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Sample records for deoxyribonucleic acid molecules

  1. Coordinate Variation in Lengths of Deoxyribonucleic Acid Molecules and Head Lengths in Morphological Variants of Bacteriophage T4

    PubMed Central

    Mosig, Gisela; Carnighan, Janet Renshaw; Bibring, Jane Baxandall; Cole, Robert; Bock, Hans-Georg Otto; Bock, Susan

    1972-01-01

    We have investigated three classes of small bacteriophage T4 particles which differ from normal T4 particles in length of their deoxyribonucleic acid (DNA), in head length, in protein content, and in density. The different particles contain DNA molecules measuring 0.90, 0.77, or 0.67, respectively, of the normal T4 length. An additional class of viable particles contains DNA molecules of 1.1 unit length. These discrete differences in DNA length correspond to discrete differences in length (but not width) of the respective heads and are roughly proportional to the resulting differences in head volumes. The measured relative dimensions of the different heads fit best the relative dimensions predicted by a quasi-icosahedral model in which the smallest T4 head corresponds to an icosahedron with a triangulation number T = 21. The mid-portion of this structure is thought to be elongated by adding successive rows of gene 23 protein hexamers, the normal T4 head having three added rows. Different mutants produce small particles of the three classes in varying proportions, but no mutant produces exclusively particles of a single class. Particles of each class, with indistinguishable DNA content, show additional minor differences in protein content, as measured by differences in buoyant density and in the relative ratio of 32P to 35S. Images PMID:5025493

  2. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... ANIMALS § 528.1070 Bc6 recombinant deoxyribonucleic acid construct. (a) Specifications and indications for use. Five copies of a human Bc6 recombinant deoxyribonucleic acid (rDNA) construct located at the GTC... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Bc6 recombinant deoxyribonucleic acid...

  3. Lambda bacteriophage-mediated transduction of ColE1 deoxyribonucleic acid having a lambda bacteriophage-cohesive end site: selection of packageable-length deoxyribonucleic acid.

    PubMed Central

    Umene, K; Shimada, K; Tsuzuki, T; Mori, R; Takagi, Y

    1979-01-01

    An in vitro recombinant ColE1-cos lambda deoxyribonucleic acid (DNA) molecule, pKY96, has 70% of the length of lambda phage DNA. The process of lambda phage-mediated transduction of pKY96 generated a small amount of transducing phage particles containing ColE1-cos lambda DNA molecules of 80 or 101% of the length of lambda phage DNA, in addition to those containing original pKY96 DNA molecules. The newly isolated larger plasmid DNAs were transduced 100 times more efficiently than pKY96 DNA. Their structures were compared with that of a prototype pKY96 DNA, and the mechanism of the formation of these molecules is discussed. Images PMID:158007

  4. recA gene product is responsible for inhibition of deoxyribonucleic acid synthesis after ultraviolet irradiation.

    PubMed Central

    Trgovcević, Z; Petranović, D; Petranović, M; Salaj-Smic, E

    1980-01-01

    Deoxyribonucleic acid synthesis after ultraviolet irradiation was studied in wild-type, uvrA, recB, recA recB, and recA Escherichia coli strains. Inhibition of deoxyribonucleic acid synthesis, which occurs almost immediately after exposing the cells to ultraviolet radiation, depends on the functional gene recA. PMID:6997276

  5. Role of deoxyribonucleic acid technology in forensic dentistry.

    PubMed

    Datta, Pankaj; Datta, Sonia Sood

    2012-01-01

    In the last few years, Deoxyribonucleic Acid (DNA) analysis methods have been applied to forensic cases. Forensic dental record comparison has been used for human identification in cases where destruction of bodily tissues or prolonged exposure to the environment has made other means of identification impractical, that is, after fire exposure or mass disaster. Teeth play an important role in identification and criminology, due to their unique characteristics and relatively high degree of physical and chemical resistance. The use of a DNA profile test in forensic dentistry offers a new perspective in human identification. The DNA is responsible for storing all the genetic material and is unique to each individual. The currently available DNA tests have high reliability and are accepted as legal proofs in courts. This article gives an overview of the evolution of DNA technology in the last few years, highlighting its importance in cases of forensic investigation.

  6. 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.

