleic acid amplification methods

    NASA Astrophysics Data System (ADS)

    Gransee, Rainer; Schneider, Tristan; Elyorgun, Deniz; Strobach, Xenia; Schunck, Tobias; Gatscha, Theresia; Höth, Julian

    2014-05-01

    Today, nucleic amplification plays a key role in modern molecular biology allowing fast and specific laboratory diagnostics testing. An ultrafast microfluidic module (allowing 30 polymeric chain reaction (PCR) cycles in 6 minutes) based on an oscillating fluid plug concept was previously developed[1]. This system allows the amplification of native genomic deoxyribonucleic acid molecules (DNA) even from whole blood samples but still lacks some functionality compared to commercial bench top systems. This work presents the actual status of the renewed and advanced system, permitting the automated optical detection of not only the fluid plug position but also fluorescence detection. The system uses light emitting diodes (LED) for illumination and a low cost CMOS web-camera for optical detection. Image data processing allows the automated process control of the overall system components. Therefore, the system enables the performance of rapid and robust nucleic acid amplifications together with the integration of real time measurement technology. This allows the amplification and simultaneous quantification of the DNA molecules. The possibility to integrate swift nucleic amplification and optical detection into complex sample-to-answer analysis platforms opens up new pathways towards fast and transportable low-cost point of care devices.

  12. Enteral n-3 fatty acids and micronutrients enhance percentage of positive neutrophil and lymphocyte adhesion molecules: a potential mediator of pressure ulcer healing in critically ill patients.

    PubMed

    Theilla, Miriam; Schwartz, Betty; Zimra, Yael; Shapiro, Haim; Anbar, Ronit; Rabizadeh, Esther; Cohen, Jonathan; Singer, Pierre

    2012-04-01

    n-3 Fatty acids are recognised as influencing both wound healing and immunity. We assessed the impact of a fish oil- and micronutrient-enriched formula (study formula) on the healing of pressure ulcers and on immune function in critically ill patients in an intensive care unit. A total of forty patients with pressure ulcers and receiving nutritional support were enrolled (intervention group, n 20, received study formula; and a control group, n 20, received an isoenergetic formula). Total and differential leucocyte count and percentage of adhesion molecule positive granulocyte and lymphocyte cells (CD11a, CD11b, CD18 and CD49b) were measured on days 0, 7 and 14. Percentage of positive lymphocytes for CD54, CD49b, CD49d and CD8 were also measured on days 0, 7 and 14. The state of pressure ulcers was assessed by using the pressure ulcer scale for healing tool score on days 7, 14 and 28 of treatment. No between-group differences in patient demographics, anthropometry or diagnostic class were observed. Patients who received the study formula showed significant increases in the percentage of positive CD18 and CD11a lymphocytes and of CD49b granulocytes as compared to controls (P < 0·05). While the severity of pressure ulcers was not significantly different between the two groups on admission, severity increased significantly over time for the control group (P < 0·05), but not for the study group. The present study suggests that a fish oil- and micronutrient-enriched formula may prevent worsening of pressure ulcers and that this effect may be mediated by an effect on adhesion molecule expression.

  13. Ribonucleic acid (RNA) biosynthesis in human cancer.

    PubMed

    Hajjawi, Omar S

    2015-01-01

    In many respects, the most remarkable chemical substances within the genome of eukaryotic cells are remarkable proteins which are the critical structural and functional units of living cells. The specifications for everything that goes in the cell are natural digital-to-digital decoding process in an archive sequence by deoxyribonucleic acid (DNA) and an articulate construction by ribonucleic acid (RNA). The products of DNA transcription are long polymers of ribonucleotides rather than deoxyribonucleotides and are termed ribonucleic acids. Certain deoxyribonucleotide sequences, or genes, give rise to transfer RNA (tRNA) and other ribosomal RNA (rRNA) when transcribed. The ribonucleotide sequences fold extensively and rRNA is associated with specific proteins to yield the essential cell components, ribosomes. Transcription of other special sequences yields messenger RNAs (mRNAs) that contain ribonucleotide sequences that will be ultimately translated into new types of amino acid sequences of functional cellular protein molecules. This switch to a different variety of cellular molecular sequences is complex, but each sequence of the three ribonucleotides specifies the insertion of one particular amino acid into the polypeptide chain under production. Whilst mRNA is considered the vehicle by which genetic information is transmitted from the genome and allocated in the appropriate cytoplasmic sites for translation into protein via cap-dependent mechanism, the actual translation depends also on the presence of other so-called household and luxury protein molecules. Recent evidence suggests RNA species are required at initiation, because treatment of cells with antibiotics or drugs that inhibit RNA synthesis cause a decrease in protein synthesis. The rRNA is necessary as a structural constituent of the ribosomes upon which translation takes place, whereas tRNA is necessary as an adaptor in amino acid activation and elongation protein chains to ribosomes. In this article

  14. Post-Training Intrahippocampal Injection of Synthetic Poly-Alpha-2,8-Sialic Acid-Neural Cell Adhesion Molecule Mimetic Peptide Improves Spatial Long-Term Performance in Mice

    ERIC Educational Resources Information Center

    Florian, Cedrick; Foltz, Jane; Norreel, Jean-Chretien; Rougon, Genevieve; Roullet, Pascal

    2006-01-01

    Several data have shown that the neural cell adhesion molecule (NCAM) is necessary for long-term memory formation and might play a role in the structural reorganization of synapses. The NCAM, encoded by a single gene, is represented by several isoforms that differ with regard to their content of alpha-2,8-linked sialic acid residues (PSA) on their…

  15. Immobilization mechanisms of deoxyribonucleic acid (DNA) to hafnium dioxide (HfO2) surfaces for biosensing applications.

    PubMed

    Fahrenkopf, Nicholas M; Rice, P Zachary; Bergkvist, Magnus; Deskins, N Aaron; Cady, Nathaniel C

    2012-10-24

    Immobilization of biomolecular probes to the sensing substrate is a critical step for biosensor fabrication. In this work we investigated the phosphate-dependent, oriented immobilization of DNA to hafnium dioxide surfaces for biosensing applications. Phosphate-dependent immobilization was confirmed on a wide range of hafnium oxide surfaces; however, a second interaction mode was observed on monoclinic hafnium dioxide. On the basis of previous materials studies on these films, DNA immobilization studies, and density functional theory (DFT) modeling, we propose that this secondary interaction is between the exposed nucleobases of single stranded DNA and the surface. The lattice spacing of monoclinic hafnium dioxide matches the base-to-base pitch of DNA. Monoclinic hafnium dioxide is advantageous for nanoelectronic applications, yet because of this secondary DNA immobilization mechanism, it could impede DNA hybridization or cause nonspecific surface intereactions. Nonetheless, DNA immobilization on polycrystalline and amorphous hafnium dioxide is predominately mediated by the terminal phosphate in an oriented manner which is desirable for biosensing applications.

  16. Epidermal growth factor inhibits radioiodine uptake but stimulates deoxyribonucleic acid synthesis in newborn rat thyroids grown in nude mice

    SciTech Connect

    Ozawa, S.; Spaulding, S.W. )

    1990-08-01

    We have studied the effect of altering the level of circulating epidermal growth factor (EGF) on the function and growth of newborn rat thyroids transplanted into nude mice. Preliminary studies confirmed that sialoadenectomy reduced circulating EGF levels in nude mice (from 0.17 +/- 0.02 to 0.09 +/- 0.02 ng/ml), and that ip injection of 5 micrograms EGF raised EGF levels (the peak level of 91.7 +/- 3.3 ng/ml was achieved at 30 min, with a subsequent half-life of about 1 h). The radioiodine uptake by newborn rat thyroid transplants in the sialoadenectomized and sham-operated animals correlated inversely with the circulating EGF levels determined when the mice were killed (r = -0.99). Low-dose TSH treatment (0.1 microU/day) generally stimulated the radioiodine uptake, but high-dose TSH groups (100 microU/day) were not significantly different from the control group. The 5-day nuclear (3H)thymidine labeling index was 6.8 +/- 0.5% IN newborn rat thyroid transplants grown in sialoadenectomized animals, 13.1 +/- 0.3% in sham-operated animals, and 16.8 +/- 0.5% in nude mice receiving 5 micrograms EGF ip daily. In general, both low-dose and high-dose TSH promoted DNA synthesis under low EGF conditions but were ineffective in the presence of higher levels of EGF. Adult rat thyroid transplants showed no significant responses. Although sialoadenectomy may alter other factors besides EGF, it appears that changes in the levels of circulating EGF within the physiological range affect the function and growth of newborn rat thyroid transplants. Circulating EGF may play a role in thyroid maturation and may also be involved in the regulation of thyroid function throughout life.

  17. Deoxyribonucleic acid of Cancer pagurus. II. Tempiate activity for a DNA-dependent DNA polymerase of eukaryotic cells

    PubMed Central

    De Recondo, Anne-Marie; Londos-Gagliardi, Danielle; Aubel-Sadron, Geneviève

    1974-01-01

    The template activity of Cancer pagurus DNA and its two components (poly d(A-T) and main component) in response to a DNA polymerase purified from regenerating rat liver has been studied and compared to the results previously obtained with synthetic templates. In the double-stranded native state, whole crab DNA and the main component were poor templates. Their replication was increased by thermal denaturation and inhibited by actinomycin. Like the synthetic copolymer poly[d(A-T)·d(T-A)], native crab poly d(A-T) could be copied and its duplication was not inhibited by actinomycin. The structural difference between native poly d(A-T) Form I, isolated on a density gradient, and partially renatured poly d(A-T) Form II, isolated on hydroxylapatite, resulted in a modification of their template activity. The kinetic studies of [3H] dGMP and [3H] dAMP incorporation confirmed the importance of single-stranded regions (particulary dC regions) in the initiation of the in vitro duplication. PMID:10793685

  18. Comparative studies on zirconia and graphene composites obtained by one-step and stepwise electrodeposition for deoxyribonucleic acid sensing.

    PubMed

    Yang, Tao; Guo, Xiuhong; Kong, Qianqian; Yang, Ruirui; Li, Qianhe; Jiao, Kui

    2013-07-01

    In this paper, the comparison of two kinds of electrochemically reduced graphene oxide (ERGNO) and zirconia composites, obtained by one-step (ZrO2-ERGNO) and stepwise (ZrO2/ERGNO) electrodeposition for DNA sensing, is systematically studied. The resulting composites were characterized by scanning electron microscopy, cyclic voltammetry, and differential pulse voltammetry. The results indicated that the ZrO2-ERGNO presented fine globular nanostructure. However, ZrO2/ERGNO presented agglomerate massive microstructure due to the absence of the oxygen-containing groups of graphene oxide, confirming the oxygen-containing groups provided a better affinity for the deposition of ZrO2. Due to the strong binding of the phosphate groups of DNA with the zirconia film, DNA probes were attached on the ZrO2-based composites. ZrO2-ERGNO/Au owning fine nanostructure presented larger surface area than microstructured ZrO2/ERGNO/Au. Moreover, compared with microstructured ZrO2/ERGNO, the nanostructured ZrO2-ERGNO provided more accessible space for immobilized DNA probe hybridization with target sequence, which consequently resulted in higher hybridization efficiency. Therefore, the ZrO2-ERGNO was chosen for fabricating DNA sensor with a limit of detection 1.21×10(-14) mol L(-1).

  19. Effect of base-pair stability of nearest-neighbor nucleotides on the fidelity of deoxyribonucleic acid synthesis.

    PubMed

    Patten, J E; So, A G; Downey, K M

    1984-04-10

    The influence of the stability of base pairs formed by nearest-neighbor nucleotides on misincorporation frequency has been studied with the large fragment of DNA polymerase I, the alternating DNA copolymers, poly(dI-dC) and poly-(dG-dC), as template-primers, and dGTP, dITP, and dCTP as substrates. We have utilized the difference in thermodynamic stability between the doubly H-bonded I X C base pair and triply H-bonded G X C base pair to examine the effects of base-pair stability of both the "preceding" and the "following" nucleotides on the frequency of insertion of a mismatched nucleotide, as well as on its stable incorporation into polynucleotide. The present studies demonstrate that the stability of the base pairs formed by nearest-neighbor nucleotides affects the frequency of incorporation of noncomplementary nucleotides. Misincorporation frequency is increased when the nearest-neighbor nucleotides form more stable base pairs with the corresponding nucleotides in the template and is decreased when they form less stable base pairs. The stability of the base pair formed by a nucleotide either preceding (5' to) or following (3' to) a misincorporated nucleotide influences misincorporation frequency, but by different mechanisms. The stability of base pairs formed by preceding nucleotides affects the rate of insertion of mismatched nucleotide but does not protect the mismatched nucleotide from removal by the 3' to 5' exonuclease activity. In contrast, the stability of a base pair formed by a following nucleotide determines whether a misincorporated nucleotide is extended or excised by affecting the ability of the enzyme to edit errors of incorporation. PMID:6722115

  20. Evaluation of non-radioactive labelling and detection of deoxyribonucleic acids. Part Two: Colorigenic methods and comparison with chemiluminescent methods.

    PubMed

    Rihn, B; Bottin, M C; Coulais, C; Martinet, N

    1995-06-01

    The diagnosis of genetic infections and cancerous diseases is carried out more and more often at a molecular level using Southern's technique which is based on the use of 32P-labelled DNA. In order to circumvent the risks and rapid decrease in radioactivity associated with these latter techniques, new colorigenic methods have been developed. In this work, we describe the use of dTTP analogues (digoxigenin-dUTP and biotin-dUTP) for the labelling of probes and detection of target DNA. Using digoxigenin-11-dUTP, 0.1 aM of a 561 bp target DNA was detected by using a modified Southern procedure. The reliability and the high sensitivity of such methods make them a good tool for DNA investigation in research as well as in testing laboratories.

  1. Three forms of gonadotropin-releasing hormone in a perciform fish (Sparus aurata): complementary deoxyribonucleic acid characterization and brain localization.

    PubMed

    Gothilf, Y; Muñoz-Cueto, J A; Sagrillo, C A; Selmanoff, M; Chen, T T; Kah, O; Elizur, A; Zohar, Y

    1996-09-01

    Three forms of GnRH-salmon (sGnRH), seabream (sb-GnRH), and chicken (cGnRH-II)-have been described in the gilthead seabream (Sparus aurata) brain, and the cDNA encoding the sbGnRH precursor was recently isolated. In the present study, the cDNAs encoding the sGnRH and cGnRH-II were isolated and characterized, and the neurons producing the three GnRHs were localized in the seabream brain. Fragments of sGnRH and cGnRH-II cDNAs were amplified by polymerase chain reaction and used as probes to isolate the full-length cDNAs from a brain cDNA library. The cDNA encoding the cGnRH-II precursor is 573 nucleotides (nt) long, and the cDNA encoding the sGnRH precursor is 1971 nt in length with an unusually long 5' untranslated region. Specific single-strand DNA probes for in situ detection of mRNA were designed according to nonconserved regions among the three GnRH c-DNAs. Localization of GnRH mRNA-producing cells in the brain revealed five distinct populations of cells: sGnRH-producing cells in the ventromedial olfactory bulbs and the terminal nerve, sbGnRH-producing cells in the preoptic area and the ventral thalamus, and cGnRH-II-producing cells in the midbrain tegmentum. The discrete sites of expression of the three forms of GnRH indicate that only sbGnRH is directly involved in the control of gonadotropin secretion. PMID:8862782

  2. Fate of transgenic deoxyribonucleic acid fragments in digesta and tissues of rabbits fed genetically modified soybean meal.

    PubMed

    Morera, P; Basiricò, L; Ronchi, B; Bernabucci, U

    2016-03-01

    Numerous animal feeding studies have investigated the presence of DNA from transgenic plants in tissues from different animal species, but the data reported are sometimes controversial. The aim of this study was to investigate the presence of transgenic DNA (tDNA) in the digesta and tissues of a meat rabbit breed fed genetically modified (GM) soybean meal. Fifteen male New Zealand White rabbits were used for the experimental trial. Ten rabbits (treated group [TG]) were fed a mixed feed containing 10% GM soybean meal and 5 rabbits (control group [CG]) received a mixed feed containing conventional soybean meal, both from weaning (28 d of age) to slaughter (80 ± 3 d). Samples of blood, liver, kidney, heart, stomach, intestine (jejunum), lateral quadricep muscle, longissimus muscle, and perirenal adipose tissue were collected to assess the possible DNA transfer from GM feed to animal tissues. Samples of stomach contents and feces were also taken to study the degradability of ingested tDNA from feed in the digestive tract of rabbit. Moreover, samples of hair were collected to determine the possible environmental contamination from feed powders present on the farm. The DNA extraction was performed using specific genomic DNA kits. All samples were monitored, by using real-time PCR, for oligonucleotide primers and probes specific for the transgenic Roundup Ready soybean 40-3-2 and for the endogenous () gene. As an internal control of rabbit tissues, the presence of the () gene was used. In this study, no fragments of tDNA were detectable in tissue DNA samples of rabbits except in the extracted DNA from stomach digesta, feces, and hair of rabbits fed with GM soybean. Similar results were found for the reference gene, whereas the presence of the gene was detected in all rabbit tissues. The lack of tDNA of soybean in rabbit tissues represents an important result, which demonstrates that meat from rabbits fed a diet containing GM feed is as that derived from rabbits fed conventional crops. The recombinant DNA recovered in the stomach digesta and in feces indicates an incomplete digestion of the soybean DNA in the gastrointestinal tract of the rabbit, whereas the presence of trace soybean transgene in the hair of the TG rabbits is suggestive of an environmental contamination. PMID:27065289

  3. Effects of Bilberry on Deoxyribonucleic Acid Damage and Oxidant-Antioxidant Balance in the Lens, Induced by Ultraviolet Radiation

    PubMed Central

    ALY, Eman Mohamed; ALI, Mervat Ahmed

    2014-01-01

    Background: This study investigated the possible protective effects of bilberry extract after exposing rat eyes to ultraviolet-B (UV-B) radiation. Methods: Four groups of rats were included in this study, each consisting of 10 Wistar rats. The first group acted as the control, and the second group was exposed to UV-B, 5 KJ/m2 (λm = 300 nm), for 15 minutes. The third group was orally administered bilberry extract (160 mg twice per day) for two weeks before exposure to the UV-B, while the fourth group was administered the same dose of bilberry extract for two weeks before euthanisation. A comet assay was used to examine DNA damage, while the malondialdehyde (MDA) level and superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and catalase (CAT), activities were measured in the lens. Results: After exposing the rats to UV-B radiation, the mean percentage tail DNA and tail moment were significantly increased (P < 0.001) when compared to the control group. In the same context, the lens tissue MDA levels and CAT activity were also significantly increased (P < 0.001). The supplementation of the bilberry extract was found to improve the comet assay parameters and enzymatic activity of the rat lens tissue. Conclusion: The administration of bilberry led to a decrease in the oxidative stress in the lens tissues and DNA damage induced by UV-B radiation in the lenses of Wistar rats. PMID:24639607

  4. Minimizing adsorption of histidine-tagged proteins for the study of protein-deoxyribonucleic acid interactions by kinetic capillary electrophoresis.

    PubMed

    Liyanage, Ruchi; Krylova, Svetlana M; Krylov, Sergey N

    2013-12-27

    Affinity interactions between DNA and proteins play a crucial role in many cellular processes. Kinetic Capillary Electrophoresis is a highly efficient tool for kinetic and equilibrium studies of protein-DNA interactions. Recombinant proteins, which are typically used for in vitro studies of protein-DNA interactions, are often expressed with a His tag to aid in their purification. In this work, we study how His tags affect Kinetic Capillary Electrophoresis analysis of protein-DNA interactions. We found that the addition of a His tag can increase or decrease protein adsorption to a bare-silica capillary wall, dependent on the protein. For Kinetic Capillary Electrophoresis measurements, it is essential to have as little protein adsorption as possible. We screened a number of capillary coatings to reduce adsorption of the His-tagged DNA mismatch repair protein MutS to the capillary wall and found that UltraTrol LN was the most effective coating. The effectiveness of the coating was confirmed with the prevention of adsorption of His-tagged fat mass and obesity-associated protein. Under typical conditions, the coating reduced protein adsorption to a level at which accurate Kinetic Capillary Electrophoresis analysis of protein-DNA interactions was possible. We further used Kinetic Capillary Electrophoresis to study how the His tag affected Kd of protein-DNA interactions for the MutS protein. Using UltraTrol LN, we found that the effect of the His tag was insignificant.

  5. Amino acid substitution at peptide-binding pockets of HLA class I molecules increases risk of severe acute GVHD and mortality

    PubMed Central

    Wang, Tao; Haagenson, Michael; Spellman, Stephen R.; Askar, Medhat; Battiwalla, Minoo; Baxter-Lowe, Lee Ann; Bitan, Menachem; Fernandez-Viña, Marcelo; Gandhi, Manish; Jakubowski, Ann A.; Maiers, Martin; Marino, Susana R.; Marsh, Steven G. E.; Oudshoorn, Machteld; Palmer, Jeanne; Prasad, Vinod K.; Reddy, Vijay; Ringden, Olle; Saber, Wael; Santarone, Stella; Schultz, Kirk R.; Setterholm, Michelle; Trachtenberg, Elizabeth; Turner, E. Victoria; Woolfrey, Ann E.; Lee, Stephanie J.; Anasetti, Claudio

    2013-01-01

    HLA disparity has a negative impact on the outcomes of hematopoietic cell transplantation (HCT). We studied the independent impact of amino acid substitution (AAS) at peptide-binding positions 9, 99, 116, and 156, and killer immunoglobulin-like receptor binding position 77 of HLA-A, B, or C, on the risks for grade 3-4 acute graft-versus-host disease (GVHD), chronic GVHD, treatment-related mortality (TRM), relapse, and overall survival. In multivariate analysis, a mismatch at HLA-C position 116 was associated with increased risk for severe acute GVHD (hazard ratio [HR] = 1.45, 95% confidence interval [CI] = 1.15-1.82, P = .0016). Mismatch at HLA-C position 99 was associated with increased transplant-related mortality (HR = 1.37, 95% CI = 1.1-1.69, P = .0038). Mismatch at HLA-B position 9 was associated with increased chronic GVHD (HR = 2.28, 95% CI = 1.36-3.82, P = .0018). No AAS were significantly associated with outcome at HLA-A. Specific AAS pair combinations with a frequency >30 were tested for association with HCT outcomes. Cysteine to tyrosine substitution at position 99 of HLA-C was associated with increased TRM (HR = 1.78, 95% = CI 1.27-2.51, P = .0009). These results demonstrate that donor-recipient mismatch for certain peptide-binding residues of the HLA class I molecule is associated with increased risk for acute and chronic GVHD and death. PMID:23982174

  6. Polysialic acid enters the cell nucleus attached to a fragment of the neural cell adhesion molecule NCAM to regulate the circadian rhythm in mouse brain.

    PubMed

    Westphal, Nina; Kleene, Ralf; Lutz, David; Theis, Thomas; Schachner, Melitta

    2016-07-01

    In the mammalian nervous system, the neural cell adhesion molecule NCAM is the major carrier of the glycan polymer polysialic acid (PSA) which confers important functions to NCAM's protein backbone. PSA attached to NCAM contributes not only to cell migration, neuritogenesis, synaptic plasticity, and behavior, but also to regulation of the circadian rhythm by yet unknown molecular mechanisms. Here, we show that a PSA-carrying transmembrane NCAM fragment enters the nucleus after stimulation of cultured neurons with surrogate NCAM ligands, a phenomenon that depends on the circadian rhythm. Enhanced nuclear import of the PSA-carrying NCAM fragment is associated with altered expression of clock-related genes, as shown by analysis of cultured neuronal cells deprived of PSA by specific enzymatic removal. In vivo, levels of nuclear PSA in different mouse brain regions depend on the circadian rhythm and clock-related gene expression in suprachiasmatic nucleus and cerebellum is affected by the presence of PSA-carrying NCAM in the cell nucleus. Our conceptually novel observations reveal that PSA attached to a transmembrane proteolytic NCAM fragment containing part of the extracellular domain enters the cell nucleus, where PSA-carrying NCAM contributes to the regulation of clock-related gene expression and of the circadian rhythm.

  7. Mobius Molecules

    ERIC Educational Resources Information Center

    Eckert, J. M.

    1973-01-01

    Discusses formation of chemical molecules via Mobius strip intermediates, and concludes that many special physics-chemical properties of the fully closed circular form (1) of polyoma DNA are explainable by this topological feature. (CC)

  8. Interstellar Molecules

    ERIC Educational Resources Information Center

    Solomon, Philip M.

    1973-01-01

    Radioastronomy reveals that clouds between the stars, once believed to consist of simple atoms, contain molecules as complex as seven atoms and may be the most massive objects in our Galaxy. (Author/DF)

  9. Interstellar molecules

    NASA Astrophysics Data System (ADS)

    Smith, D.

    1987-09-01

    Some 70 different molecular species have so far been detected variously in diffuse interstellar clouds, dense interstellar clouds, and circumstellar shells. Only simple (diatomic and triatomic) species exist in diffuse clouds because of the penetration of destructive UV radiations, whereas more complex (polyatomic) molecules survive in dense clouds as a result of the shielding against this UV radiation provided by dust grains. A current list of interstellar molecules is given together with a few other molecular species that have so far been detected only in circumstellar shells. Also listed are those interstellar species that contain rare isotopes of several elements. The gas phase ion chemistry is outlined via which the observed molecules are synthesized, and the process by which enrichment of the rare isotopes occurs in some interstellar molecules is described.

  10. Modeling Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.

  11. Enumerating molecules.

    SciTech Connect

    Visco, Donald Patrick, Jr.; Faulon, Jean-Loup Michel; Roe, Diana C.

    2004-04-01

    This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.

  12. Ice photochemistry as a source of amino acids and other organic molecules in meteorites, and implications for the origin of life and the search for life in the Solar System

    NASA Technical Reports Server (NTRS)

    Bernstein, Max

    2005-01-01

    The tons of extraterrestrial organic material that come to the Earth every day probably helped to made the Earth habitable, and possibly played a role in the origin of life. At the astrochemistry lab (http://www.astrochem.orq) we investigate the formation and distribution of organic molecules in space and consider the impact such molecules may have on the habitability of planets and the search for life in the Solar System. The organic compounds in meteorites include amino acids, aromatics of various sorts including purine and pyrimidine bases, and fatty acids that form bi-layer vesicles. The origin of many of these species remains mysterious, but in recent years we and others have performed experiments that suggest low temperature radiation chemistry could account for the presence and deuterium enrichment of many of these molecules. . I will present our laboratory experiments that show the viability of low temperature radiation chemistry as a source of organic molecules such as;amino acids (Nature, 2002, 416, 401-403), amphiphiles (Astrobiology, 2003, 2, 371, Proc. Nat. Acad. Sci. 2001, 98, 815), quinones (Science, 1999, 283, 1135) and other functionalized aromatic compounds (Meteoritics, 2001, 36, 351 ; Astrophysical Journal., 2003, 582, L25), some of which were invoked as potential biomarkers in the Alan Hills 84001 Martian meteorite. Understanding how components of proteins and DNA could form in sterile space environments is also of relevance to our search for life elsewhere in the Solar System, the great task now ahead of NASA. If we find evidence of Life elsewhere in the Solar System it will probably be in form of chemical biomarkers, quintessentially biological molecules that indicate the presence of micro-organisms. While most people think of molecules such as amino acids, and nucleo-bases as good candidate biomarkers, these molecules are produced non-biotically in space and are expected to be present on the surface of other planets even in the absence of

  13. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study.

    PubMed

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2015-09-01

    The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  14. Depletion of Polysialic Acid from Neural Cell Adhesion Molecule (PSA-NCAM) Increases CA3 Dendritic Arborization and Increases Vulnerability to Excitotoxicity

    PubMed Central

    McCall, Trudy; Weil, Zachary M.; Nacher, Juan; Bloss, Erik B.; El Marouf, Abderrahman; Rutishauser, Urs; McEwen, Bruce S.

    2012-01-01

    Chronic immobilization stress (CIS) shortens apical dendritic trees of CA3 pyramidal neurons in the hippocampus of the male rat, and dendritic length may be a determinant of vulnerability to stress. Expression of the polysialylated form of neural cell adhesion molecule (PSA-NCAM) in the hippocampal formation is increased by stress, while PSA removal by Endoneuraminidase-N (endo-N) is known to cause the mossy fibers to defasciculate and synapse ectopically in their CA3 target area. We show here that enzymatic removal of PSA produced a remarkable expansion of dendritic arbors of CA3 pyramidal neurons, with a lesser effect in CA1. This expansion eclipsed the CIS-induced shortening of CA3 dendrites, with the expanded dendrites of both no-stress-endo-N and CIS-endo-N rats being longer than those in no-stress-control rats and much longer than those in CIS-control rats. As predicted by the hypothesis that ENDO-N-induced dendritic expansion might increase vulnerability to excitotoxic challenge, systemic injection with kainic acid, showed markedly increased neuronal degeneration, as assessed by fluorojade B histochemistry, in rats that had been treated with ENDO-N compared to vehicle treated rats throughout the entire hippocampal formation. PSA removal also exacerbated the CIS-induced reduction in body weight and abolished effects of CIS on NPY and NR2B mRNA levels. These findings support the hypothesis that CA3 arbor plasticity plays a protective role during prolonged stress and clarify the role of PSA-NCAM in stress-induced dendritic plasticity. PMID:23219884

  15. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study.

    PubMed

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2015-09-01

    The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  16. Electrocatalytic oxidation of small organic molecules in acid medium: enhancement of activity of noble metal nanoparticles and their alloys by supporting or modifying them with metal oxides

    PubMed Central

    Kulesza, Pawel J.; Pieta, Izabela S.; Rutkowska, Iwona A.; Wadas, Anna; Marks, Diana; Klak, Karolina; Stobinski, Leszek; Cox, James A.

    2013-01-01

    Different approaches to enhancement of electrocatalytic activity of noble metal nanoparticles during oxidation of small organic molecules (namely potential fuels for low-temperature fuel cells such as methanol, ethanol and formic acid) are described. A physical approach to the increase of activity of catalytic nanoparticles (e.g. platinum or palladium) involves nanostructuring to obtain highly dispersed systems of high surface area. Recently, the feasibility of enhancing activity of noble metal systems through the formation of bimetallic (e.g. PtRu, PtSn, and PdAu) or even more complex (e.g. PtRuW, PtRuSn) alloys has been demonstrated. In addition to possible changes in the electronic properties of alloys, specific interactions between metals as well as chemical reactivity of the added components have been postulated. We address and emphasize here the possibility of utilization of noble metal and alloyed nanoparticles supported on robust but reactive high surface area metal oxides (e.g. WO3, MoO3, TiO2, ZrO2, V2O5, and CeO2) in oxidative electrocatalysis. This paper concerns the way in which certain inorganic oxides and oxo species can act effectively as supports for noble metal nanoparticles or their alloys during electrocatalytic oxidation of hydrogen and representative organic fuels. Among important issues are possible changes in the morphology and dispersion, as well as specific interactions leading to the improved chemisorptive and catalytic properties in addition to the feasibility of long time operation of the discussed systems. PMID:24443590

  17. Electrocatalytic oxidation of small organic molecules in acid medium: enhancement of activity of noble metal nanoparticles and their alloys by supporting or modifying them with metal oxides.

    PubMed

    Kulesza, Pawel J; Pieta, Izabela S; Rutkowska, Iwona A; Wadas, Anna; Marks, Diana; Klak, Karolina; Stobinski, Leszek; Cox, James A

    2013-11-01

    Different approaches to enhancement of electrocatalytic activity of noble metal nanoparticles during oxidation of small organic molecules (namely potential fuels for low-temperature fuel cells such as methanol, ethanol and formic acid) are described. A physical approach to the increase of activity of catalytic nanoparticles (e.g. platinum or palladium) involves nanostructuring to obtain highly dispersed systems of high surface area. Recently, the feasibility of enhancing activity of noble metal systems through the formation of bimetallic (e.g. PtRu, PtSn, and PdAu) or even more complex (e.g. PtRuW, PtRuSn) alloys has been demonstrated. In addition to possible changes in the electronic properties of alloys, specific interactions between metals as well as chemical reactivity of the added components have been postulated. We address and emphasize here the possibility of utilization of noble metal and alloyed nanoparticles supported on robust but reactive high surface area metal oxides (e.g. WO3, MoO3, TiO2, ZrO2, V2O5, and CeO2) in oxidative electrocatalysis. This paper concerns the way in which certain inorganic oxides and oxo species can act effectively as supports for noble metal nanoparticles or their alloys during electrocatalytic oxidation of hydrogen and representative organic fuels. Among important issues are possible changes in the morphology and dispersion, as well as specific interactions leading to the improved chemisorptive and catalytic properties in addition to the feasibility of long time operation of the discussed systems.

  18. 'Escentric' molecules.

    PubMed

    Schön, Geza

    2008-06-01

    Can a fragrance be revolutionary? In this commentary, the creation of two unusual, extravagant fine fragrances, 'escentric01' and 'molecule01', is described. In response to the fantasy components found in release notes of many recent perfume launches, both center around a single real fragrance raw material, the transparent woody aroma chemical 'Iso E Super' (1+2). The perfume 'escentric01' contains 65% of it, accompanied by Trisamber (3), red pepper, lime oil, incense and musks, while 'molecule01' consists exclusively of 'Iso E Super' (1+2). The elegant woody note lives here its own eccentric life--the revolution starts.

  19. Infrared linear dichroism investigations of deoxyribonucleic complexes with histones H2B and H3.

    PubMed

    Liquier, J; Taboury, J; Taillandier, E; Brahms, J

    1977-07-12

    Complexes between DNA and histones H2B and H3 were studies by means of infrared linear dichroism in a wide range of histone to DNA ratios and of different relative humidities. The measurement of the dichroic ratios allows one to determine the secondary structure of DNA in the complexes. It is shown that the progressive addition of histone H2B or H3 to DNA inhibits the structural B leads to A transition and DNA remains in a B-type form at low relative humidity. A new simple method is proposed to evaluate the amount of A or B forms of DNA when both structures are present. It is found that the B leads to A transition is fully inhibited when only one molecule of H2B or H3 histone is bound per about three or four turns of DNA helix, respectively. It is proposed that about four to three turns of DNA helix represent the "critical length of DNA" (minimum "cooperative unit") for the B leads to A transition.

  20. 77 FR 68133 - Guidance for Industry: Use of Nucleic Acid Tests on Pooled and Individual Samples From Donors of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-15

    ... November 28, 2011 (76 FR 72950), FDA announced the availability of the draft guidance of the same title...) deoxyribonucleic acid (DNA) and recommendations for product testing and disposition, donor management, methods for... screen blood donors for HBV DNA. FDA is also providing these blood establishments with...

  1. Antibacterial Nitroacridine, Nitroakridin 3582: Binding to Nucleic Acids In Vitro and Effects on Selected Cell-Free Model Systems of Macromolecular Biosynthesis

    PubMed Central

    Wolfe, Alan D.; Cook, Thomas M.; Hahn, Fred E.

    1971-01-01

    Nitroakridin 3582 (NA) formed complexes with native deoxyribonucleic acid (DNA) and with transfer ribonucleic acid (tRNA) species from Escherichia coli. Spectrophotometric titrations of NA with these nucleic acids produced numerical results from which nonlinear adsorption isotherms were derived. These curves indicated the existence of more than one class of binding sites on the polymers to which NA was bound by more than one process. The stoichiometry of strong binding of NA to double helical DNA was in agreement with a conventional value (1 ligand molecule per 4.2 component nucleotides) for complete intercalation binding. NA inhibited the DNA-dependent DNA polymerase I and RNA polymerase reactions, the first strongly and the second appreciably. These inhibitions corresponded to the extents to which NA inhibits DNA and RNA biosyntheses in vivo. Evidently, NA interferes with the template function of DNA. The drug also inhibited the polymerization of phenylalanine in a cell-free E. coli ribosome-polyuridylic acid [poly (U)] system. The effect paralleled an inhibition of the poly (U)-directed binding of phenylalanyl tRNA to ribosomes. Ethidium bromide acted similarly. The antimalarial drug, chloroquine, stimulated polyphenylalanine synthesis, apparently as a result of stimulating the poly (U)-directed binding of phenylalanyl tRNA to ribosomes. PMID:4945180

  2. Influence of dietary supplementation with long-chain n-3 or n-6 polyunsaturated fatty acids on blood inflammatory cell populations and functions and on plasma soluble adhesion molecules in healthy adults.

    PubMed

    Thies, F; Miles, E A; Nebe-von-Caron, G; Powell, J R; Hurst, T L; Newsholme, E A; Calder, P C

    2001-11-01

    Greatly increasing the amounts of flaxseed oil [rich in alpha-linolenic acid (ALNA)] or fish oil (FO); [rich in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)] in the diet can decrease inflammatory cell functions and so might impair host defense. The objective of this study was to determine the effect of dietary supplementation with moderate levels of ALNA, gamma-linolenic acid (GLA), arachidonic acid (ARA), DHA, or FO on inflammatory cell numbers and functions and on circulating levels of soluble adhesion molecules. Healthy subjects aged 55 to 75 yr consumed nine capsules per day for 12 wk. The capsules contained placebo oil (an 80:20 mix of palm and sunflowerseed oils) or blends of placebo oil with oils rich in ALNA, GLA, ARA, or DHA or FO. Subjects in these groups consumed 2 g ALNA; approximately 700 mg GLA, ARA, or DHA; or 1 g EPA plus DHA (720 mg EPA + 280 mg DHA) daily from the capsules. Total fat intake from the capsules was 4 g per day. None of the treatments affected inflammatory cell numbers in the bloodstream; neutrophil and monocyte phagocytosis or respiratory burst in response to E. coli; production of tumor necrosis factor-alpha, interleukin-1beta, and interleukin-6 in response to bacterial lipopolysaccharide; or plasma concentrations of soluble intercellular adhesion molecule-1. In contrast, the ALNA and FO treatments decreased the plasma concentrations of soluble vascular cell adhesion molecule-1 (16 and 28% decrease, respectively) and soluble E-selectin (23 and 17% decrease, respectively). It is concluded that, in contrast to previous reports using higher amounts of these fatty acids, a moderate increase in consumption of long-chain n-6 or n-3 polyunsaturated fatty acids does not significantly affect inflammatory cell numbers or neutrophil and monocyte responses in humans and so would not be expected to cause immune impairment. Furthermore, we conclude that moderate levels of ALNA and FO, which could be incorporated into the diet, can

  3. Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond

    PubMed Central

    Staniforth, Michael; Stavros, Vasilios G.

    2013-01-01

    In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach. PMID:24204191

  4. Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond.

    PubMed

    Staniforth, Michael; Stavros, Vasilios G

    2013-11-01

    In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach.

  5. Walking molecules.

    PubMed

    von Delius, Max; Leigh, David A

    2011-07-01

    Movement is intrinsic to life. Biologists have established that most forms of directed nanoscopic, microscopic and, ultimately, macroscopic movements are powered by molecular motors from the dynein, myosin and kinesin superfamilies. These motor proteins literally walk, step by step, along polymeric filaments, carrying out essential tasks such as organelle transport. In the last few years biological molecular walkers have inspired the development of artificial systems that mimic aspects of their dynamics. Several DNA-based molecular walkers have been synthesised and shown to walk directionally along a track upon sequential addition of appropriate chemical fuels. In other studies, autonomous operation--i.e. DNA-walker migration that continues as long as a complex DNA fuel is present--has been demonstrated and sophisticated tasks performed, such as moving gold nanoparticles from place-to-place and assistance in sequential chemical synthesis. Small-molecule systems, an order of magnitude smaller in each dimension and 1000× smaller in molecular weight than biological motor proteins or the walker systems constructed from DNA, have also been designed and operated such that molecular fragments can be progressively transported directionally along short molecular tracks. The small-molecule systems can be powered by light or chemical fuels. In this critical review the biological motor proteins from the kinesin, myosin and dynein families are analysed as systems from which the designers of synthetic systems can learn, ratchet concepts for transporting Brownian substrates are discussed as the mechanisms by which molecular motors need to operate, and the progress made with synthetic DNA and small-molecule walker systems reviewed (142 references). PMID:21416072

  6. An effective nanosensor for organic molecules based on water-soluble mercaptopropionic acid-capped CdTe nanocrystals with potential application in high-throughput screening and high-resolution optical microscopy.

    PubMed

    Lau, Pick-Chung; Norwood, Robert A; Mansuripur, Masud; Peyghambarian, Nasser

    2014-07-01

    Specially-treated glass substrates coated with a thin film of water soluble mercaptopropionic acid (MPA) capped CdTe nanocrystals (NCs) were prepared and found to undergo photoluminescence changes by as much as 40% when micro-droplets of organic molecules were placed in the nanometer-range proximity of the NCs. This imaging technique involving close proximity between a nano-crystal and an organic molecule is found to provide a 2 × -3 × enhanced contrast ratio over the conventional method of fluorescence imaging. Photoluminescence of NCs is recoverable upon removal of the organic molecules, therefore validating these NCs as potential all-optical organic molecular nanosensors. Upon optimization and with proper instrumentation, these nano-crystals could eventually serve as point-detectors for purposes of super-resolution optical microscopy. No solvents are required for the proposed sensing mechanism since all solutions were dried under argon flow. Fluorophores and fluorescent proteins were investigated, including fluorescein, Rhodamine 6G, and green fluorescent protein (GFP). Furthermore, NC photoluminescence changes were systematically quantified as a function of the solution pH and of the organic molecule concentration. Long duration (> 40 minutes) continuous excitation studies were conducted in order to evaluate the reliability of the proposed sensing scheme.

  7. An effective nanosensor for organic molecules based on water-soluble mercaptopropionic acid-capped CdTe nanocrystals with potential application in high-throughput screening and high-resolution optical microscopy

    PubMed Central

    Lau, Pick-Chung; Norwood, Robert A.; Mansuripur, Masud; Peyghambarian, Nasser

    2014-01-01

    Specially-treated glass substrates coated with a thin film of water soluble mercaptopropionic acid (MPA) capped CdTe nanocrystals (NCs) were prepared and found to undergo photoluminescence changes by as much as 40% when micro-droplets of organic molecules were placed in the nanometer-range proximity of the NCs. This imaging technique involving close proximity between a nano-crystal and an organic molecule is found to provide a 2 × –3 × enhanced contrast ratio over the conventional method of fluorescence imaging. Photoluminescence of NCs is recoverable upon removal of the organic molecules, therefore validating these NCs as potential all-optical organic molecular nanosensors. Upon optimization and with proper instrumentation, these nano-crystals could eventually serve as point-detectors for purposes of super-resolution optical microscopy. No solvents are required for the proposed sensing mechanism since all solutions were dried under argon flow. Fluorophores and fluorescent proteins were investigated, including fluorescein, Rhodamine 6G, and green fluorescent protein (GFP). Furthermore, NC photoluminescence changes were systematically quantified as a function of the solution pH and of the organic molecule concentration. Long duration (> 40 minutes) continuous excitation studies were conducted in order to evaluate the reliability of the proposed sensing scheme. PMID:25071975

  8. Tumor suppressor molecules and methods of use

    DOEpatents

    Welch, Peter J.; Barber, Jack R.

    2004-09-07

    The invention provides substantially pure tumor suppressor nucleic acid molecules and tumor suppressor polypeptides. The invention also provides hairpin ribozymes and antibodies selective for these tumor suppressor molecules. Also provided are methods of detecting a neoplastic cell in a sample using detectable agents specific for the tumor suppressor nucleic acids and polypeptides.

  9. Essential fatty acids and their metabolites could function as endogenous HMG-CoA reductase and ACE enzyme inhibitors, anti-arrhythmic, anti-hypertensive, anti-atherosclerotic, anti-inflammatory, cytoprotective, and cardioprotective molecules.

    PubMed

    Das, Undurti N

    2008-01-01

    Lowering plasma low density lipoprotein-cholesterol (LDL-C), blood pressure, homocysteine, and preventing platelet aggregation using a combination of a statin, three blood pressure lowering drugs such as a thiazide, a beta blocker, and an angiotensin converting enzyme (ACE) inhibitor each at half standard dose; folic acid; and aspirin-called as polypill- was estimated to reduce cardiovascular events by approximately 80%. Essential fatty acids (EFAs) and their long-chain metabolites: gamma-linolenic acid (GLA), dihomo-GLA (DGLA), arachidonic acid, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) and other products such as prostaglandins E1 (PGE1), prostacyclin (PGI2), PGI3, lipoxins (LXs), resolvins, protectins including neuroprotectin D1 (NPD1) prevent platelet aggregation, lower blood pressure, have anti-arrhythmic action, reduce LDL-C, ameliorate the adverse actions of homocysteine, show anti-inflammatory actions, activate telomerase, and have cytoprotective properties. Thus, EFAs and their metabolites show all the classic actions expected of the "polypill". Unlike the proposed "polypill", EFAs are endogenous molecules present in almost all tissues, have no significant or few side effects, can be taken orally for long periods of time even by pregnant women, lactating mothers, and infants, children, and adults; and have been known to reduce the incidence cardiovascular diseases including stroke. In addition, various EFAs and their long-chain metabolites not only enhance nitric oxide generation but also react with nitric oxide to yield their respective nitroalkene derivatives that produce vascular relaxation, inhibit neutrophil degranulation and superoxide formation, inhibit platelet activation, and possess PPAR-gamma ligand activity and release NO, thus prevent platelet aggregation, thrombus formation, atherosclerosis, and cardiovascular diseases. Based on these evidences, I propose that a rational combination of omega-3 and omega-6 fatty acids and the

  10. Modulation of Pb-induced stress in Prosopis shoots through an interconnected network of signaling molecules, phenolic compounds and amino acids.

    PubMed

    Zafari, Somaieh; Sharifi, Mohsen; Ahmadian Chashmi, Najmeh; Mur, Luis A J

    2016-02-01

    Lead (Pb) is a hazardous heavy metal present in the environment which elicits oxidative stress in plants. To characterize the physiological and biochemical basis of Pb tolerance, Prosopis farcta seedlings were exposed to Hoagland's solutions at six different Pb concentrations (0, 80, 160, 320, 400 and 480 μM) for different periods of time. As expected, application of Pb significantly increased hydrogen peroxide (H2O2) content. In response, P. farcta deployed the antioxidative defence mechanisms with significantly higher activities of superoxide dismutase (SOD), enzymes related to H2O2 removal, and also the increases in proline as a solute marker of stress. Increases were observed in nitric oxide (NO) production which could also act in triggering defense functions to detoxify Pb. Enhanced phenylalanine ammonia-lyase (PAL) activity at early days of exposure to Pb was correlated with increases in phenolic compounds. Significant increases in phenolic acids and flavonoids; daidzein, vitexin, ferulic acid and salicylic acid were observed with Pb treatment. Furthermore, the stress effects were followed by changes in free amino acid content and composition. Aspartic acid and glycine content was increased but glutamic acid significantly decreased. It is likely that stress signal transduction by NO and H2O2 mediated defence responses to Pb by coordination of antioxidative system and metabolic pathways of phenylpropanoid and amino acids.

  11. Transcription of fractionated mammalian chromatin by mammalian ribonucleic acid polymerase. Demonstration of temperature-dependent rifampicin-resistant initiation sites in euchromatin deoxyribonucleic acid

    PubMed Central

    Chesterton, C. James; Coupar, Barbara E. H.; Butterworth, Peter H. W.

    1974-01-01

    The chromatin fractionation method of Frenster et al. (1963) as modified by Leake et al. (1972) was used to prepare fragments of euchromatin from rat liver nuclei. These remain soluble in 5mm-MgCl2, and contain DNA of maximum mol.wt. 1×106–2×106. The fragments were separated from condensable chromatin on a sucrose gradient. Euchromatin contains endogenous DNA-dependent RNA polymerase, and most of the nascent RNA labelled in vivo or in vitro. Euchromatin fragments allow initiation of transcription by added purified rat liver form-B RNA polymerase and contain temperature-dependent rifampicin-resistant initiation sites for the form-B enzyme. These findings indicate that transcription of the euchromatin regions of interphase chromosomes is not initiated in condensed chromatin, but is initiated within the euchromatin stretches. Condensable chromatin also contains most of these activities, but is not associated with nascent RNA. PMID:4464858

  12. Inhibition of hepatic deoxyribonucleic acid-dependent ribonucleic acid polymerases by the exotoxin of Bacillus thuringiensis in comparison with the effects of α-amanitin and cordycepin

    PubMed Central

    Smuckler, Edward A.; Hadjiolov, Asen A.

    1972-01-01

    The action of Bacillus thuringiensis exotoxin, a structural analogue of ATP, on mouse liver DNA-dependent RNA polymerases was studied and its effects were compared with those of α-amanitin and cordycepin. (1) Administration of exotoxin in vivo caused a marked decrease in RNA polymerase activity of isolated nuclei at various concentrations of Mg2+, Mn2+ and (NH4)2SO4. A similar action was recorded after addition of exotoxin to isolated nuclei from control or exotoxin-treated mice. (2) Chromatographic separation of nuclear RNA polymerases from mice treated in vivo with exotoxin showed a drastic decrease of the peak of nucleoplasmic RNA polymerase, whereas the peak of nucleolar RNA polymerase remained unaltered. The same effect was observed after administration of α-amanitin in vivo, but cordycepin did not alter the relative amounts of the two main RNA polymerase peaks. (3) Administration of exotoxin in vivo did not alter the template activity of isolated DNA or chromatin tested with different fractions of RNA polymerase from control or exotoxin-treated mice. (4) Addition of exotoxin to isolated liver RNA polymerases inhibited both enzyme fractions. However, the α-amanitin-sensitive RNA polymerase was also 50–100-fold more sensitive to exotoxin inhibition than was the α-amanitin-insensitive RNA polymerase. Kinetic analysis indicated the exotoxin produces a competitive inhibition with ATP on the nucleolar enzyme, but a mixed type of inhibition with nucleoplasmic enzyme. The results obtained indicate that the B. thuringiensis exotoxin inhibits liver RNA synthesis by affecting nuclear RNA polymerases, showing a preferential inhibition of the nucleoplasmic α-amanitin-sensitive RNA polymerase. ImagesFig. 7. PMID:4539593

  13. Effect of an exotoxin from Bacillus thuringiensis on deoxyribonucleic acid-dependent ribonucleic acid polymerase in nuclei from adult Sarcophaga bullata. Unusual behaviour of eukaryotic polymerases to inhibitors.

    PubMed

    Beebee, T J; Bond, R P

    1973-09-01

    The DNA-dependent RNA polymerase activities in nuclei isolated from adult Sarcophaga bullata are unusual in their responses to metal ions, ionic strength and inhibitors. There is an activity that is sensitive both to rifamycin and to alpha-amanitin. The activity is less sensitive to Bacillus thuringiensis exotoxin than is larval polymerase, and low concentration of exotoxin provoke a slight stimulation.

  14. Effect of in ovo feeding of folic acid on the folate metabolism, immune function and epigenetic modification of immune effector molecules of broiler.

    PubMed

    Li, Shizhao; Zhi, Lihui; Liu, Yanli; Shen, Jing; Liu, Lei; Yao, Junhu; Yang, Xiaojun

    2016-02-14

    This study was conducted to investigate the effect of in ovo feeding (IOF) of folic acid on the folate metabolism, immune function and the involved epigenetic modification of broilers. A total of 400 (Cobb) hatching eggs were randomly divided into four groups (0, 50, 100 and 150 µg injection of folic acid at embryonic age 11 d), and chicks hatched from each treatment were randomly divided into six replicates with 12 broilers/replicate after incubation. The results indicated that, in ovo, 100- and 150-µg folic acid injections improved the hatchability. The average daily gain and feed conversion ratio increased in the 150-µg group during the late growth stage. Simultaneously, in the 100- and 150-µg groups, an increase was observed in hepatic folate content and the expression of methylenetetrahydrofolate reductase (d1 and 42) and methionine synthase reductase (d21). IgG and IgM concentrations, as well as plasma lysozyme activity of broilers, showed a marked increase along with increasing folic acid levels. The splenic expression levels of IL-2 and IL-4 were up-regulated, whereas that of IL-6 was down-regulated, in the 100- and 150-µg folic acid treatment groups. In addition, histone methylation in IL-2 and IL-4 promoters exhibited an enrichment of H3K4m2 but a loss of H3K9me2 with the increased amount of folic acid additive. In contrast, a decrease in H3K4m2 and an increase in H3K9me2 were observed in the IL-6 promoter in folic acid treatments. Furthermore, in ovo, the 150-µg folic acid injection improved the chromatin tightness of the IL-2 and IL-4 promoter regions. Our findings suggest that IOF of 150 µg of folic acid can improve the growth performance and folate metabolism of broilers, and enhance the relationship between immune function and epigenetic regulation of immune genes, which are involved with the alterations in chromatin conformation and histone methylation in their promoters.

  15. Effect of in ovo feeding of folic acid on the folate metabolism, immune function and epigenetic modification of immune effector molecules of broiler.

    PubMed

    Li, Shizhao; Zhi, Lihui; Liu, Yanli; Shen, Jing; Liu, Lei; Yao, Junhu; Yang, Xiaojun

    2016-02-14

    This study was conducted to investigate the effect of in ovo feeding (IOF) of folic acid on the folate metabolism, immune function and the involved epigenetic modification of broilers. A total of 400 (Cobb) hatching eggs were randomly divided into four groups (0, 50, 100 and 150 µg injection of folic acid at embryonic age 11 d), and chicks hatched from each treatment were randomly divided into six replicates with 12 broilers/replicate after incubation. The results indicated that, in ovo, 100- and 150-µg folic acid injections improved the hatchability. The average daily gain and feed conversion ratio increased in the 150-µg group during the late growth stage. Simultaneously, in the 100- and 150-µg groups, an increase was observed in hepatic folate content and the expression of methylenetetrahydrofolate reductase (d1 and 42) and methionine synthase reductase (d21). IgG and IgM concentrations, as well as plasma lysozyme activity of broilers, showed a marked increase along with increasing folic acid levels. The splenic expression levels of IL-2 and IL-4 were up-regulated, whereas that of IL-6 was down-regulated, in the 100- and 150-µg folic acid treatment groups. In addition, histone methylation in IL-2 and IL-4 promoters exhibited an enrichment of H3K4m2 but a loss of H3K9me2 with the increased amount of folic acid additive. In contrast, a decrease in H3K4m2 and an increase in H3K9me2 were observed in the IL-6 promoter in folic acid treatments. Furthermore, in ovo, the 150-µg folic acid injection improved the chromatin tightness of the IL-2 and IL-4 promoter regions. Our findings suggest that IOF of 150 µg of folic acid can improve the growth performance and folate metabolism of broilers, and enhance the relationship between immune function and epigenetic regulation of immune genes, which are involved with the alterations in chromatin conformation and histone methylation in their promoters. PMID:26586196

  16. A DFT study of the acid-base properties of anatase TiO2 and tetragonal ZrO2 by adsorption of CO and CO2 probe molecules

    NASA Astrophysics Data System (ADS)

    Chen, Hsin-Yi Tiffany; Tosoni, Sergio; Pacchioni, Gianfranco

    2016-10-01

    We have performed a comparative study of the acid-base characteristics of the surfaces of anatase TiO2 and tetragonal ZrO2. To this end we performed DFT + U calculations on CO and CO2 probe molecules adsorbed both on terraces and steps of the two oxides. For titania, CO adsorption results in a moderate adsorption energy (about - 0.3 eV) and in a positive shift of the Csbnd O stretching frequency (about + 40 cm- 1), typical of Lewis acid sites, with no clear difference in the acidity between terraces or steps. For zirconia we found a similar CO binding energy as for titania, and a CO vibrational shift that depends on the location of the Zr cation: negligible on terraces, similar to TiO2 on steps. We conclude that the acidic properties are similar in the two oxide surfaces. Things are different for CO2 adsorption. On titania the interaction is weak and surface carbonates compete with physisorbed CO2, indicating a weak basic character. On the contrary, on zirconia three types of stable carbonates have been identified. Their vibrational frequencies are consistent with IR measurements reported in the literature. The most stable species forms on steps of the t-ZrO2 surface and consists of a CO32 - unit which lies flat on the surface with the O atoms pointing towards three Zr ions. The species forms spontaneously by extraction of a lattice oxygen by an incoming CO2 molecule. The different reactivity points towards a much more pronounced basic character of zirconia compared to titania, at least if measured by CO2 adsorption.

  17. Hydrothermal crystal growth and Vernier structures of the metal benzenedicarboxylates MIL-47 and MIL-53 containing guest molecules of benzenecarboxylic acid

    NASA Astrophysics Data System (ADS)

    Wang, Xiqu; Jacobson, Allan J.

    2016-04-01

    The nanoporous frameworks VO(bdc), MIL-47, and M(OH)(bdc), MIL-53; bdc=1,4-benzenedicarboxylate, can absorb various guest species in their channels. As synthesized, the channels are filled with H2bdc molecules that have been reported to be disordered, except for [In(OH)bdc](H2bdc)3/4, 1, which has a inorganic-organic hybrid Vernier structure with the H2bdc molecules forming an ordered sublattice. Based on X-ray data from large single crystals grown by hydrothermal techniques, similar Vernier structures have been found for MIL-47, [VO(bdc)](H2bdc)5/7, 2, MIL-53Al, [Al(OH)(bdc)](H2bdc)11/16, 3, and MIL-53Ga, [Ga(OH)(bdc)](H2bdc)12/17, 4. The Vernier structures of 2-4 at room temperature were determined based on superstructure unit cells that index both host and guest sublattices: 2, space group P21, a=23.903(2), b=17.191(2), c=25.722(2) Å, β=105.914(8)°; 3, P21/n, a=105.224(4), b=12.2441(5), c=17.0143(6) Å, β=89.99(1)°; 4, P21, a=114.562(5), b=12.1503(5), c=17.4275(7) Å, β=89.99(1)°. The number of guest H2bdc molecules per framework metal ion is determined by the ratio of the repeat distances of the two sublattices which depends on the size of the metal ion in the octahedral chain. The octahedral chains are parallel to [201] in 2, and to [100] in 3 and 4. Remarkably, all atoms in 3 and 4 show significant sinusoidal modulations transverse to the chain axis.

  18. Searching for new NO-donor aspirin-like molecules: a new class of nitrooxy-acyl derivatives of salicylic acid.

    PubMed

    Lazzarato, Loretta; Donnola, Monica; Rolando, Barbara; Marini, Elisabetta; Cena, Clara; Coruzzi, Gabriella; Guaita, Elena; Morini, Giuseppina; Fruttero, Roberta; Gasco, Alberto; Biondi, Stefano; Ongini, Ennio

    2008-03-27

    A new class of products in which the phenol group of salicylic acid is linked to alkanoyl moieties bearing nitrooxy functions has been synthesized and studied for their polyvalent actions. The products were stable in acid and neutral media, while they were hydrolyzed in human serum. Their half-lives were dependent upon the structure of alkanoyl moieties. The products showed anti-inflammatory activities similar to aspirin when tested in the carrageenan-induced paw edema assay in the rat. Interestingly, unlike aspirin, they showed reduced or no gastrotoxicity in a lesion model in rats at equimolar doses. A number of them were able to inhibit platelet aggregation induced by collagen in human platelet-rich plasma. All of the products were capable of relaxing rat aortic strips precontracted with phenylephrine in a concentration-dependent manner. Selected members of this new class of nonsteroidal anti-inflammatory drugs might represent possible safer alternatives to aspirin in different clinical settings.

  19. Proteins Are the Body's Worker Molecules

    MedlinePlus

    ... Each "bead" is a small molecule called an amino acid. There are 20 standard amino acids, each with its own shape, size, and properties. Proteins typically contain from 50 to 2,000 amino acids hooked end-to-end in many combinations. Each ...

  20. Proposed formation mechanism and active species of hydrogen molecules generated from a novel magnesium-citric acid-hydroxypropyl cellulose coating (MgCC) material

    NASA Astrophysics Data System (ADS)

    Kobayashi, Shigeki; Chikuma, Toshiyuki; Chiba, Kazuyoshi; Tsuchiya, Daisuke; Hirai, Tomomitsu

    2016-02-01

    The presence of acids is known to accelerate the reaction (Mg + 2H2O = Mg(OH)2 + H2). We developed a novel Mg-citric acid coating (MgCC) material produced by milling Mg powder coated with hydroxypropyl cellulose (HPC); because of its H2 generation, this material could be used in antioxidant therapy and antiaging applications. After milling in the presence of citric acid, this material produced H2-rich water upon addition to cooled water. Although the reaction was considered to involve a two-electron transfer from Mg to 2H2O, the role of the acid in H2 generation remains incompletely understood. To clarify the reaction mechanism, we performed studies on the deuterium kinetic isotope effects (KIE) and electron spin resonance (ESR). We observed differences in the concentration ratios, such as H2/D2 > 1 and H2/(H2 + D2 + HD) > 1, involved in H2, D2, and (H2 + D2 + HD) production, and found that adducts with hydrogen atoms (Hrad) were not obtained from the spin-trapping reaction between 5-(2, 2-Dimethyl-1,3-propoxy cyclophosphoryl)-5-methyl-1-pyrroline N-oxide (CYPMPO) and the MgCC material. The H2, D2, and HD produced from MgCC were identified by using a gas chromatograph connected to a mass spectrometer. The spin-trapping techniques showed that the Hrad adducts formed by the reaction of NaBH4 with CYPMPO could not be observed from reaction of MGCC with CYPMPO in H2O. The data suggest that the rate-controlling step and proposed transition state (TS) exist in the reaction pathway of the O-H bond cleavage and H-H bond formation. A TS of a structure such as [Mg(OH2)2]∗ could be expected in the reaction pathway between Mg and 2H2O by density functional theory calculations. Also, these results show that H2 generation is accelerated in the presence of acids because the activation energy of the TS is significantly smaller than that of H2O.

  1. Proposed formation mechanism and active species of hydrogen molecules generated from a novel magnesium-citric acid-hydroxypropyl cellulose coating (MgCC) material

    NASA Astrophysics Data System (ADS)

    Kobayashi, Shigeki; Chikuma, Toshiyuki; Chiba, Kazuyoshi; Tsuchiya, Daisuke; Hirai, Tomomitsu

    2016-02-01

    The presence of acids is known to accelerate the reaction (Mg + 2H2O = Mg(OH)2 + H2). We developed a novel Mg-citric acid coating (MgCC) material produced by milling Mg powder coated with hydroxypropyl cellulose (HPC); because of its H2 generation, this material could be used in antioxidant therapy and antiaging applications. After milling in the presence of citric acid, this material produced H2-rich water upon addition to cooled water. Although the reaction was considered to involve a two-electron transfer from Mg to 2H2O, the role of the acid in H2 generation remains incompletely understood. To clarify the reaction mechanism, we performed studies on the deuterium kinetic isotope effects (KIE) and electron spin resonance (ESR). We observed differences in the concentration ratios, such as H2/D2 > 1 and H2/(H2 + D2 + HD) > 1, involved in H2, D2, and (H2 + D2 + HD) production, and found that adducts with hydrogen atoms (Hrad) were not obtained from the spin-trapping reaction between 5-(2, 2-Dimethyl-1,3-propoxy cyclophosphoryl)-5-methyl-1-pyrroline N-oxide (CYPMPO) and the MgCC material. The H2, D2, and HD produced from MgCC were identified by using a gas chromatograph connected to a mass spectrometer. The spin-trapping techniques showed that the Hrad adducts formed by the reaction of NaBH4 with CYPMPO could not be observed from reaction of MGCC with CYPMPO in H2O. The data suggest that the rate-controlling step and proposed transition state (TS) exist in the reaction pathway of the O-H bond cleavage and H-H bond formation. A TS of a structure such as [Mg(OH2)2]∗ could be expected in the reaction pathway between Mg and 2H2O by density functional theory calculations. Also, these results show that H2 generation is accelerated in the presence of acids because the activation energy of the TS is significantly smaller than that of H2O.

  2. Discovery of molecules for the treatment of neuropathic pain: synthesis, antiallodynic and antihyperalgesic activities of 5-(4-nitrophenyl)furoic-2-acid hydrazones.

    PubMed

    Yogeeswari, Perumal; Menon, Niloufer; Semwal, Arvind; Arjun, Muralidharan; Sriram, Dharmarajan

    2011-07-01

    Neuropathic pain is a chronic pain condition that occurs and persists in a heterogeneous group of etiologically different diseases characterized by a primary lesion or dysfunction of the peripheral or central nervous system. Current treatment options do not provide adequate relief for many patients and a significant number of the agents used have dose limiting side effects. During the course of our work on the synthesis and screening of new drugs for the treatment of neuropathic pain, we have identified 5-(4-nitrophenyl)furoic-2-acid hydrazones which showed significant antiallodynic and antihyperalgesic activities in a chronic constriction injury (CCI) model of neuropathic pain in rat. Synthesized compounds thus represent a promising lead for new drug development for the treatment of neuropathic pain. PMID:21536354

  3. New developments in hydrogen bonding acidity and basicity of small organic molecules for the prediction of physical and ADMET properties. Part 2. The universal solvation equation.

    PubMed

    Oliferenko, Polina V; Oliferenko, Alexander A; Poda, Gennadiy; Palyulin, Vladimir A; Zefirov, Nikolay S; Katritzky, Alan R

    2009-03-01

    Theoretical quantifications of hydrogen bonding (HB) basicities and acidities, originally developed for aliphatic systems (J. Chem. Inf. Comput. Sci. 2004, 44, 1042-1055), are now extended to cover aromatic, heterocyclic, anionic, cationic and zwitter-ionic molecular fragments, thus encompassing a majority of druggable chemical space. The addition of terms accounting for cavity formation, polarity, hydrophobicity, and resonance allowed us to derive a new equation able to predict accurately free energies of solvation of diverse solutes, interphase transfers, and aqueous solubilities (log S(w)). We thus provide a "universal solvation equation" (USE) available for the accurate estimation of desolvation energies in protein-ligand docking, for the prediction of many physical and ADMET properties, and for studying fluid phase equilibria.

  4. Probing radiation damage by alternated current conductivity as a method to characterize electron hopping conduction in DNA molecules

    NASA Astrophysics Data System (ADS)

    Gomes, Paulo J.; Coelho, Margarida; Dionísio, Madalena; António Ribeiro, Paulo; Raposo, Maria

    2012-09-01

    Analysis of AC electrical conductivity of deoxyribonucleic acid (DNA) thin films, irradiated with ultraviolet (UV) light, revealed that electrical conduction arises from DNA chain electron hopping between base-pairs and phosphate groups. The hopping distance calculated from correlated barrier hopping model equals the distance between DNA base-pairs, which is consistent with the loss of conductivity with irradiation time arising from a decrease in phosphates groups. In the high frequency regime, at a given frequency, real part of conductivity strongly depends on irradiation time particularly for low dose levels suggesting the use of DNA based films for UV radiation sensors.

  5. Probing radiation damage by alternated current conductivity as a method to characterize electron hopping conduction in DNA molecules

    SciTech Connect

    Gomes, Paulo J.; Coelho, Margarida; Antonio Ribeiro, Paulo; Raposo, Maria; Dionisio, Madalena

    2012-09-17

    Analysis of AC electrical conductivity of deoxyribonucleic acid (DNA) thin films, irradiated with ultraviolet (UV) light, revealed that electrical conduction arises from DNA chain electron hopping between base-pairs and phosphate groups. The hopping distance calculated from correlated barrier hopping model equals the distance between DNA base-pairs, which is consistent with the loss of conductivity with irradiation time arising from a decrease in phosphates groups. In the high frequency regime, at a given frequency, real part of conductivity strongly depends on irradiation time particularly for low dose levels suggesting the use of DNA based films for UV radiation sensors.

  6. Self-assembled structures of 4‧-([2,2‧:6‧,2″-terpyridine]-4‧-yl)-[1,1‧-phenyl]-4-carboxylic acid molecules induced by metal atoms on ag(111) surface

    NASA Astrophysics Data System (ADS)

    Ling, Jie; Lu, Yan; Liu, Lacheng; Liu, Xiaoqing; Wang, Li

    2016-07-01

    The self-assembled supramolecular structures of 4‧-([2,2‧:6‧,2″-terpyridine]-4‧-yl)-[1,1‧-phenyl]-4-carboxylic acid (Y) molecules on Ag(111) surface induced by metal elements have been studied by scanning tunneling microscopy. After annealing, the as-deposited monolayer of Y molecules shows four kinds of well-ordered structures due to the competition between dipole interaction, hydrogen bonding and Van der Waals interaction. Introduced Cu atoms drive ordered monolayer into a self-assembled supramolecular structure with bright spots. Deposited Ag atoms cause the monolayer change to a windmill shape self-assembled supramolecular structure. Though the Cu and Ag are in the same group of the periodic table, a Cu atom connects two COOH groups and an Ag atom trends to bind to three COOH groups during the formation of metal-organic bonding within both induced structures. Such result suggests that the self-assembled structures formed by metal-organic coordination bonding can be controlled by choosing the number of metal-organic coordination bonds, which can be helpful to design metal-organic molecular architectures comprising functional building blocks.

  7. Functional N-methyl-D-aspartate receptors in O-2A glial precursor cells: a critical role in regulating polysialic acid-neural cell adhesion molecule expression and cell migration

    PubMed Central

    1996-01-01

    The capacity for long-distance migration of the oligodendrocyte precursor cell, oligodendrocyte-type 2 astrocyte (O-2A), is essential for myelin formation. To study the molecular mechanisms that control this process, we used an in vitro migration assay that uses neurohypophysial explants. We provide evidence that O-2A cells in these preparations express functional N-methyl-D-aspartate (NMDA) receptors, most likely as homomeric complexes of the NR1 subunit. We show that NMDA evokes an increase in cytosolic Ca2+ that can be blocked by the NMDA receptor antagonist AP-5 and by Mg2+. Blocking the activity of these receptors dramatically diminished O-2A cell migration from explants. We also show that NMDA receptor activity is necessary for the expression by O-2A cells of the highly sialylated polysialic acid- neural cell adhesion molecule (PSA-NCAM) that is required for their migration. Thus, glutamate or glutamate receptor ligands may regulate O- 2A cell migration by modulating expression of PSA-NCAM. These studies demonstrate how interactions between ionotropic receptors, intracellular signaling, and cell adhesion molecule expression influence cell surface properties, which in turn are critical determinants of cell migration. PMID:8978823

  8. A mixture of amino acids and other small molecules present in the serum suppresses the growth of murine and human tumors in vivo.

    PubMed

    Kulcsár, Gyula; Gaál, Dezső; Kulcsár, Péter I; Schulcz, Ákos; Czömpöly, Tamás

    2013-03-01

    Previously we have hypothesized that the small molecules which are selectively accumulated in cancer cells might participate in a non-immunological antitumor surveillance mechanism. We demonstrated earlier that a mixture of experimentally selected substances ("active mixture", AM: L-arginine, L-histidine, L-methionine, L-phenylalanine, L-tyrosine, L-tryptophan, L-ascorbate, D-biotin, pyridoxine, riboflavin, adenine, L(-)malate) possesses a selective toxic effect in vitro on a variety of tumor cell lines, and we have shown that the AM selectively induces apoptosis of cancer cells in vitro. To explore the in vivo significance of our earlier findings we examined the antitumor effect of AM in Colon 26 murine colorectal adenocarcinoma, B16 murine melanoma, MXT murine mammary carcinoma, S180 murine sarcoma, P388 murine lymphoid leukemia, HL-60 human promyeloid leukemia, PC-3 human prostate carcinoma, and HT-29 human colon carcinoma tumor models. Treatment of tumor bearing mice with AM inhibited the growth of the tumors investigated, with an inhibitory effect ranging from 40 to 69%. The AM had a comparable antitumor effect with 5-fluorouracil and cisplatin in the Colon-26 tumor model, and combined treatment with AM and 5-fluorouracil or cisplatin resulted in an enhanced tumor growth inhibitory effect. The AM induced apoptosis through the mitochondrial pathway and induced G1 arrest in PC-3 cells and increased the number of apoptotic cells in PC-3 xenografts. These findings suggest that the AM might offer an interesting perspective in the treatment of cancer and in combination with other treatments may offer hope for a more effective cancer therapy.

  9. Role of the deposition temperature on the self-assembly of the non-planar molecule benzene-1,3,5-triphosphonic acid (BTP) at the liquid-solid interface.

    PubMed

    Nguyen, Doan Chau Yen; Smykalla, Lars; Nguyen, Thi Ngoc Ha; Mehring, Michael; Hietschold, Michael

    2016-09-21

    Benzene-1,3,5-triphosphonic acid (BTP) contains three non-planar phosphonic acid groups which enable three-dimensional hydrogen bonding. Because of these versatile 3D functional groups, BTP is an interesting intermediate to design both 2D and 3D supramolecular hydrogen-bonded architectures and organic-inorganic hybrid frameworks. However, the adsorption of BTP has surprisingly not been the subject of scanning tunneling microscopy (STM) investigations so far. Here a STM study of the adsorption pattern of BTP as obtained from deposition out of a solution in undecanol on an interface to highly-oriented pyrolytic graphite (HOPG) is presented. Furthermore, the influence of the substrate temperature during the deposition from solution on the self-assembly is investigated. High-resolution STM images reveal that the BTB molecules usually form various structures by co-adsorption with undecanol and that the BTP molecules as parts of self-assembled aggregates adsorb with their benzene ring planes tilted with respect to the substrate plane. The specific supramolecular pattern and the 2D packing density of BTP can be precisely tuned by adjusting the initial substrate temperature during deposition. The experimental results are compared to corresponding model structures obtained from semi-empirical simulations and explained by the influence of temperature on the concentration at the solution-solid interface and the kinetics of the self-assembly process. Based on these results, the control of the deposition substrate temperature has been proven to be a versatile tool to control the polymorphism of molecular patterns deposited out of solutions. PMID:27530556

  10. Role of the deposition temperature on the self-assembly of the non-planar molecule benzene-1,3,5-triphosphonic acid (BTP) at the liquid-solid interface.

    PubMed

    Nguyen, Doan Chau Yen; Smykalla, Lars; Nguyen, Thi Ngoc Ha; Mehring, Michael; Hietschold, Michael

    2016-09-21

    Benzene-1,3,5-triphosphonic acid (BTP) contains three non-planar phosphonic acid groups which enable three-dimensional hydrogen bonding. Because of these versatile 3D functional groups, BTP is an interesting intermediate to design both 2D and 3D supramolecular hydrogen-bonded architectures and organic-inorganic hybrid frameworks. However, the adsorption of BTP has surprisingly not been the subject of scanning tunneling microscopy (STM) investigations so far. Here a STM study of the adsorption pattern of BTP as obtained from deposition out of a solution in undecanol on an interface to highly-oriented pyrolytic graphite (HOPG) is presented. Furthermore, the influence of the substrate temperature during the deposition from solution on the self-assembly is investigated. High-resolution STM images reveal that the BTB molecules usually form various structures by co-adsorption with undecanol and that the BTP molecules as parts of self-assembled aggregates adsorb with their benzene ring planes tilted with respect to the substrate plane. The specific supramolecular pattern and the 2D packing density of BTP can be precisely tuned by adjusting the initial substrate temperature during deposition. The experimental results are compared to corresponding model structures obtained from semi-empirical simulations and explained by the influence of temperature on the concentration at the solution-solid interface and the kinetics of the self-assembly process. Based on these results, the control of the deposition substrate temperature has been proven to be a versatile tool to control the polymorphism of molecular patterns deposited out of solutions.

  11. Glossary

    MedlinePlus

    ... caused by disorders of oxidative phosphorylation, including mitochondrial DNA depletion syndromes. APHASIA : Impaired or absent language function, ... functions due to a disease or disease process. DNA : Deoxyribonucleic acid; a two-stranded molecule that contain ...

  12. Combined Transcriptomics and Chemical-Genetics Reveal Molecular Mode of Action of Valproic acid, an Anticancer Molecule using Budding Yeast Model

    PubMed Central

    Golla, Upendarrao; Joseph, Deepthi; Tomar, Raghuvir Singh

    2016-01-01

    Valproic acid (VA) is a pharmacologically important histone deacetylase inhibitor that recently garnered attention as an anticancer agent. Since the molecular mechanisms behind the multiple effects of VA are unclear, this study was aimed to unravel the comprehensive cellular processes affected by VA and its molecular targets in vivo using budding yeast as a model organism. Interestingly, genome-wide transcriptome analysis of cells treated with VA showed differential regulation of 30% of the genome. Functional enrichment analysis of VA transcriptome evidenced alteration of various cellular processes including cell cycle, cell wall biogenesis, DNA repair, ion homeostasis, metabolism, stress response, transport and ribosomal biogenesis, etc. Moreover, our genetic screening analysis revealed VA molecular targets belonging to oxidative and osmotic stress, DNA repair, cell wall integrity, and iron homeostasis. Further, our results demonstrated the activation of mitogen-activated protein kinases (MAPKs) Hog1 (p38) and Slt2 (p44/42) upon VA treatment. Our results also exhibited that VA acts through alteration of mitochondrial, ER architecture and functions. Especially, VA effects were neutralized in cells lacking lipid particles. Altogether, our results deciphered the novel molecular insights and mechanistic links to strengthen our knowledge on diverse cellular effects of VA along with its probable therapeutic targets and detoxification approaches. PMID:27734932

  13. Combined free nitrous acid and hydrogen peroxide pre-treatment of waste activated sludge enhances methane production via organic molecule breakdown

    PubMed Central

    Zhang, Tingting; Wang, Qilin; Ye, Liu; Batstone, Damien; Yuan, Zhiguo

    2015-01-01

    This study presents a novel pre-treatment strategy using combined free nitrous acid (FNA i.e. HNO2) and hydrogen peroxide (H2O2) to enhance methane production from WAS, with the mechanisms investigated bio-molecularly. WAS from a full-scale plant was treated with FNA alone (1.54 mg N/L), H2O2 alone (10–80 mg/g TS), and their combinations followed by biochemical methane potential tests. Combined FNA and H2O2 pre-treatment substantially enhanced methane potential of WAS by 59–83%, compared to 13–23% and 56% with H2O2 pre-treatment alone and FNA pre-treatment alone respectively. Model-based analysis indicated the increased methane potential was mainly associated with up to 163% increase in rapidly biodegradable fraction with combined pre-treatment. The molecular weight distribution and chemical structure analyses revealed the breakdown of soluble macromolecules with the combined pre-treatment caused by the deamination and oxidation of the typical functional groups in proteins, polysaccharides and phosphodiesters. These changes likely improved the biodegradability of WAS. PMID:26565653

  14. Anti-dormant mycobacterial activity and target molecule of melophlins, tetramic acid derivatives isolated from a marine sponge of Melophlus sp.

    PubMed

    Arai, Masayoshi; Yamano, Yoshi; Kamiya, Kentaro; Setiawan, Andi; Kobayashi, Motomasa

    2016-07-01

    Tuberculosis (TB), caused by Mycobacterium tuberculosis infection, is a major world health problem that is responsible for the deaths of 1.5 million people each year. In addition, the requirement for long-term therapy to cure TB complicates treatment of the disease. One of the major reasons for the extended chemotherapeutic regimens and wide epidemicity of TB is that M. tuberculosis has the ability to persist in a dormant state. We therefore established a new screening system to search for substances with activity against dormant mycobacteria using M. smegmatis and M. bovis BCG cultivated in medium containing propionate as sole carbon source to induce dormancy. Subsequently, melophlins A (1), G (2), H (3), and I (4), tetramic acid derivatives, were re-discovered from the Indonesian marine sponge of Melophlus sp. as anti-dormant mycobacterial substances. Moreover, target analysis of melophlin A indicated that it targeted the BCG1083 protein of putative exopolyphosphatase and the BCG1321c protein of diadenosine 5',5‴-P(1),P(4)-tetraphosphate phosphorylase. PMID:27193014

  15. The Fe(III) and Ga(III) coordination chemistry of 3-(1-hydroxymethylidene) and 3-(1-hydroxydecylidene)-5-(2-hydroxyethyl)pyrrolidine-2,4-dione: Novel tetramic acid degradation products of homoserine lactone bacterial quorum sensing molecules

    PubMed Central

    Romano, Ariel A.; Hahn, Tobias; Davis, Nicole; Lowery, Colin A.; Struss, Anjali K.; Janda, Kim D.; Böttger, Lars H.; Matzanke, Berthold F.; Carrano, Carl J.

    2011-01-01

    Bacteria use small diffusible molecules to exchange information in a process called quorum sensing (QS). An important class of quorum sensing molecules used by Gram-negative bacteria is the family of N-acylhomoserine lactones (HSL). It was recently discovered that a degradation product of the QS molecule 3-oxo-C12-homoserine lactone, the tetramic acid 3-(1-hydroxydecylidene)-5-(2-hydroxyethyl)pyrrolidine-2,4-dione, is a potent antibacterial agent, thus implying roles for QS outside of simply communication. Because these tetramic acids also appear to bind iron with appreciable affinity it was suggested that metal binding might contribute to their biological activity. Here, using a variety of spectroscopic tools, we describe the coordination chemistry of both the methylidene and decylidene tetramic acid derivatives with Fe(III) and Ga(III) and discuss the potential biological significance of such metal binding. PMID:22178671

  16. The Fe(III) and Ga(III) coordination chemistry of 3-(1-hydroxymethylidene) and 3-(1-hydroxydecylidene)-5-(2-hydroxyethyl)pyrrolidine-2,4-dione: novel tetramic acid degradation products of homoserine lactone bacterial quorum sensing molecules.

    PubMed

    Romano, Ariel A; Hahn, Tobias; Davis, Nicole; Lowery, Colin A; Struss, Anjali K; Janda, Kim D; Böttger, Lars H; Matzanke, Berthold F; Carrano, Carl J

    2012-02-01

    Bacteria use small diffusible molecules to exchange information in a process called quorum sensing (QS). An important class of quorum sensing molecules used by Gram-negative bacteria is the family of N-acylhomoserine lactones (HSL). It was recently discovered that a degradation product of the QS molecule 3-oxo-C(12)-homoserine lactone, the tetramic acid 3-(1-hydroxydecylidene)-5-(2-hydroxyethyl)pyrrolidine-2,4-dione, is a potent antibacterial agent, thus implying roles for QS outside of simply communication. Because these tetramic acids also appear to bind iron with appreciable affinity it was suggested that metal binding might contribute to their biological activity. Here, using a variety of spectroscopic tools, we describe the coordination chemistry of both the methylidene and decylidene tetramic acid derivatives with Fe(III) and Ga(III) and discuss the potential biological significance of such metal binding.

  17. The Fe(III) and Ga(III) coordination chemistry of 3-(1-hydroxymethylidene) and 3-(1-hydroxydecylidene)-5-(2-hydroxyethyl)pyrrolidine-2,4-dione: novel tetramic acid degradation products of homoserine lactone bacterial quorum sensing molecules.

    PubMed

    Romano, Ariel A; Hahn, Tobias; Davis, Nicole; Lowery, Colin A; Struss, Anjali K; Janda, Kim D; Böttger, Lars H; Matzanke, Berthold F; Carrano, Carl J

    2012-02-01

    Bacteria use small diffusible molecules to exchange information in a process called quorum sensing (QS). An important class of quorum sensing molecules used by Gram-negative bacteria is the family of N-acylhomoserine lactones (HSL). It was recently discovered that a degradation product of the QS molecule 3-oxo-C(12)-homoserine lactone, the tetramic acid 3-(1-hydroxydecylidene)-5-(2-hydroxyethyl)pyrrolidine-2,4-dione, is a potent antibacterial agent, thus implying roles for QS outside of simply communication. Because these tetramic acids also appear to bind iron with appreciable affinity it was suggested that metal binding might contribute to their biological activity. Here, using a variety of spectroscopic tools, we describe the coordination chemistry of both the methylidene and decylidene tetramic acid derivatives with Fe(III) and Ga(III) and discuss the potential biological significance of such metal binding. PMID:22178671

  18. Attenuation of lipid peroxidation by antioxidants in rat-1 fibroblasts: comparison of the lipid peroxidation reporter molecules cis-parinaric acid and C11-BODIPY(581/591) in a biological setting.

    PubMed

    Drummen, Gregor P C; Makkinje, Miriam; Verkleij, Arie J; Op den Kamp, Jos A F; Post, Jan A

    2004-03-22

    Lipid peroxidation is a major factor in the pathogenesis of many disease states. To detect the initial stages of lipid peroxidation or evaluate antioxidant efficacy, cis-parinaric acid (cis-PnA) has been successfully used and thoroughly validated. However, cis-PnA is not very well suited for medium throughput screening of antioxidants in living cells. We recently introduced and validated a lipid peroxidation reporter molecule, C11-BODIPY(581/591). To further explore this probe, we evaluated the protective effect of 12 natural antioxidants in rat-1 fibroblasts subjected to 50 microM cumene-hydroperoxide using both probes. The same pecking order for the individual antioxidant efficacies was obtained: alpha-tocopherol approximately gamma-tocopherol > quercetin approximately lycopene > kaempferol > palm oil > hydroxy-tyrosol > > alpha-carotene = beta-carotene = lutein = tyrosol = chlorogenic acid. This validates the accuracy of the C11-BODIPY(581/591) method and shows that this assay is an accurate and highly flexible method for indexing lipid peroxidation or determining antioxidant efficacy in living cells in a medium throughput scenario. The antioxidant efficacy was compared with their one-electron reduction potential, hydrophobicity and Trolox C equivalent antioxidant capacity. Our results show that although these parameters are valuable for determining structure-function relationships, they have limited predictive value for antioxidant efficacy in vivo.

  19. Amino acid-derived 1,2-benzisothiazolinone derivatives as novel small-molecule antifungal inhibitors: identification of potential genetic targets.

    PubMed

    Alex, Deepu; Gay-Andrieu, Francoise; May, Jared; Thampi, Linta; Dou, Dengfeng; Mooney, Aileen; Groutas, William; Calderone, Richard

    2012-09-01

    We have identified four synthetic compounds (DFD-VI-15, BD-I-186, DFD-V-49, and DFD-V-66) from an amino acid-derived 1,2-benzisothiazolinone (BZT) scaffold that have reasonable MIC(50) values against a panel of fungal pathogens. These compounds have no structural similarity to existing antifungal drugs. Three of the four compounds have fungicidal activity against Candida spp., Cryptococcus neoformans, and several dermatophytes, while one is fungicidal to Aspergillus fumigatus. The kill rates of our compounds are equal to those in clinical usage. The BZT compounds remain active against azole-, polyene-, and micafungin-resistant strains of Candida spp. A genetics-based approach, along with phenotype analysis, was used to begin mode of action (MOA) studies of one of these compounds, DFD-VI-15. The genetics-based screen utilized a homozygous deletion collection of approximately 4,700 Saccharomyces cerevisiae mutants. We identified mutants that are both hypersensitive and resistant. Using FunSpec, the hypersensitive mutants and a resistant ace2 mutant clustered within a category of genes related directly or indirectly to mitochondrial functions. In Candida albicans, the functions of the Ace2p transcription factor include the regulation of glycolysis. Our model is that DFD-VI-15 targets a respiratory pathway that limits energy production. Supporting this hypothesis are phenotypic data indicating that DFD-VI-15 causes increased cell-reactive oxidants (ROS) and a decrease in mitochondrial membrane potential. Also, the same compound has activity when cells are grown in a medium containing glycerol (mitochondrial substrate) but is much less active when cells are grown anaerobically.

  20. Amino Acid-Derived 1,2-Benzisothiazolinone Derivatives as Novel Small-Molecule Antifungal Inhibitors: Identification of Potential Genetic Targets

    PubMed Central

    Alex, Deepu; Gay-Andrieu, Francoise; May, Jared; Thampi, Linta; Dou, Dengfeng; Mooney, Aileen; Groutas, William

    2012-01-01

    We have identified four synthetic compounds (DFD-VI-15, BD-I-186, DFD-V-49, and DFD-V-66) from an amino acid-derived 1,2-benzisothiazolinone (BZT) scaffold that have reasonable MIC50 values against a panel of fungal pathogens. These compounds have no structural similarity to existing antifungal drugs. Three of the four compounds have fungicidal activity against Candida spp., Cryptococcus neoformans, and several dermatophytes, while one is fungicidal to Aspergillus fumigatus. The kill rates of our compounds are equal to those in clinical usage. The BZT compounds remain active against azole-, polyene-, and micafungin-resistant strains of Candida spp. A genetics-based approach, along with phenotype analysis, was used to begin mode of action (MOA) studies of one of these compounds, DFD-VI-15. The genetics-based screen utilized a homozygous deletion collection of approximately 4,700 Saccharomyces cerevisiae mutants. We identified mutants that are both hypersensitive and resistant. Using FunSpec, the hypersensitive mutants and a resistant ace2 mutant clustered within a category of genes related directly or indirectly to mitochondrial functions. In Candida albicans, the functions of the Ace2p transcription factor include the regulation of glycolysis. Our model is that DFD-VI-15 targets a respiratory pathway that limits energy production. Supporting this hypothesis are phenotypic data indicating that DFD-VI-15 causes increased cell-reactive oxidants (ROS) and a decrease in mitochondrial membrane potential. Also, the same compound has activity when cells are grown in a medium containing glycerol (mitochondrial substrate) but is much less active when cells are grown anaerobically. PMID:22687516

  1. Amino acid-derived 1,2-benzisothiazolinone derivatives as novel small-molecule antifungal inhibitors: identification of potential genetic targets.

    PubMed

    Alex, Deepu; Gay-Andrieu, Francoise; May, Jared; Thampi, Linta; Dou, Dengfeng; Mooney, Aileen; Groutas, William; Calderone, Richard

    2012-09-01

    We have identified four synthetic compounds (DFD-VI-15, BD-I-186, DFD-V-49, and DFD-V-66) from an amino acid-derived 1,2-benzisothiazolinone (BZT) scaffold that have reasonable MIC(50) values against a panel of fungal pathogens. These compounds have no structural similarity to existing antifungal drugs. Three of the four compounds have fungicidal activity against Candida spp., Cryptococcus neoformans, and several dermatophytes, while one is fungicidal to Aspergillus fumigatus. The kill rates of our compounds are equal to those in clinical usage. The BZT compounds remain active against azole-, polyene-, and micafungin-resistant strains of Candida spp. A genetics-based approach, along with phenotype analysis, was used to begin mode of action (MOA) studies of one of these compounds, DFD-VI-15. The genetics-based screen utilized a homozygous deletion collection of approximately 4,700 Saccharomyces cerevisiae mutants. We identified mutants that are both hypersensitive and resistant. Using FunSpec, the hypersensitive mutants and a resistant ace2 mutant clustered within a category of genes related directly or indirectly to mitochondrial functions. In Candida albicans, the functions of the Ace2p transcription factor include the regulation of glycolysis. Our model is that DFD-VI-15 targets a respiratory pathway that limits energy production. Supporting this hypothesis are phenotypic data indicating that DFD-VI-15 causes increased cell-reactive oxidants (ROS) and a decrease in mitochondrial membrane potential. Also, the same compound has activity when cells are grown in a medium containing glycerol (mitochondrial substrate) but is much less active when cells are grown anaerobically. PMID:22687516

  2. Interaction of aflatoxin B1 and cyclopiazonic acid toxicities.

    PubMed

    Yates, I E; Cole, R J; Giles, J L; Dorner, J W

    1987-01-01

    Toxic properties of the mycotoxins cyclopiazonic acid and aflatoxin B1 have been analyzed separately and in combination by monitoring their effects on luminescence in the marine bacterium Photobacterium phosphoreum, Strain NCMB 844. Genotoxicity was analyzed with a dark mutant of this organism whose reversion to the bioluminescent condition is stimulated by compounds attacking guanine sites in deoxyribonucleic acids. In this assay, cyclopiazonic acid, unlike aflatoxin B1, is not enhanced by cyclopiazonic acid when the two mycotoxins are assayed in combination. Cytotoxicity was assessed by the diminution of bioluminescence in a separate assay system with strain NRRLB-1177 of P. phosphoreum. Cyclopiazonic acid is more cytotoxic than aflatoxin B1, and concentrations of cyclopiazonic acid required for cytotoxicity decreases with time, whereas aflatoxin B1 cytotoxic expression does not change significantly with time under most assay conditions. Aflatoxin B1 and cyclopiazonic acid assayed as a dose pair indicate that these mycotoxins elicit their effects by independent modes of action.

  3. Physics of Molecules

    NASA Astrophysics Data System (ADS)

    Williams, D.; Murdin, P.

    2000-11-01

    Many varieties of molecule have been detected in the Milky Way and in other galaxies. The processes by which these molecules are formed and destroyed are now broadly understood (see INTERSTELLAR CHEMISTRY). These molecules are important components of galaxies in two ways. Firstly, radiation emitted by molecules enables us to trace the presence of diffuse gas, to infer its physical properties and ...

  4. Organic Molecules in Meteorites

    NASA Astrophysics Data System (ADS)

    Martins, Zita

    2015-08-01

    Carbonaceous meteorites are primitive samples from the asteroid belt, containing 3-5wt% organic carbon. The exogenous delivery of organic matter by carbonaceous meteorites may have contributed to the organic inventory of the early Earth. The majority (>70%) of the meteoritic organic material consist of insoluble organic matter (IOM) [1]. The remaining meteoritic organic material (<30%) consists of a rich organic inventory of soluble organic compounds, including key compounds important in terrestrial biochemistry [2-4]. Different carbonaceous meteorites contain soluble organic molecules with different abundances and distributions, which may reflect the extension of aqueous alteration or thermal metamorphism on the meteorite parent bodies. Extensive aqueous alteration on the meteorite parent body may result on 1) the decomposition of α-amino acids [5, 6]; 2) synthesis of β- and γ-amino acids [2, 6-9]; 3) higher relative abundances of alkylated polycyclic aromatic hydrocarbons (PAHs) [6, 10]; and 4) higher L-enantiomer excess (Lee) value of isovaline [6, 11, 12].The soluble organic content of carbonaceous meteorites may also have a contribution from Fischer-Tropsch/Haber-Bosch type gas-grain reactions after the meteorite parent body cooled to lower temperatures [13, 14].The analysis of the abundances and distribution of the organic molecules present in meteorites helps to determine the physical and chemical conditions of the early solar system, and the prebiotic organic compounds available on the early Earth.[1] Cody and Alexander (2005) GCA 69, 1085. [2] Cronin and Chang (1993) in: The Chemistry of Life’s Origin. pp. 209-258. [3] Martins and Sephton (2009) in: Amino acids, peptides and proteins in organic chemistry. pp. 1-42. [4] Martins (2011) Elements 7, 35. [5] Botta et al. (2007) MAPS 42, 81. [6] Martins et al. (2015) MAPS, in press. [7] Cooper and Cronin (1995) GCA 59, 1003. [8] Glavin et al. (2006) MAPS. 41, 889. [9] Glavin et al. (2011) MAPS 45, 1948. [10

  5. Inhibition of fatty acid amide hydrolase and cyclooxygenase-2 increases levels of endocannabinoid related molecules and produces analgesia via peroxisome proliferator-activated receptor-alpha in a model of inflammatory pain.

    PubMed

    Jhaveri, Maulik D; Richardson, Denise; Robinson, Ian; Garle, Michael J; Patel, Annie; Sun, Yan; Sagar, Devi R; Bennett, Andrew J; Alexander, Stephen P H; Kendall, David A; Barrett, David A; Chapman, Victoria

    2008-07-01

    The antinociceptive effects of the endocannabinoids (ECs) are enhanced by inhibiting catabolic enzymes such as fatty acid amide hydrolase (FAAH). The physiological relevance of the metabolism of ECs by other pathways, such as cyclooxygenase-2 (COX2) is less clear. To address this question we compared the effects of local inhibition of FAAH versus COX2 (URB597 and nimesulide, respectively) on inflammatory hyperalgesia and levels of endocannabinoids and related molecules in the hindpaw. Inflammatory hyperalgesia was measured following intraplantar injection of carrageenan. Effects of intraplantar injection of URB597 (25 microg and 100 microg) or nimesulide (50 microg) on hyperalgesia and hindpaw levels of anandamide (AEA), 2-arachidonoylglycerol (2AG) and N-palmitoylethanolamine (PEA) were determined. Although both doses of URB597 increased levels of AEA and 2AG in the carrageenan inflamed hindpaw, only the lower dose of URB597 attenuated hyperalgesia (P<0.05). Nimesulide attenuated both hyperalgesia and hindpaw oedema (P<0.001, P<0.01, respectively) and increased levels of PEA (P<0.05) in the hindpaw. Since both AEA and PEA are ligands for peroxisome proliferator-activated receptor-alpha (PPARalpha), the effects of the PPARalpha antagonist GW6471 on nimesulide- and URB597-mediated effects were studied. GW6471, but not a PPARgamma antagonist, blocked the inhibitory effects of nimesulide and URB597 on hyperalgesia. Our data suggest that both COX2 and FAAH play a role in the metabolism of endocannabinoids and related molecules. The finding that PPARalpha antagonism blocked the inhibitory effects of nimesulide and URB597 suggests that PPARalpha contributes to their antinociceptive effects in the carrageenan model of inflammatory hyperalgesia.

  6. Electrorheological crystallization of proteins and other molecules

    DOEpatents

    Craig, George D.; Rupp, Bernhard

    1996-01-01

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an x-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the x-ray diffraction pattern.

  7. Electrorheological crystallization of proteins and other molecules

    DOEpatents

    Craig, G.D.; Rupp, B.

    1996-06-11

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an X-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the X-ray diffraction pattern. 4 figs.

  8. Increase in liver nuclear tri-iodothyronine receptors associated with increased deoxyribonucleic acid by long-term administration of tri-iodothyronine in thyroidectomized rats

    PubMed Central

    Nakamura, Hirotoshi; Hamada, Satoshi; Imura, Hiroo

    1979-01-01

    The effect of long-term administration of small amounts of tri-iodothyronine was examined on the nuclear tri-iodothyronine receptors in rat liver. The maximal binding capacity (Cmax.) and association constant (Ka) of the receptors were determined in thyroidectomized rats given vehicle alone (group A), 2μg of tri-iodothyronine/100g body wt. (group B) or 7μg of tri-iodothyronine/100g body wt. (group C) for 2 weeks. Scatchard analyses with correction for the amount of endogenous tri-iodothyronine revealed that Cmax. values per g of liver were increased to 1.5 and 2.7 times the control value in groups B and C respectively. Since concentrations of DNA per g of liver were significantly increased in the two groups of hormone-treated rats, Cmax. values per mg of DNA were nearly the same in group B, but still increased significantly in group C compared with group A. Ka values remained unchanged in all three groups of animals. Mitochondrial α-glycerophosphate dehydrogenase activity was 9.6 and 28.7 times as high in groups B and C, respectively, as in group A. Concentrations of endogenous tri-iodothyronine bound to non-histone protein were substantially increased in groups B and C, although concentrations of serum tri-iodothyronine remained rather low. The results obtained indicate that the long-term administration of tri-iodothyronine in small doses induces an increase in the nuclear receptors associated with increased DNA with and without accompanying a relative increase in the receptor concentration in thyroidectomized rats. Also the hormonal effect is closely related to the total number of the nuclear receptors and the concentrations of nuclear tri-iodothyronine bound to the receptors rather than the serum tri-iodothyronine concentrations. PMID:230825

  9. Metronomic Adjuvant Chemotherapy Improves Treatment Outcome in Nasopharyngeal Carcinoma Patients With Postradiation Persistently Detectable Plasma Epstein-Barr Virus Deoxyribonucleic Acid

    SciTech Connect

    Twu, Chih-Wen; Wang, Wen-Yi; Chen, Chien-Chih; Liang, Kai-Li; Jiang, Rong-San; Wu, Ching-Te; Shih, Yi-Ting; Lin, Po-Ju; Liu, Yi-Chun; Lin, Jin-Ching

    2014-05-01

    Purpose: To investigate the effects of adjuvant chemotherapy in nasopharyngeal carcinoma (NPC) patients with persistently detectable plasma Epstein-Barr virus DNA (pEBV DNA) after curative radiation therapy plus induction/concurrent chemotherapy. Methods and Materials: The study population consisted of 625 NPC patients with available pEBV DNA levels before and after treatment. Eighty-five patients with persistently detectable pEBV DNA after 1 week of completing radiation therapy were eligible for this retrospective study. Of the 85 patients, 33 were administered adjuvant chemotherapy consisting of oral tegafur-uracil (2 capsules twice daily) for 12 months with (n=4) or without (n=29) preceding intravenous chemotherapy of mitomycin-C, epirubicin, and cisplatin. The remaining 52 patients who did not receive adjuvant chemotherapy served as the control group. Results: Baseline patient characteristics at diagnosis (age, sex, pathologic type, performance status, T classification, N classification, and overall stage), as well as previous treatment modality, were comparable in both arms. After a median follow-up of 70 months for surviving patients, 45.5% (15 of 33 patients) with adjuvant chemotherapy and 71.2% (37 of 52 patients) without adjuvant chemotherapy experienced tumor relapses (P=.0323). There were a significant reduction in distant failure (P=.0034) but not in local or regional recurrence. The 5-year overall survival rate was 71.6% for patients with adjuvant chemotherapy and 28.7% for patients without adjuvant chemotherapy (hazard ratio 0.27; 95% confidence interval 0.17-0.55; P<.0001). Conclusions: Our retrospective data showed that adjuvant chemotherapy can reduce distant failure and improve overall survival in NPC patients with persistently detectable pEBV DNA after curative radiation therapy plus induction/concurrent chemotherapy.

  10. Mechanism of deoxyribonucleic acid breakage induced by 4'-(9-acridinylamino)methanesulfon-m-anisidide and copper: role for cuprous ion and oxygen free radicals

    SciTech Connect

    Wong, A.; Huang, C.H.; Crooke, S.T.

    1984-06-19

    4-(9-Acridinylamino)methanesulfon-m-anisidide (mAMSA) interacts with Cu(II) ions, as indicated by changes in the mAMSA absorption spectrum induced by Cu(II). The spectral changes are due to the oxidation of mAMSA by Cu(II), resulting in an oxidized mAMSA product and Cu(I). Cu(I) plays an important role in the mAMSA-Cu(II)-induced DNA breakage, since in the presence of neocuproine the DNA breakage is inhibited. Up to 200 ..mu..M, Cu(I) by itself is virtually ineffective, in contrast to the mixture of mAMSA and Cu(II). This suggests that mAMSA, aside from reducing Cu(II) to Cu(I), may play a role in mediating DNA breakage. The DNA breakage was reduced in partially anaerobic conditions, indicating the involvement of molecular oxygen. Catalase and 4,5-dihydroxy-1,2-benzenedisulfonate inhibited the DNA breakage completely, indicating that hydrogen peroxide and superoxide radicals mediate DNA breakage. 1,3-Diazabicyclo(2.2.2)octane partially inhibited the breakage, suggesting that singlet oxygen is involved. The available evidence supports a mechanism indicating the formation of a DNA x mAMSA x Cu(II) ternary complex and the subsequent oxidation-reduction of the complex to form DNA x mAQDI x Cu(I). The oxidation of the complexed Cu(I) may result in reduction of oxygen to oxygen free radicals which induce DNA breaks.

  11. R Factor Proteins Synthesized in Escherichia coli Minicells: Incorporation Studies with Different R Factors and Detection of Deoxyribonucleic Acid-Binding Proteins1

    PubMed Central

    Levy, Stuart B.

    1974-01-01

    Analysis of the protein synthesized by Escherichia coli minicells containing R factors demonstrated a variety of low- and high-molecular-weight polypeptides in sodium dodecyl sulfate (SDS)-polyacrylamide gels. Only half of this protein was released into a soluble fraction on lysis of these minicells. The other half remained associated with the minicell envelope. The efficiency of precursor incorporation into protein and the kinds of proteins synthesized changed with the age of the minicells at the time of harvest. About 1 to 2% of the soluble R factor-coded protein bound to calf thymus, E. coli, or R factor DNA-cellulose. Although most of these proteins were excluded from Sephadex G-100 columns, they migrated chiefly as low-molecular-weight-polypeptides (13,000 to 15,000) in SDS-polyacrylamide gels. Additional DNA-binding proteins that appeared to be higher-molecular-weight peptides were noted in extracts from younger minicells. At least one protein, identified as an SDS band, appeared to bind selectively to R factor DNA-cellulose. Minicells with R factors also contained DNA-binding proteins of cell origin, including the core RNA polymerase. No such binding proteins were found in R− minicells. These studies suggest that: (i) R factors code for proteins that may be involved in their own DNA metabolism; (ii) R factor DNA-binding proteins may be associated with larger host cell DNA-binding proteins or subunits of larger R factor proteins; and (iii) the age of the minicell influences the extent of protein synthesis and the kinds of proteins synthesized by R factors in minicells. Images PMID:4612023

  12. Semiconductor sensor embedded microfluidic chip for protein biomarker detection using a bead-based immunoassay combined with deoxyribonucleic acid strand labeling.

    PubMed

    Lin, Yen-Heng; Peng, Po-Yu

    2015-04-15

    Two major issues need to be addressed in applying semiconductor biosensors to detecting proteins in immunoassays. First, the length of the antibody on the sensor surface surpasses the Debye lengths (approximately 1 nm, in normal ionic strength solution), preventing certain specifically bound proteins from being tightly attached to the sensor surface. Therefore, these proteins do not contribute to the sensor's surface potential change. Second, these proteins carry a small charge and can be easily affected by the pH of the surrounding solution. This study proposes a magnetic bead-based immunoassay using a secondary antibody to label negatively charged DNA fragments for signal amplification. An externally imposed magnetic force attaches the analyte tightly to the sensor surface, thereby effectively solving the problem of the analyte protein's distance to the sensor surface surpassing the Debye lengths. In addition, a normal ion intensity buffer can be used without dilution for the proposed method. Experiments revealed that the sensitivity can be improved by using a longer DNA fragment for labeling and smaller magnetic beads as solid support for the antibody. By using a 90 base pair DNA label, the signal was 15 times greater than that without labeling. In addition, by using a 120 nm magnetic bead, a minimum detection limit of 12.5 ng mL(-1) apolipoprotein A1 can be measured. Furthermore, this study integrates a semiconductor sensor with a microfluidic chip. With the help of microvalves and micromixers in the chip, the length of the mixing step for each immunoassay has been reduced from 1h to 20 min, and the sample volume has been reduced from 80 μL to 10 μL. In practice, a protein biomarker in a urinary bladder cancer patient's urine was successfully measured using this technique. This study provides a convenient and effective method to measure protein using a semiconductor sensor.

  13. Rapid deoxyribonucleic acid analysis by allele-specific polymerase chain reaction for detection of mutations in the steroid 21-hydroxylase gene

    SciTech Connect

    Wilson, R.C.; Wei, J.Q.; Cheng, K.C.

    1995-05-01

    Rapid DNA analysis based on allele-specific polymerase chain reaction (PCR) using mutation site-specific primers was developed to detect mutations in the CYP21 gene known to cause steroid 21-hydroxylase deficiency. In contrast to the previous method, in which PCR of genomic DNA was followed by dot blot analysis with radio active probes and multiple rounds of stripping and reprobing for each of the 8 most common mutation sites, the results using this new method were immediately visualized after the PCR run by ethidium bromide-stained agarose gel electrophoresis. Using allele-specific PCR, mutation(s) were identified on 148 affected chromosomes out of 160 tested. Although mutation(s) were identified on only one chromosome of 11 of these patients, their parents showed a consistent pattern on DNA analysis. The only exception was that in one family, in which the parents each had a detectable mutation, a mutation was detected on only one allele of the patient. Most likely there is a mutation in the patient`s other allele that could have arisen de novo or was inherited from the parent and was not evident in the transmitting parent`s phenotype. When compared with the dot blot procedure, allele-specific PCR is more rapid, less labor-intensive, and avoids the use of radioactivity. 26 refs., 3 figs., 2 tabs.

  14. Existing and emerging detection technologies for DNA (Deoxyribonucleic Acid) finger printing, sequencing, bio- and analytical chips: a multidisciplinary development unifying molecular biology, chemical and electronics engineering.

    PubMed

    Kumar Khanna, Vinod

    2007-01-01

    The current status and research trends of detection techniques for DNA-based analysis such as DNA finger printing, sequencing, biochips and allied fields are examined. An overview of main detectors is presented vis-à-vis these DNA operations. The biochip method is explained, the role of micro- and nanoelectronic technologies in biochip realization is highlighted, various optical and electrical detection principles employed in biochips are indicated, and the operational mechanisms of these detection devices are described. Although a diversity of biochips for diagnostic and therapeutic applications has been demonstrated in research laboratories worldwide, only some of these chips have entered the clinical market, and more chips are awaiting commercialization. The necessity of tagging is eliminated in refractive-index change based devices, but the basic flaw of indirect nature of most detection methodologies can only be overcome by generic and/or reagentless DNA sensors such as the conductance-based approach and the DNA-single electron transistor (DNA-SET) structure. Devices of the electrical detection-based category are expected to pave the pathway for the next-generation DNA chips. The review provides a comprehensive coverage of the detection technologies for DNA finger printing, sequencing and related techniques, encompassing a variety of methods from the primitive art to the state-of-the-art scenario as well as promising methods for the future.

  15. Electrochemical deoxyribonucleic acid biosensor based on electrodeposited graphene and nickel oxide nanoparticle modified electrode for the detection of salmonella enteritidis gene sequence.

    PubMed

    Sun, Wei; Wang, Xiuli; Lu, Yongxi; Gong, Shixing; Qi, Xiaowei; Lei, Bingxin; Sun, Zhenfan; Li, Guangjiu

    2015-04-01

    In this paper a new electrochemical DNA biosensor was prepared by using graphene (GR) and nickel oxide (NiO) nanocomposite modified carbon ionic liquid electrode (CILE) as the substrate electrode. GR and NiO nanoparticles were electrodeposited on the CILE surface step-by-step to get the nanocomposite. Due to the strong affinity of NiO with phosphate groups of ssDNA, oligonucleotide probe with a terminal 5'-phosphate group could be attached on the surface of NiO/GR/CILE, which could further hybridize with the target ssDNA sequence. Methylene blue (MB) was used as the electrochemical indicator for monitoring the hybridization reaction. Under the optimal conditions the reduction peak current of MB was proportional to the concentration of salmonella enteritidis gene sequence in the range from 1.0×10(-13) to 1.0×10(-6)molL(-1) with a detection limit as 3.12×10(-14)molL(-1). This electrochemical DNA sensor exhibited good discrimination ability to one-base and three-base mismatched ssDNA sequences, and the polymerase chain reaction amplification product of salmonella enteritidis gene sequences were further detected with satisfactory results. PMID:25686924

  16. Electrochemical deoxyribonucleic acid biosensor based on electrodeposited graphene and nickel oxide nanoparticle modified electrode for the detection of salmonella enteritidis gene sequence.

    PubMed

    Sun, Wei; Wang, Xiuli; Lu, Yongxi; Gong, Shixing; Qi, Xiaowei; Lei, Bingxin; Sun, Zhenfan; Li, Guangjiu

    2015-04-01

    In this paper a new electrochemical DNA biosensor was prepared by using graphene (GR) and nickel oxide (NiO) nanocomposite modified carbon ionic liquid electrode (CILE) as the substrate electrode. GR and NiO nanoparticles were electrodeposited on the CILE surface step-by-step to get the nanocomposite. Due to the strong affinity of NiO with phosphate groups of ssDNA, oligonucleotide probe with a terminal 5'-phosphate group could be attached on the surface of NiO/GR/CILE, which could further hybridize with the target ssDNA sequence. Methylene blue (MB) was used as the electrochemical indicator for monitoring the hybridization reaction. Under the optimal conditions the reduction peak current of MB was proportional to the concentration of salmonella enteritidis gene sequence in the range from 1.0×10(-13) to 1.0×10(-6)molL(-1) with a detection limit as 3.12×10(-14)molL(-1). This electrochemical DNA sensor exhibited good discrimination ability to one-base and three-base mismatched ssDNA sequences, and the polymerase chain reaction amplification product of salmonella enteritidis gene sequences were further detected with satisfactory results.

  17. Deoxyribonucleic Acid and Other Words Students Avoid Speaking Aloud: Evaluating the Role of Pronunciation on Participation in Secondary School Science Classroom Conversations

    NASA Astrophysics Data System (ADS)

    Beck, Stacie Elizabeth

    Student's verbal participation in science classrooms is an essential element in building the skills necessary for proficiency in scientific literacy and discourse. The myriad of new, multisyllabic vocabulary terms introduced in one year of secondary school biology instruction can overwhelm students and further impede the self-efficacy needed for concise constructions of scientific explanations and arguments. Factors inhibiting students' inclination to answer questions, share ideas and respond to peers in biology classrooms include confidence and self-perceived competence in appropriately speaking the language of science. Providing students with explicit, engaging instruction in methods to develop vocabulary for use in expressing conclusions is critical for expanding comprehension of science concepts. This study fused the recommended strategies for engaging vocabulary instruction with linguistic practices for teaching pronunciation to examine the relationship between a student's ability to pronounce challenging bio-terminology and their propensity to speak in teacher-led, guided classroom discussions. Interviews, surveys, and measurements quantifying and qualifying students' participation in class discussions before and after explicit instruction in pronunciation were used to evaluate the potential of this strategy as an appropriate tool for increasing students' self-efficacy and willingness to engage in biology classroom conversations. The findings of this study showed a significant increase in student verbal participation in classroom discussions after explicit instruction in pronunciation combined with vocabulary literacy strategies. This research also showed an increase in the use of vocabulary words in student comments after the intervention.

  18. High-Sensitivity C-Reactive Protein Complements Plasma Epstein-Barr Virus Deoxyribonucleic Acid Prognostication in Nasopharyngeal Carcinoma: A Large-Scale Retrospective and Prospective Cohort Study

    SciTech Connect

    Tang, Lin-Quan; Li, Chao-Feng; Chen, Qiu-Yan; Zhang, Lu; Lai, Xiao-Ping; He, Yun; Xu, Yun-Xiu-Xiu; Hu, Dong-Peng; Wen, Shi-Hua; Peng, Yu-Tuan; Chen, Wen-Hui; Liu, Huai; Guo, Shan-Shan; Liu, Li-Ting; Li, Jing; Zhang, Jing-Ping; and others

    2015-02-01

    Purpose: To evaluate the effects of combining the assessment of circulating high-sensitivity C-reactive protein (hs-CRP) with that of Epstein-Barr virus DNA (EBV DNA) in the pretherapy prognostication of nasopharyngeal carcinoma (NPC). Patients and Methods: Three independent cohorts of NPC patients (training set of n=3113, internal validation set of n=1556, and prospective validation set of n=1668) were studied. Determinants of disease-free survival, distant metastasis–free survival, and overall survival were assessed by multivariate analysis. Hazard ratios and survival probabilities of the patient groups, segregated by clinical stage (T1-2N0-1M0, T3-4N0-1M0, T1-2N2-3M0, and T3-4N2-3M0) and EBV DNA load (low or high) alone, and also according to hs-CRP level (low or high), were compared. Results: Elevated hs-CRP and EBV DNA levels were significantly correlated with poor disease-free survival, distant metastasis–free survival, and overall survival in both the training and validation sets. Associations were similar and remained significant after excluding patients with cardiovascular disease, diabetes, and chronic hepatitis B. Patients with advanced-stage disease were segregated by high EBV DNA levels and high hs-CRP level into a poorest-risk group, and participants with either high EBV DNA but low hs-CRP level or high hs-CRP but low EBV DNA values had poorer survival compared with the bottom values for both biomarkers. These findings demonstrate a significant improvement in the prognostic ability of conventional advanced NPC staging. Conclusion: Baseline plasma EBV DNA and serum hs-CRP levels were significantly correlated with survival in NPC patients. The combined interpretation of EBV DNA with hs-CRP levels led to refinement of the risks for the patient subsets, with improved risk discrimination in patients with advanced-stage disease.

  19. Synthesis and characterization of various ruthenium small molecules and metallopolymers for potential use in photovoltaic devices and luminescence properties of N-heterocyclic carbenes and trifluoro methylated tris(pyrazolyl)borate silver (I) acid-base adducts

    NASA Astrophysics Data System (ADS)

    Chitikuri, Shylaja

    This thesis with its 66 pages, 1 table, 29 figures and 47 references, deals with two major topics involving structure and properties of selected metal complexes and their use in electronic devices. The first chapter discusses the development of ruthenium-based metallopolymer and small molecular complexes toward possible utilization as active materials for solar cells. Such complexes have been found to be good "black absorbers" with solid-state absorption that spans the entire visible region into the near-infrared, representing an impressive overlap with the solar radiation that is more favorable than common molecular solar cell active materials. The second chapter includes photophysical studies of different metallo N-heterocyclic carbenes and acid-base adducts comprising fluorinated tris(pyrazolyl)borate silver(I) complexes coordinated to different solvent and aromatic molecules. These species have been investigated and found to exhibit unusual photophysical properties, including metal-free phosphorescence at room temperature with high quantum yield, multi-color emission from a single compound, and selective sensing of temperature and hazardous vapors.

  20. Cytometry of deoxyribonuclei acid content and morphology of mammalian sperm

    SciTech Connect

    Gledhill, B.L.

    1983-01-01

    Because spermatogenesis is exquisitely sensitive to external influences, sperm can serve as a biological dosimeter. Advances in interpreting induced sperm abnormalities require a better understanding of sperm characteristics. This report reviews the application of several methods for automated, quantitative detection of shape changes, methods that are faster and more sensitive than conventional subjective technqiues. Variability of sperm deoxyribonucleic acid content as a bioassay of genetic damage is explored, and limitations of the bioassay are discussed. New flow cytometric techniques that could lead to sexing mammalian sperm are examined.

  1. [Endothelial cell adhesion molecules].

    PubMed

    Ivanov, A N; Norkin, I A; Puchin'ian, D M; Shirokov, V Iu; Zhdanova, O Iu

    2014-01-01

    The review presents current data concerning the functional role of endothelial cell adhesion molecules belonging to different structural families: integrins, selectins, cadherins, and the immunoglobulin super-family. In this manuscript the regulatory mechanisms and factors of adhesion molecules expression and distribution on the surface of endothelial cells are discussed. The data presented reveal the importance of adhesion molecules in the regulation of structural and functional state of endothelial cells in normal conditions and in pathology. Particular attention is paid to the importance of these molecules in the processes of physiological and pathological angiogenesis, regulation of permeability of the endothelial barrier and cell transmigration.

  2. Theoretical studies on the coupling interactions in H2SO4···HOO˙···(H2O)n (n = 0-2) clusters: toward understanding the role of water molecules in the uptake of HOO˙ radical by sulfuric acid aerosols.

    PubMed

    Li, Ping; Ma, Zhiying; Wang, Weihua; Zhai, Yazhou; Sun, Haitao; Bi, Siwei; Bu, Yuxiang

    2011-01-21

    A detailed knowledge of coupling interactions among sulfuric acid (H(2)SO(4)), the hydroperoxyl radical (HOO˙), and water molecules (H(2)O) is crucial for the better understanding of the uptake of HOO˙ radicals by sulfuric acid aerosols at different atmospheric humidities. In the present study, the equilibrium structures, binding energies, equilibrium distributions, and the nature of the coupling interactions in H(2)SO(4)···HOO˙···(H(2)O)(n) (n = 0-2) clusters have been systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, energy decomposition analyses, and ab initio molecular dynamics. Two binary, five ternary, and twelve tetramer clusters possessing multiple intermolecular H-bonds have been located on their potential energy surfaces. Two different modes for water molecules have been observed to influence the coupling interactions between H(2)SO(4) and HOO˙ through the formations of intermolecular H-bonds with or without breaking the original intermolecular H-bonds in the binary H(2)SO(4)···HOO˙ cluster. It was found that the introduction of one or two water molecules can efficiently enhance the interactions between H(2)SO(4) and HOO˙, implying the positive role of water molecules in the uptake of the HOO˙ radical by sulfuric acid aerosols. Additionally, the coupling interaction modes of the most stable clusters under study have been verified by the ab initio molecular dynamics. PMID:21052607

  3. Molecules between the Stars.

    ERIC Educational Resources Information Center

    Verschuur, Gerrit L.

    1987-01-01

    Provides a listing of molecules discovered to date in the vast interstellar clouds of dust and gas. Emphasizes the recent discoveries of organic molecules. Discusses molecular spectral lines, MASERs (microwave amplification by stimulated emission of radiation), molecular clouds, and star birth. (TW)

  4. The missing organic molecules on Mars.

    PubMed

    Benner, S A; Devine, K G; Matveeva, L N; Powell, D H

    2000-03-14

    GC-MS on the Viking 1976 Mars missions did not detect organic molecules on the Martian surface, even those expected from meteorite bombardment. This result suggested that the Martian regolith might hold a potent oxidant that converts all organic molecules to carbon dioxide rapidly relative to the rate at which they arrive. This conclusion is influencing the design of Mars missions. We reexamine this conclusion in light of what is known about the oxidation of organic compounds generally and the nature of organics likely to come to Mars via meteorite. We conclude that nonvolatile salts of benzenecarboxylic acids, and perhaps oxalic and acetic acid, should be metastable intermediates of meteoritic organics under oxidizing conditions. Salts of these organic acids would have been largely invisible to GC-MS. Experiments show that one of these, benzenehexacarboxylic acid (mellitic acid), is generated by oxidation of organic matter known to come to Mars, is rather stable to further oxidation, and would not have been easily detected by the Viking experiments. Approximately 2 kg of meteorite-derived mellitic acid may have been generated per m(2) of Martian surface over 3 billion years. How much remains depends on decomposition rates under Martian conditions. As available data do not require that the surface of Mars be very strongly oxidizing, some organic molecules might be found near the surface of Mars, perhaps in amounts sufficient to be a resource. Missions should seek these and recognize that these complicate the search for organics from entirely hypothetical Martian life.

  5. The missing organic molecules on Mars

    PubMed Central

    Benner, Steven A.; Devine, Kevin G.; Matveeva, Lidia N.; Powell, David H.

    2000-01-01

    GC-MS on the Viking 1976 Mars missions did not detect organic molecules on the Martian surface, even those expected from meteorite bombardment. This result suggested that the Martian regolith might hold a potent oxidant that converts all organic molecules to carbon dioxide rapidly relative to the rate at which they arrive. This conclusion is influencing the design of Mars missions. We reexamine this conclusion in light of what is known about the oxidation of organic compounds generally and the nature of organics likely to come to Mars via meteorite. We conclude that nonvolatile salts of benzenecarboxylic acids, and perhaps oxalic and acetic acid, should be metastable intermediates of meteoritic organics under oxidizing conditions. Salts of these organic acids would have been largely invisible to GC-MS. Experiments show that one of these, benzenehexacarboxylic acid (mellitic acid), is generated by oxidation of organic matter known to come to Mars, is rather stable to further oxidation, and would not have been easily detected by the Viking experiments. Approximately 2 kg of meteorite-derived mellitic acid may have been generated per m2 of Martian surface over 3 billion years. How much remains depends on decomposition rates under Martian conditions. As available data do not require that the surface of Mars be very strongly oxidizing, some organic molecules might be found near the surface of Mars, perhaps in amounts sufficient to be a resource. Missions should seek these and recognize that these complicate the search for organics from entirely hypothetical Martian life. PMID:10706606

  6. The missing organic molecules on Mars

    NASA Technical Reports Server (NTRS)

    Benner, S. A.; Devine, K. G.; Matveeva, L. N.; Powell, D. H.

    2000-01-01

    GC-MS on the Viking 1976 Mars missions did not detect organic molecules on the Martian surface, even those expected from meteorite bombardment. This result suggested that the Martian regolith might hold a potent oxidant that converts all organic molecules to carbon dioxide rapidly relative to the rate at which they arrive. This conclusion is influencing the design of Mars missions. We reexamine this conclusion in light of what is known about the oxidation of organic compounds generally and the nature of organics likely to come to Mars via meteorite. We conclude that nonvolatile salts of benzenecarboxylic acids, and perhaps oxalic and acetic acid, should be metastable intermediates of meteoritic organics under oxidizing conditions. Salts of these organic acids would have been largely invisible to GC-MS. Experiments show that one of these, benzenehexacarboxylic acid (mellitic acid), is generated by oxidation of organic matter known to come to Mars, is rather stable to further oxidation, and would not have been easily detected by the Viking experiments. Approximately 2 kg of meteorite-derived mellitic acid may have been generated per m(2) of Martian surface over 3 billion years. How much remains depends on decomposition rates under Martian conditions. As available data do not require that the surface of Mars be very strongly oxidizing, some organic molecules might be found near the surface of Mars, perhaps in amounts sufficient to be a resource. Missions should seek these and recognize that these complicate the search for organics from entirely hypothetical Martian life.

  7. Conformational dynamics of peptide T molecule

    NASA Astrophysics Data System (ADS)

    Akverdieva, Gulnare; Godjayev, Niftali; Akyuz, Sevim

    2002-05-01

    Using a method of the theoretical conformational analysis, a conformational dynamics of the side chains of the amino acid residues of peptide T, a competitor of the human immuno-deficiency virus in the binding to human T cells, was investigated. For this purpose, the conformational maps of the potential surfaces were constructed over the angles of the side chains for the preferable conformations of peptide T molecule. Permissible deviations of these angles from the optimal values were determined. It has been found that the angles of the side chains of the amino acid residues involved in physiologically active fragment Thr4-Thr8 are more rigid than in the other segment of the molecule. This fact confirms the existence of such a regular structure as β-turn revealed previously in studies of the spatial structure of the peptide T molecule.

  8. Asparagusic acid.

    PubMed

    Mitchell, Stephen C; Waring, Rosemary H

    2014-01-01

    Asparagusic acid (1,2-dithiolane-4-carboxylic acid) is a simple sulphur-containing 5-membered heterocyclic compound that appears unique to asparagus, though other dithiolane derivatives have been identified in non-food species. This molecule, apparently innocuous toxicologically to man, is the most probable culprit responsible for the curious excretion of odorous urine following asparagus ingestion. The presence of the two adjacent sulphur atoms leads to an enhanced chemical reactivity, endowing it with biological properties including the ability to substitute potentially for α-lipoic acid in α-keto-acid oxidation systems. This brief review collects the scattered data available in the literature concerning asparagusic acid and highlights its properties, intermediary metabolism and exploratory applications.

  9. Asparagusic acid.

    PubMed

    Mitchell, Stephen C; Waring, Rosemary H

    2014-01-01

    Asparagusic acid (1,2-dithiolane-4-carboxylic acid) is a simple sulphur-containing 5-membered heterocyclic compound that appears unique to asparagus, though other dithiolane derivatives have been identified in non-food species. This molecule, apparently innocuous toxicologically to man, is the most probable culprit responsible for the curious excretion of odorous urine following asparagus ingestion. The presence of the two adjacent sulphur atoms leads to an enhanced chemical reactivity, endowing it with biological properties including the ability to substitute potentially for α-lipoic acid in α-keto-acid oxidation systems. This brief review collects the scattered data available in the literature concerning asparagusic acid and highlights its properties, intermediary metabolism and exploratory applications. PMID:24099657

  10. Linking ultracold polar molecules.

    PubMed

    Avdeenkov, A V; Bohn, John L

    2003-01-31

    We predict that pairs of polar molecules can be weakly bound together in an ultracold environment, provided that a dc electric field is present. The field that links the molecules together also strongly influences the basic properties of the resulting dimer, such as its binding energy and predissociation lifetime. Because of their long-range character, these dimers will be useful in disentangling cold collision dynamics of polar molecules. As an example, we estimate the microwave photoassociation yield for OH-OH cold collisions.

  11. Interlocked molecules: Aqueous assembly

    NASA Astrophysics Data System (ADS)

    Bai, Linyi; Zhao, Yanli

    2015-12-01

    The quantitative self-assembly of mechanically interlocked molecules in water, instead of organic solvents, opens up the possibility of such systems being used in a biological context where their functions can be interfaced with biomolecular systems.

  12. Single-Molecule Enzymology

    SciTech Connect

    Xie, Xiaoliang; Lu, H PETER.

    1999-06-04

    Viewing a movie of an enzyme molecule made from molecular dynamics (MD) simulation, we see incredible details of molecular motions, be it a change of the conformation or the action of a chemical reaction.

  13. Of Molecules and Models.

    ERIC Educational Resources Information Center

    Brinner, Bonnie

    1992-01-01

    Presents an activity in which models help students visualize both the DNA process and transcription. After constructing DNA, RNA messenger, and RNA transfer molecules; students model cells, protein synthesis, codons, and RNA movement. (MDH)

  14. How Acidic Is Carbonic Acid?

    PubMed

    Pines, Dina; Ditkovich, Julia; Mukra, Tzach; Miller, Yifat; Kiefer, Philip M; Daschakraborty, Snehasis; Hynes, James T; Pines, Ehud

    2016-03-10

    Carbonic, lactic, and pyruvic acids have been generated in aqueous solution by the transient protonation of their corresponding conjugate bases by a tailor-made photoacid, the 6-hydroxy-1-sulfonate pyrene sodium salt molecule. A particular goal is to establish the pK(a) of carbonic acid H2CO3. The on-contact proton transfer (PT) reaction rate from the optically excited photoacid to the carboxylic bases was derived, with unprecedented precision, from time-correlated single-photon-counting measurements of the fluorescence lifetime of the photoacid in the presence of the proton acceptors. The time-dependent diffusion-assisted PT rate was analyzed using the Szabo-Collins-Kimball equation with a radiation boundary condition. The on-contact PT rates were found to follow the acidity order of the carboxylic acids: the stronger was the acid, the slower was the PT reaction to its conjugate base. The pK(a) of carbonic acid was found to be 3.49 ± 0.05 using both the Marcus and Kiefer-Hynes free energy correlations. This establishes H2CO3 as being 0.37 pK(a) units stronger and about 1 pK(a) unit weaker, respectively, than the physiologically important lactic and pyruvic acids. The considerable acid strength of intact carbonic acid indicates that it is an important protonation agent under physiological conditions. PMID:26862781

  15. Striking similarities are exhibited by two small Epstein-Barr virus-encoded ribonucleic acids and the adenovirus-associated ribonucleic acids VAI and VAII

    SciTech Connect

    Rosa, M.D.; Gottlieb, E.; Lerner, M.R.; Steitz, J.A.

    1981-09-01

    The nucleotide sequence of the region of the Epstein-Barr virus genome that specified two small ribonucleic acids (RNAs), EBER 1 and EBER 2, has been determined. Both of these RNAs are encoded by the right-hand 1,000 base pairs of the EcoRI J fragment of EBV deoxyribonucleic acid. EBER 1 is 166 (167) nucleotides long and EBER 2 is 172 +- 1 nucleotides long; the heterogeneity resides at the 3' termini. The EBER genes are separated by 161 base pairs and are transcribed from the same deoxyribonucleic acid strand. In vitro, both EBER genes can be transcribed by RNA polymerase III; sequences homologous to previously identified RNA polymerase III intragenic transcription control regions are present. Striking similarities are therefore apparent both between the EBERs and the two adenovirus-associated RNAs, VAI and VAII, and between the regions of the two viral genomes that specify these small RNAs. We have shown that VAII RNA as well as VAI RNA and the EBERs exist in ribonucleoprotein complexes which are precipitable by anti-La antibodies associated with systemic lupus erythematosus. Finally the authors have demonstrated that the binding of protein(s) from uninfected cells confers antigenicity on each of the four virus-encoded small RNAs.

  16. Newly detected molecules in dense interstellar clouds.

    PubMed

    Irvine, W M; Avery, L W; Friberg, P; Matthews, H E; Ziurys, L M

    1988-01-01

    The last year or so has seen the identification of several new interstellar molecules, including C2S, C3S, C5H, C6H, and (probably) HC2CHO in the cold, dark cloud TMC-1; and the discovery of the first interstellar phosphorous-containing molecule, PN, in the Orion "plateau" source. Further interesting results include the observations of 13C3H2 and C3HD, and the first detection of HCOOH (formic acid) in a cold cloud.

  17. The origin of life. [genetically important molecules

    NASA Technical Reports Server (NTRS)

    Horowitz, N. H.; Hubbard, J. S.

    1974-01-01

    Research in the areas of precambrian paleontology, chemical evolution of genetically important monomers, prebiotic dehydration-condensation reactions, organic compounds in meteorites and interstellar space, and biological exploration of the planets is summarized. Fossils in precambrian cherts and findings of eukaryotic cells are described, and recent investigations of prebiotic conditions, energy sources, and starting materials for genetic molecules are outlined. Studies of homogeneous and heterogeneous dehydrations and of nonaqueous thermal dehydrations are described. The detection of amino acids, purines, and pyrimidines in meteorites and of biologically significant molecules in interstellar clouds is discussed, as well as the possibilities of life on Jupiter, Mars, and Titan.

  18. Photochemistry of interstellar molecules

    NASA Technical Reports Server (NTRS)

    Stief, L. J.

    1971-01-01

    The photochemistry of two diatomic and eight polyatomic molecules is discussed quantitatively. For an interstellar molecule, the lifetime against photodecomposition depends upon the absorption cross section, the quantum yield or probability of dissociation following photon absorption, and the interstellar radiation field. The constant energy density of Habing is used for the unobserved regions of interstellar radiation field, and the field in obscuring clouds is estimated by combining the constant flux with the observed interstellar extinction curve covering the visible and ultraviolet regions. Lifetimes against photodecomposition in the unobscured regions and as a function of increasing optical thickness in obscuring clouds are calculated for the ten species. The results show that, except for CO, all the molecules have comparable lifetimes of less than one hundred years. Thus they can exist only in dense clouds and can never have been exposed to the unobscured radiation. The calculations further show that the lifetimes in clouds of moderate opacity are of the order of one million years.

  19. MOLECULES IN {eta} CARINAE

    SciTech Connect

    Loinard, Laurent; Menten, Karl M.; Guesten, Rolf; Zapata, Luis A.; Rodriguez, Luis F.

    2012-04-10

    We report the detection toward {eta} Carinae of six new molecules, CO, CN, HCO{sup +}, HCN, HNC, and N{sub 2}H{sup +}, and of two of their less abundant isotopic counterparts, {sup 13}CO and H{sup 13}CN. The line profiles are moderately broad ({approx}100 km s{sup -1}), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO{sup +} do not appear to be underabundant in {eta} Carinae. On the other hand, molecules containing nitrogen or the {sup 13}C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of {eta} Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  20. Atomic branching in molecules

    NASA Astrophysics Data System (ADS)

    Estrada, Ernesto; Rodríguez-Velázquez, Juan A.; Randić, Milan

    A graph theoretic measure of extended atomic branching is defined that accounts for the effects of all atoms in the molecule, giving higher weight to the nearest neighbors. It is based on the counting of all substructures in which an atom takes part in a molecule. We prove a theorem that permits the exact calculation of this measure based on the eigenvalues and eigenvectors of the adjacency matrix of the graph representing a molecule. The definition of this measure within the context of the Hückel molecular orbital (HMO) and its calculation for benzenoid hydrocarbons are also studied. We show that the extended atomic branching can be defined using any real symmetric matrix, as well as any Hermitian (self-adjoint) matrix, which permits its calculation in topological, geometrical, and quantum chemical contexts.

  1. Sol-gel method for encapsulating molecules

    DOEpatents

    Brinker, C. Jeffrey; Ashley, Carol S.; Bhatia, Rimple; Singh, Anup K.

    2002-01-01

    A method for encapsulating organic molecules, and in particular, biomolecules using sol-gel chemistry. A silica sol is prepared from an aqueous alkali metal silicate solution, such as a mixture of silicon dioxide and sodium or potassium oxide in water. The pH is adjusted to a suitably low value to stabilize the sol by minimizing the rate of siloxane condensation, thereby allowing storage stability of the sol prior to gelation. The organic molecules, generally in solution, is then added with the organic molecules being encapsulated in the sol matrix. After aging, either a thin film can be prepared or a gel can be formed with the encapsulated molecules. Depending upon the acid used, pH, and other processing conditions, the gelation time can be from one minute up to several days. In the method of the present invention, no alcohols are generated as by-products during the sol-gel and encapsulation steps. The organic molecules can be added at any desired pH value, where the pH value is generally chosen to achieve the desired reactivity of the organic molecules. The method of the present invention thereby presents a sufficiently mild encapsulation method to retain a significant portion of the activity of the biomolecules, compared with the activity of the biomolecules in free solution.

  2. Single Molecule Manipulation

    NASA Astrophysics Data System (ADS)

    Kiang, Ching-Hwa

    2011-10-01

    Single-molecule manipulation studies open a door for a close-up investigation of complex biological interactions at the molecular level. In these studies, single biomolecules are pulled while their force response is being monitored. The process is often nonequilibrium, and interpretation of the results has been challenging. We used the atomic force microscope to pull proteins and DNA, and determined the equilibrium properties of the molecules using the recently derived nonequilibrium work theorem. I will present applications of the technique in areas ranging from fundamental biological problems such as DNA mechanics, to complex medical processes such as the mechanical activation of von Willebrand Factor, a key protein in blood coagulation.

  3. Plasmonic nanostructures: artificial molecules.

    PubMed

    Wang, Hui; Brandl, Daniel W; Nordlander, Peter; Halas, Naomi J

    2007-01-01

    This Account describes a new paradigm for the relationship between the geometry of metallic nanostructures and their optical properties. While the interaction of light with metallic nanoparticles is determined by their collective electronic or plasmon response, a compelling analogy exists between plasmon resonances of metallic nanoparticles and wave functions of simple atoms and molecules. Based on this insight, an entire family of plasmonic nanostructures, artificial molecules, has been developed whose optical properties can be understood within this picture: nanoparticles (nanoshells, nanoeggs, nanomatryushkas, nanorice), multi-nanoparticle assemblies (dimers, trimers, quadrumers), and a nanoparticle-over-metallic film, an electromagnetic analog of the spinless Anderson model. PMID:17226945

  4. Spin transport in molecules studied by Fe3O4/molecule nanoparticles

    NASA Astrophysics Data System (ADS)

    Yue, F. J.; Wang, S.; Wu, D.

    2013-05-01

    In this work, we synthesize single molecular layer coated Fe3O4 nanoparticles to form the network of the molecular junction spin valves. The Fe3O4 nanoparticles chemically bond with molecules without any physically absorbed molecules, leading to one monolayer molecule coated on nanoparticles. The magnetoresistance (MR) of cold-pressed Fe3O4/oleic acid nanoparticles is more than two times larger than bare Fe3O4 nanoparticles, indicating weaker spin scattering in molecules. Furthermore, the MR ratio is as high as ˜21 % at room temperature for Fe3O4/alkane molecule nanoparticles. Interestingly, even though the resistance spans about two decades as the alkane molecular length varies from 0.7 to 2.5 nm, the MR ratio stays approximately constant. This molecular length independent spin valve MR, originated from the weaker hyperfine interaction strength of the σ-electrons in alkane molecules, entails room-temperature spin-conserving transport in molecular materials. Using the size of ˜500 nm Fe3O4 nanoparticles, a large MR is achieved in a relatively low magnetic field. This feature opens a door for the development of future spin-based molecular electronics. Moreover, spin injection at the interface of Fe3O4/stearic acid molecule is investigated in a comparative study between Fe3O4 nanoparticles chemically bonded (ChemNPs) and physically absorbed (PhyNPs) molecules. A MR of 12 % at room temperature is observed in ChemNPs, in sharp contrast to the zero MR ratio in PhyNPs, reflecting that the chemical bonding is crucial for spin injection. These results show that the hybrid nanoparticles provide a simple approach to study the spin transport in molecules.

  5. Controllably local gene delivery mediated by polyelectrolyte multilayer films assembled from gene-loaded nanopolymersomes and hyaluronic acid

    PubMed Central

    Teng, Wei; Wang, Qinmei; Chen, Ying; Huang, Hongzhang

    2014-01-01

    To explore a spatiotemporally controllable gene delivery system with high efficiency and safety, polyelectrolyte multilayer (PEM) films were constructed on titanium or quartz substrates via layer-by-layer self-assembly technique by using plasmid deoxyribonucleic acid-loaded lipopolysaccharide–amine nanopolymersomes (pNPs) as polycations and hyaluronic acid (HA) as polyanions. pNPs were chosen because they have high transfection efficiency (>95%) in mesenchymal stem cells (MSCs) and induce significant angiogenesis in zebrafish in conventional bolus transfection. The assembly process of PEM films was confirmed by analyses of quartz crystal microbalance with dissipation, X-ray photoelectron spectroscopy, infrared, contact angle, and zeta potential along with atomic force microscopy observation. Quartz crystal microbalance with dissipation analysis reveals that this film grows in an exponential mode, pNPs are the main contributor to the film mass, and the film mass can be modulated in a relatively wide range (1.0–29 μg/cm2) by adjusting the deposition layer number. Atomic force microscopy observation shows that the assembly leads to the formation of a patterned film with three-dimensional tree-like nanostructure, where the branches are composed of beaded chains (pNP beads are strung on HA molecular chains), and the incorporated pNPs keep structure intact. In vitro release experiment shows that plasmid deoxyribonucleic acid can be gradually released from films over 14 days, and the released plasmid deoxyribonucleic acid exists in a complex form. In vitro cell experiments demonstrate that PEM films can enhance the adhesion and proliferation of MSCs and efficiently transfect MSCs in situ in vitro for at least 4 days. Our results suggest that a (pNPs/HA)n system can mediate efficient transfection in stem cells in a spatially and temporally controllable pattern, highlighting its huge potential in local gene therapy. PMID:25378927

  6. Boric acid catalyzed chemoselective esterification of alpha-hydroxycarboxylic acids.

    PubMed

    Houston, Todd A; Wilkinson, Brendan L; Blanchfield, Joanne T

    2004-03-01

    Boric acid catalyzes the selective esterification of alpha-hydroxycarboxylic acids without causing significant esterification to occur with other carboxylic acids. The procedure is simple, high-yielding, and applicable to the esterification of alpha-hydroxy carboxylates in the presence of other carboxylic acids including beta-hydroxyacids within the same molecule. [reaction: see text

  7. Modelling water molecules inside cyclic peptide nanotubes

    NASA Astrophysics Data System (ADS)

    Tiangtrong, Prangsai; Thamwattana, Ngamta; Baowan, Duangkamon

    2016-03-01

    Cyclic peptide nanotubes occur during the self-assembly process of cyclic peptides. Due to the ease of synthesis and ability to control the properties of outer surface and inner diameter by manipulating the functional side chains and the number of amino acids, cyclic peptide nanotubes have attracted much interest from many research areas. A potential application of peptide nanotubes is their use as artificial transmembrane channels for transporting ions, biomolecules and waters into cells. Here, we use the Lennard-Jones potential and a continuum approach to study the interaction of a water molecule in a cyclo[(- D-Ala- L-Ala)_4-] peptide nanotube. Assuming that each unit of a nanotube comprises an inner and an outer tube and that a water molecule is made up of a sphere of two hydrogen atoms uniformly distributed over its surface and a single oxygen atom at the centre, we determine analytically the interaction energy of the water molecule and the peptide nanotube. Using this energy, we find that, independent of the number of peptide units, the water molecule will be accepted inside the nanotube. Once inside the nanotube, we show that a water molecule prefers to be off-axis, closer to the surface of the inner nanotube. Furthermore, our study of two water molecules inside the peptide nanotube supports the finding that water molecules form an array of a 1-2-1-2 file inside peptide nanotubes. The theoretical study presented here can facilitate thorough understanding of the behaviour of water molecules inside peptide nanotubes for applications, such as artificial transmembrane channels.

  8. Algebraic theory of molecules

    NASA Technical Reports Server (NTRS)

    Iachello, Franco

    1995-01-01

    An algebraic formulation of quantum mechanics is presented. In this formulation, operators of interest are expanded onto elements of an algebra, G. For bound state problems in nu dimensions the algebra G is taken to be U(nu + 1). Applications to the structure of molecules are presented.

  9. Diversity in Biological Molecules

    ERIC Educational Resources Information Center

    Newbury, H. John

    2010-01-01

    One of the striking characteristics of fundamental biological processes, such as genetic inheritance, development and primary metabolism, is the limited amount of variation in the molecules involved. Natural selective pressures act strongly on these core processes and individuals carrying mutations and producing slightly sub-optimal versions of…

  10. Halley's polymeric organic molecules

    NASA Technical Reports Server (NTRS)

    Huebner, W. F.; Boice, D. C.; Korth, A.

    1989-01-01

    The detection of polymeric organic compounds in the mass spectrum of Comet Halley obtained with the Positive Ion Cluster Composition analyzer on Giotto are examined. It is found that, in addition to polyoxymethylene, other polymers and complex molecules may exist in the comet. It is suggested that polymerized hydrogen cyanide may be a source for the observed CN and NH2 jets.

  11. Mighty Molecule Models

    ERIC Educational Resources Information Center

    Brown, Tom; Rushton, Greg; Bencomo, Marie

    2008-01-01

    As part of the SMATHematics Project: The Wonder of Science, The Power of Mathematics--a collaborative partnership between Kennesaw State University and two local school districts, fifth graders had the opportunity to puzzle out chemical formulas of propane, methanol, and other important molecules. In addition, they explored properties that…

  12. OMG: Open Molecule Generator

    PubMed Central

    2012-01-01

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck. PMID:22985496

  13. OMG: Open Molecule Generator.

    PubMed

    Peironcely, Julio E; Rojas-Chertó, Miguel; Fichera, Davide; Reijmers, Theo; Coulier, Leon; Faulon, Jean-Loup; Hankemeier, Thomas

    2012-01-01

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck. PMID:22985496

  14. OMG: Open Molecule Generator.

    PubMed

    Peironcely, Julio E; Rojas-Chertó, Miguel; Fichera, Davide; Reijmers, Theo; Coulier, Leon; Faulon, Jean-Loup; Hankemeier, Thomas

    2012-09-17

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.

  15. Isolation and Characterization of Simian Virus 40 Ribonucleic Acid

    PubMed Central

    Weinberg, R. A.; Warnaar, S. O.; Winocour, E.

    1972-01-01

    Deoxyribonucleic acid-ribonucleic acid (RNA) hybridization in formamide was used to isolate simian virus 40-specific RNA. Early in the lytic cycle, a 19S viral RNA species was observed. Late in the lytic cycle, 16S and 19S viral species were found. The 16S and 19S species of viral RNA were localized in the cytoplasm. High-molecular-weight heterogeneous RNA, containing viral sequences, was isolated from the nuclear fraction of infected cells late in the lytic cycle. This RNA may contain non-viral sequences linked to viral sequences. The formamide hybridization technique can be used to isolate intact late lytic viral RNA which is at least 99% pure. PMID:4342237

  16. Bacterial invasion reconstructed molecule by molecule

    SciTech Connect

    Werner, James H

    2009-01-01

    We propose to visualize the initial stages of bacterial infection of a human host cell with unmatched spatial and temporal resolution. This work will develop a new capability for the laboratory (super-resolution optical imaging), will test unresolved scientific hypotheses regarding host-pathogen interaction dynamics, and leverages state of the art 3D molecular tracking instrumentation developed recently by our group. There is much to be gained by applying new single molecule tools to the important and familiar problem of pathogen entry into a host cell. For example, conventional fluorescence microscopy has identified key host receptors, such as CD44 and {alpha}5{beta}1 integrin, that aggregate near the site of Salmonella typhimurium infection of human cells. However, due to the small size of the bacteria ({approx} 2 {micro}m) and the diffraction of the emitted light, one just sees a fluorescent 'blob' of host receptors that aggregate at the site of attachment, making it difficult to determine the exact number of receptors present or whether there is any particular spatial arrangement of the receptors that facilitates bacterial adhesion/entry. Using newly developed single molecule based super-resolution imaging methods, we will visualize how host receptors are directed to the site of pathogen adhesion and whether host receptors adopt a specific spatial arrangement for successful infection. Furthermore, we will employ our 3D molecular tracking methods to follow the injection of virulence proteins, or effectors, into the host cell by the pathogen Type III secretion system (TTSS). We expect these studies to provide mechanistic insights into the early events of pathogen infection that have here-to-fore been technically beyond our reach. Our Research Goals are: Goal 1--Construct a super-resolution fluorescence microscope and use this new capability to image the spatial distribution of different host receptors (e.g. CD44, as {alpha}5{beta}1 integrin) at the point of

  17. Molecules for Fluorescence Detection of Specific Chemicals

    NASA Technical Reports Server (NTRS)

    Fedor, Steve

    2008-01-01

    A family of fluorescent dye molecules has been developed for use in on-off fluorescence detection of specific chemicals. By themselves, these molecules do not fluoresce. However, when exposed to certain chemical analytes in liquid or vapor forms, they do fluoresce (see figure). These compounds are amenable to fixation on or in a variety of substrates for use in fluorescence-based detection devices: they can be chemically modified to anchor them to porous or non-porous solid supports or can be incorporated into polymer films. Potential applications for these compounds include detection of chemical warfare agents, sensing of acidity or alkalinity, and fluorescent tagging of proteins in pharmaceutical research and development. These molecules could also be exploited for use as two-photon materials for photodynamic therapy in the treatment of certain cancers and other diseases. A molecule in this family consists of a fluorescent core (such as an anthracene or pyrene) attached to two end groups that, when the dye is excited by absorption of light, transfer an electron to the core, thereby quenching the fluorescence. The end groups can be engineered so that they react chemically with certain analytes. Upon reaction, electrons on the end groups are no longer available for transfer to the core and, consequently, the fluorescence from the core is no longer quenched. The chemoselectivity of these molecules can be changed by changing the end groups. For example, aniline end groups afford a capability for sensing acids or acid halides (including those contained in chemical warfare agents). Pyridine or bipyridyl end groups would enable sensing of metal ions. Other chemicals that can be selectively detected through suitable choice of end groups include glucose and proteins. Moreover, the fluorescent cores can be changed to alter light-absorption and -emission characteristics: anthracene cores fluoresce at wavelengths around 500 nm, whereas perylene cores absorb and emit at

  18. Langmuir Films of Chiral Molecules on Mercury

    SciTech Connect

    Tamam, L.; Menahem, T; Mastai, Y; Sloutskin, E; Yefet, S; Deustch, M

    2009-01-01

    Homo- and heterochiral Langmuir films of a chiral derivative of stearic acid are studied in situ on the surface of liquid mercury as a function of surface coverage by surface tensiometry and surface-specific synchrotron X-ray diffraction and reflectivity. A transition from a phase of surface-parallel molecules to a phase of standing-up molecules is found. The former shows no surface-parallel long-range order. The standing-up phase of both homochiral and heterochiral compositions exhibit long-range order. However, the former has an oblique unit cell with parallel molecular planes, and the later has a centered rectangular unit cell with a herringbone molecular packing. For both cases, the standing-up molecules are tilted by 44 from the surface normal and pack at a density of 19.5 Angstroms2/molecule in the plane normal to the molecular long axis. Important differences are found, and discussed, between this behavior and that of a Langmuir film of the nonchiral stearic acid on mercury.

  19. Single-molecule electrophoresis

    SciTech Connect

    Castro, A.; Shera, E.B.

    1995-09-15

    A novel method for the detection and identification of single molecules in solution has been devised, computer simulated, and experimentally achieved. The technique involves the determination of electrophoretic velocities by measuring the time required for individual molecules to travel a fixed distance between two laser beams. Computer simulations of the process were performed before-hand in order to estimate the experimental feasibility of the method and to determine the optimum values for the various experimental parameters. Examples of the use of the technique for the ultrasensitive detection and identification of rhodamine-6G, a mixture of DNA restriction fragments, and a mixture of proteins in aqueous solution are presented. 20 refs., 8 figs.

  20. Cometary Parent Molecules

    NASA Astrophysics Data System (ADS)

    Feldman, Paul

    1990-12-01

    We propose to use HRS observations of a suitable target-of-opportunity comet to study two outstanding problems related to the composition of the volatile component of the cometary nucleus. These problems concern two species, CO and S2, which have been observed in the cometary coma and identified as "parent" molecules sublimating directly from the nucleus. Both of these molecules have their principal fluorescent emissions in the vaccuum ultraviolet. The high spectral resolution will allow the determination of the rotational temperature of CO, which is diagnostic of the source temperature and the excitation mechanism of the observed emission. The determination of the abundance of both CO and S2 in the primarily water ice of the nucleus can serve to constrain current models of comet formation in the primordial solar nebula.

  1. Small molecule annotation for the Protein Data Bank.

    PubMed

    Sen, Sanchayita; Young, Jasmine; Berrisford, John M; Chen, Minyu; Conroy, Matthew J; Dutta, Shuchismita; Di Costanzo, Luigi; Gao, Guanghua; Ghosh, Sutapa; Hudson, Brian P; Igarashi, Reiko; Kengaku, Yumiko; Liang, Yuhe; Peisach, Ezra; Persikova, Irina; Mukhopadhyay, Abhik; Narayanan, Buvaneswari Coimbatore; Sahni, Gaurav; Sato, Junko; Sekharan, Monica; Shao, Chenghua; Tan, Lihua; Zhuravleva, Marina A

    2014-01-01

    The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors.

  2. Small molecule annotation for the Protein Data Bank.

    PubMed

    Sen, Sanchayita; Young, Jasmine; Berrisford, John M; Chen, Minyu; Conroy, Matthew J; Dutta, Shuchismita; Di Costanzo, Luigi; Gao, Guanghua; Ghosh, Sutapa; Hudson, Brian P; Igarashi, Reiko; Kengaku, Yumiko; Liang, Yuhe; Peisach, Ezra; Persikova, Irina; Mukhopadhyay, Abhik; Narayanan, Buvaneswari Coimbatore; Sahni, Gaurav; Sato, Junko; Sekharan, Monica; Shao, Chenghua; Tan, Lihua; Zhuravleva, Marina A

    2014-01-01

    The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors. PMID:25425036

  3. Photonic Molecule Lasers Revisited

    NASA Astrophysics Data System (ADS)

    Gagnon, Denis; Dumont, Joey; Déziel, Jean-Luc; Dubé, Louis J.

    2014-05-01

    Photonic molecules (PMs) formed by coupling two or more optical resonators are ideal candidates for the fabrication of integrated microlasers, photonic molecule lasers. Whereas most calculations on PM lasers have been based on cold-cavity (passive) modes, i.e. quasi-bound states, a recently formulated steady-state ab initio laser theory (SALT) offers the possibility to take into account the spectral properties of the underlying gain transition, its position and linewidth, as well as incorporating an arbitrary pump profile. We will combine two theoretical approaches to characterize the lasing properties of PM lasers: for two-dimensional systems, the generalized Lorenz-Mie theory will obtain the resonant modes of the coupled molecules in an active medium described by SALT. Not only is then the theoretical description more complete, the use of an active medium provides additional parameters to control, engineer and harness the lasing properties of PM lasers for ultra-low threshold and directional single-mode emission. We will extend our recent study and present new results for a number of promising geometries. The authors acknowledge financial support from NSERC (Canada) and the CERC in Photonic Innovations of Y. Messaddeq.

  4. The Chemical Structure and Acid Deterioration of Paper.

    ERIC Educational Resources Information Center

    Hollinger, William K., Jr.

    1984-01-01

    Describes the chemical structure of paper, including subatomic particles, atoms and molecules, and the forces that bond atoms into molecules, molecules into chains, chains into sheets, and sheets into layers. Acid is defined, and the deleterious role of acid in breaking the forces that bond atoms into molecules is detailed. (EJS)

  5. Isomerization reactions on single adsorbed molecules.

    PubMed

    Morgenstern, Karina

    2009-02-17

    Molecular switches occur throughout nature. In one prominent example, light induces the isomerization of retinal from the compact 11-cis form to the elongated all-trans form, a conversion that triggers the transformation of light into a neural impulse in the eye. Applying these natural principles to synthetic systems offers a promising way to construct smaller and faster nanoelectronic devices. In such systems, electronic switches are essential components for storage and logical operations. The development of molecular switches on the single-molecule level would represent a major step toward incorporating molecules as building units into nanoelectronic circuits. Molecular switches must be both reversible and bistable. To meet these requirements, a molecule must have at least two different thermally stable forms and a way to repeatedly interconvert between those forms based on changes in light, heat, pressure, magnetic or electric fields, pH, mechanical forces, or electric currents. The conversion should be connected to a measurable change in electronic, optical, magnetic, or mechanical properties. Because isomers can differ significantly in physical and chemical properties, isomerization could serve as a molecular switching mechanism. Integration of molecular switches into larger circuits will probably require arranging them on surfaces, which will require a better understanding of isomerization reactions in these environments. In this Account, we describe our scanning tunneling microscopy studies of the isomerization of individual molecules adsorbed on metal surfaces. Investigating chlorobenzene and azobenzene derivatives on the fcc(111) faces of Ag, Cu, and Au, we explored the influence of substituents and the substrate on the excitation mechanism of the isomerization reaction induced by inelastically tunneling electrons. We achieved an irreversible configurational (cis-trans) isomerization of individual 4-dimethyl-amino-azobenzene-4-sulfonic acid molecules on Au

  6. Replica amplification of nucleic acid arrays

    DOEpatents

    Church, George M.

    2002-01-01

    A method of producing a plurality of a nucleic acid array, comprising, in order, the steps of amplifying in situ nucleic acid molecules of a first randomly-patterned, immobilized nucleic acid array comprising a heterogeneous pool of nucleic acid molecules affixed to a support, transferring at least a subset of the nucleic acid molecules produced by such amplifying to a second support, and affixing the subset so transferred to the second support to form a second randomly-patterned, immobilized nucleic acid array, wherein the nucleic acid molecules of the second array occupy positions that correspond to those of the nucleic acid molecules from which they were amplified on the first array, so that the first array serves as a template to produce a plurality, is disclosed.

  7. Laboratory studies of astrophysical molecules

    NASA Astrophysics Data System (ADS)

    Wang, Haiyan

    There is growing evidence that the molecules necessary for the evolution of life on earth arrived from the interstellar medium. The study of these molecules is therefore of great current interest. Two major types of signals from interstellar space, so-called unidentified interstellar infrared emission bands and the diffuse interstellar absorption bands, have intrigued and puzzled astrochemists for decades. This work has been concentrated on how to contribute to an understanding of the origins of these perplexing signals from space and help identify other molecules that may exist in outer space. Matrix isolation spectroscopy (infrared and ultraviolet-visible) combined with theoretical calculations has been employed throughout this research. Fourier transform infrared absorption spectroscopic measurements, aided by theoretical calculations and 13 C-isotope shifts, have led to the identification of eight heretofore unknown C n S m clusters: C 2 S, C 6 S, C 7 S, C 7 S 2 , C 9 S 2 , C 11 S 2 , C 13 S 2 , and C 15 S 2 . Infrared absorption studies of xenon polycarbon clusters aid in understanding the special electronic structure and reactivity of carbon clusters, which might be associated with the formation mechanism of Buckyball (C 60 ). Reaction of C3 with benzene and ammonia might be involved in the formation of more complex molecular structures, including polycyclic aromatic hydrocarbons (PAHs) and biomolecules such as the amino acids. High resolution vibrational and electronic spectra of neutral dibenzo [b,def]chrysene and its ions in 12 K argon matrices have been recorded. Spectral assignments were supported by high level theoretical calculations. A mixture of the neutral and ionic infrared spectra of dibenzo[b,def]chrysene resembles the unidentified IR bands in the reflection nebula NGC 7023. Anharmonic frequency calculations for neutral and cationic naphthalene, phenanthrene and anthracene using density functional theory have been carried out for the first time

  8. Watching single molecules dance

    NASA Astrophysics Data System (ADS)

    Mehta, Amit Dinesh

    Molecular motors convert chemical energy, from ATP hydrolysis or ion flow, into mechanical motion. A variety of increasingly precise mechanical probes have been developed to monitor and perturb these motors at the single molecule level. Several outstanding questions can be best approached at the single molecule level. These include: how far does a motor progress per energy quanta consumed? how does its reaction cycle respond to load? how many productive catalytic cycles can it undergo per diffusional encounter with its track? and what is the mechanical stiffness of a single molecule connection? A dual beam optical trap, in conjunction with in vitro ensemble motility assays, has been used to characterize two members of the myosin superfamily: muscle myosin II and chick brain myosin V. Both move the helical polymer actin, but myosin II acts in large ensembles to drive muscle contraction or cytokinesis, while myosin V acts in small numbers to transport vesicles. An optical trapping apparatus was rendered sufficiently precise to identify a myosin working stroke with 1nm or so, barring systematic errors such as those perhaps due to random protein orientations. This and other light microscopic motility assays were used to characterize myosin V: unlike myosin II this vesicle transport protein moves through many increments of travel while remaining strongly bound to a single actin filament. The step size, stall force, and travel distance of myosin V reveal a remarkably efficient motor capable of moving along a helical track for over a micrometer without significantly spiraling around it. Such properties are fully consistent with the putative role of an organelle transport motor, present in small numbers to maintain movement over long ranges relative to cellular size scales. The contrast between myosin II and myosin V resembles that between a human running on the moon and one walking on earth, where the former allows for faster motion when in larger ensembles but for less

  9. Neutron Nucleic Acid Crystallography.

    PubMed

    Chatake, Toshiyuki

    2016-01-01

    The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination. PMID:26227050

  10. Neutron Nucleic Acid Crystallography.

    PubMed

    Chatake, Toshiyuki

    2016-01-01

    The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

  11. Molecules in crystals

    NASA Astrophysics Data System (ADS)

    Spackman, Mark A.

    2013-04-01

    Hirshfeld surface analysis has developed from the serendipitous discovery of a novel partitioning of the crystal electron density into discrete molecular fragments, to a suite of computational tools used widely for the identification, analysis and discussion of intermolecular interactions in molecular crystals. The relationship between the Hirshfeld surface and very early ideas on the internal structure of crystals is outlined, and applications of Hirshfeld surface analysis are presented for three molecules of historical importance in the development of modern x-ray crystallography: hexamethylbenzene, hexamethylenetetramine and diketopiperazine.

  12. Ultra-cold molecule production.

    SciTech Connect

    Ramirez-Serrano, Jamie; Chandler, David W.; Strecker, Kevin; Rahn, Larry A.

    2005-12-01

    The production of Ultra-cold molecules is a goal of many laboratories through out the world. Here we are pursuing a unique technique that utilizes the kinematics of atomic and molecular collisions to achieve the goal of producing substantial numbers of sub Kelvin molecules confined in a trap. Here a trap is defined as an apparatus that spatially localizes, in a known location in the laboratory, a sample of molecules whose temperature is below one degree absolute Kelvin. Further, the storage time for the molecules must be sufficient to measure and possibly further cool the molecules. We utilize a technique unique to Sandia to form cold molecules from near mass degenerate collisions between atoms and molecules. This report describes the progress we have made using this novel technique and the further progress towards trapping molecules we have cooled.

  13. The Molecules of Life.

    ERIC Educational Resources Information Center

    Weinberg, Robert A.

    1985-01-01

    New advances in molecular biology have established a biotechnology industry and have changed ways people think about living things. In support of this theme, a discussion on historical development and current practice of gene cloning is presented. The role of nucleic acids, viruses, and therapeutic intervention is also considered. (DH)

  14. Melatonin: a multitasking molecule.

    PubMed

    Reiter, Russel J; Tan, Dun-Xian; Fuentes-Broto, Lorena

    2010-01-01

    Melatonin (N-acetyl-5-methoxytryptamine) has revealed itself as an ubiquitously distributed and functionally diverse molecule. The mechanisms that control its synthesis within the pineal gland have been well characterized and the retinal and biological clock processes that modulate the circadian production of melatonin in the pineal gland are rapidly being unravelled. A feature that characterizes melatonin is the variety of mechanisms it employs to modulate the physiology and molecular biology of cells. While many of these actions are mediated by well-characterized, G-protein coupled melatonin receptors in cellular membranes, other actions of the indole seem to involve its interaction with orphan nuclear receptors and with molecules, for example calmodulin, in the cytosol. Additionally, by virtue of its ability to detoxify free radicals and related oxygen derivatives, melatonin influences the molecular physiology of cells via receptor-independent means. These uncommonly complex processes often make it difficult to determine specifically how melatonin functions to exert its obvious actions. What is apparent, however, is that the actions of melatonin contribute to improved cellular and organismal physiology. In view of this and its virtual absence of toxicity, melatonin may well find applications in both human and veterinary medicine.

  15. Omega 3 (n-3) fatty acids down-regulate nuclear factor-kappa B (NF-κB) gene and blood cell adhesion molecule expression in patients with homozygous sickle cell disease.

    PubMed

    Daak, Ahmed A; Elderdery, Abozer Y; Elbashir, Leana M; Mariniello, Katia; Mills, Jeremy; Scarlett, Garry; Elbashir, Mustafa I; Ghebremeskel, Kebreab

    2015-06-01

    Chronic inflammation and reduced blood levels of omega-3 fatty acids (n-3) are known characteristics of sickle cell disease (SCD).The anti-inflammatory properties of n-3 fatty acids are well recognized. Omega-3 treated (n = 24), hydroxyurea (HU) treated (n = 18), and n-3 untreated (n=21) homozygous SCD patients (HbSS) and healthy (HbAA) controls (n = 25) matched for age (5-16 years), gender and socioeconomic status were studied. According to age (5-10) or (11-16) years, two or three capsules containing 277.8 mg docosahexaenoic (DHA) and 39.0mg eicosapentaenoic (EPA) or high oleic acid placebo (41%) were assigned to n-3 treated and n-3 untreated groups, respectively. Hydroxyurea treated group was on dosage more than 20 mg/kg/day. The effect of supplementation on systemic and blood cell markers of inflammation was investigated. The n-3 treated group had higher levels of DHA and EPA (p < 0.001) and lower white blood cell count and monocyte integrin (p < 0.05) compared with the n-3 untreated. No difference was detected between the two groups regarding C-reactive protein, granulocytes integrin and selectin, plasma tumour necrosis factor-α and interleukin-10. The n-3 treated group had lowered nuclear factor-kappa B (NF-κB) gene expression compared to n-3 untreated and HU treated groups (p < 0.05). This study provides evidence that supplementation with n-3 fatty acids may ameliorate inflammation and blood cell adhesion in patients with SCD.

  16. Molecules Best Paper Award 2013.

    PubMed

    McPhee, Derek J

    2013-02-05

    Molecules has started to institute a "Best Paper" award to recognize the most outstanding papers in the area of natural products, medicinal chemistry and molecular diversity published in Molecules. We are pleased to announce the second "Molecules Best Paper Award" for 2013.

  17. Complex molecules in galactic dust cores: Biologically interesting molecules and dust chemistry

    NASA Astrophysics Data System (ADS)

    Liu, Shen-Yuan

    2000-06-01

    The astronomical study of molecules has been an essential research field since the development of radio astronomy. Presently nearly 120 molecules have been identified in interstellar and circumstellar environments. The complexity of molecular species, and particularly organic molecules, that can be synthesized in the interstellar medium (ISM) leads to one interesting and important subfield in interstellar molecular studies, namely, the search and study for molecules of possible biological interest. Observationally, complex and most saturated molecules are observed exclusively toward compact hot, dense regions, often called ``hot cores'', in molecular clouds. To account for the observed amount of saturated organic molecules, interstellar dust particles play an important role. It has often been suggested that solid state reactions on grain surfaces provide an efficient way to synthesis saturated organic molecules. The objective of this study is to obtain observational data on biologically interesting molecules and to study important complex interstellar molecules. Since hot molecular cores are inherently compact, interferometric observations are therefore an ideal approach to study these sources. All our observations were all made with the Berkeley-Illinois-Maryland-Association (BIMA) Array. We conducted the first survey of formic acid (HCOOH) with an interferometric array, and identified at least three sources. HCOOH is found with column densities above 1015 cm-2 in these sources. The correlation between HCOOH and HCOOCH3 emission implies a surface chemistry origin of HCOOH. Details of the results are given in Chapter 2. Meanwhile, we continued to search for molecules of biological interest, namely urea, acetic acid, and glycine. In Chapter 3, the results of column density limits set by our observations are discussed. We have also investigated properties of individual hot molecular cores. It is very important to obtain the physical and chemical properties of these

  18. Origins of the handedness of biological molecules.

    PubMed

    Mason, S F

    1991-01-01

    Pasteur (1860) showed that many organic molecules form enantiomeric pairs with non-superposable mirror-image shapes, characterized by their oppositely signed optical rotation but otherwise apparently identical. Equal numbers of left-handed and right-handed molecules resulted from laboratory synthesis, whereas biosynthetic processes afforded only one of the two enantiomers, leading Pasteur to conclude that biosynthesis involves a chiral force. Fischer demonstrated (1890-1919) that functional biomolecules are composed specifically of the D-sugars and the L-amino acids and that the laboratory synthetic reactions of such molecules propagate with chiral stereoselectivity. Given a primordial enantiomer, biomolecular homochirality follows without the intervention of a chiral natural force, except prebiotically. Chiral forces known at the time were found to be even handed on a time and space average, exemplifying parity conservation (1927). The weak nuclear force, shown to violate parity (1956), was unified with electro-magnetism in the electroweak force (1970). Ab initio estimations including the chiral electroweak force indicate that the L-amino acids and the D-sugars are more stable than the corresponding enantiomers. The small energy difference between these enantiomeric pairs, with Darwinian reaction kinetics in a flow reactor, account for the choice of biomolecular handedness made when life began.

  19. Sulfuric acid as autocatalyst in the formation of sulfuric acid.

    PubMed

    Torrent-Sucarrat, Miquel; Francisco, Joseph S; Anglada, Josep M

    2012-12-26

    Sulfuric acid can act as a catalyst of its own formation. We have carried out a computational investigation on the gas-phase formation of H(2)SO(4) by hydrolysis of SO(3) involving one and two water molecules, and also in the presence of sulfuric acid and its complexes with one and two water molecules. The hydrolysis of SO(3) requires the concurrence of two water molecules, one of them acting as a catalyzer, and our results predict an important catalytic effect, ranging between 3 and 11 kcal·mol(-1) when the catalytic water molecule is substituted by a sulfuric acid molecule or one of its hydrates. In these cases, the reaction products are either bare sulfuric acid dimer or sulfuric acid dimer complexed with a water molecule. There are broad implications from these new findings. The results of the present investigation show that the catalytic effect of sulfuric acid in the SO(3) hydrolysis can be important in the Earth's stratosphere, in the heterogeneous formation of sulfuric acid and in the formation of aerosols, in H(2)SO(4) formation by aircraft engines, and also in understanding the formation of sulfuric acid in the atmosphere of Venus.

  20. Forces in molecules.

    PubMed

    Hernández-Trujillo, Jesús; Cortés-Guzmán, Fernando; Fang, De-Chai; Bader, Richard F W

    2007-01-01

    Chemistry is determined by the electrostatic forces acting within a collection of nuclei and electrons. The attraction of the nuclei for the electrons is the only attractive force in a molecule and is the force responsible for the bonding between atoms. This is the attractive force acting on the electrons in the Ehrenfest force and on the nuclei in the Feynman force, one that is countered by the repulsion between the electrons in the former and by the repulsion between the nuclei in the latter. The virial theorem relates these forces to the energy changes resulting from interactions between atoms. All bonding, as signified by the presence of a bond path, has a common origin in terms of the mechanics determined by the Ehrenfest, Feynman and virial theorems. This paper is concerned in particular with the mechanics of interaction encountered in what are classically described as 'nonbonded interactions'--are atoms that 'touch' bonded or repelling one another?