  7. Unambiguous typing of canine adenovirus isolates by deoxyribonucleic acid restriction-endonuclease analysis.

    PubMed Central

    Assaf, R; Marsolais, G; Yelle, J; Hamelin, C

    1983-01-01

    Viral deoxyribonucleic acid extracted from a limited number of cells infected with canine adenovirus type 1 or type 2 was cleaved with several restriction endonucleases. Agarose gel electrophoresis of the limit digests showed stable differences between the canine adenovirus type 1 and type 2 cleavage patterns. Rapid and accurate typing of large numbers of clinical isolates may thus be done by deoxyribonucleic acid restriction-endonuclease analysis. Images Fig. 1. Fig. 2. PMID:6321002

  8. PENICILLIN RESISTANCE OF COMPETENT CELLS IN DEOXYRIBONUCLEIC ACID TRANSFORMATION OF BACILLUS SUBTILIS.

    PubMed

    NESTER, E W

    1964-04-01

    Nester, E. W. (University of Washington, Seattle). Penicillin resistance of competent cells in deoxyribonucleic acid transformation of Bacillus subtilis. J. Bacteriol. 87:867-875. 1964.-Transformants are resistant to penicillin killing for several hours after deoxyribonucleic acid (DNA) addition. The present study indicates that this resistance is a consequence of such cells still remaining competent and is not the result of any interaction of donor DNA with the recipient cell. The following data support this conclusion: (i) the frequency of transformation can be increased five- to tenfold if penicillin acts on a competent culture prior to DNA addition; (ii) the percentage of competent cells in such a penicillin-treated culture calculated on the basis of a random coincidence of DNA molecules entering the same cell increases some 25-fold over that of a penicillin-nontreated population; (iii) the kinetics of penicillin killing of a recipient culture are identical whether or not transforming DNA has been added; (iv) the extent of killing by penicillin is related to the level of competence of the recipient culture; and (v) the kinetics of appearance and disappearance of competence in a population as well as in individual cells indicate that a cell may remain competent for 3 to 4 hr.

  9. Stabilizing and destabilizing effects of arginine on deoxyribonucleic acid.

    PubMed

    Arakawa, Tsutomu; Hirano, Atsushi; Shiraki, Kentaro; Kita, Yoshiko; Koyama, A Hajime

    2010-03-01

    Aqueous arginine solution now finds a wide range of applications in biotechnology fields, including protein refolding, chromatography and virus inactivation. While progress has been made for mechanistic understanding of the effects of arginine on proteins, we have little understanding on how arginine inactivates viruses. One of the viral components is nucleic acid. We have examined the effects of arginine on the structure and thermal stability of calf thymus deoxyribonucleic acid (DNA) using circular dichroism (CD). Both NaCl and arginine reduced CD intensity. At low concentrations, arginine showed a stronger effect on CD intensity than NaCl. Both NaCl and arginine sharply increased the melting temperature at low concentrations (below 0.25 M). However, they had an opposite effect at higher concentrations. Above this concentration, NaCl gradually increased the melting temperature, leading to the onset melting temperature above 90 degrees C. On the other hand, the thermal stability in the presence of arginine reached a maximum at 0.2-0.5 M, after which further addition of arginine caused decreased melting temperature. It is most likely that the increased melting temperature at low concentration is due to electrostatic stabilization of DNA structure by both NaCl and arginine and that the opposite effects at higher salt concentration are due to salt-specific effects, i.e., stabilizing (salting-out) effects of NaCl and destabilizing (salting-in) effects of arginine. Solubility measurements of nucleic acid bases showed that arginine, but not NaCl, increases the solubilities of the bases, supporting their effects on DNA stability at higher concentration.

  10. Excretion of glutamic acid in Citrobacter intermedius C3 associated with plasmid deoxyribonucleic acid.

    PubMed Central

    Jofre, J; Prieto, M J; Tomás, J; Parés, R

    1979-01-01

    Several mutants of Citrobacter intermedius C3 lacking both the ability to synthesize proline and the ability to excrete glutamic acid were isolated by treatment with nitrosoguanidine. No revertants for either characteristic were obtained from these mutants. The ability to excrete glutamic acid was transferred to those mutants with very high frequencies in mating experience by using auxotropic excreting strains as donors. Moreover, the ability to synthesize proline was transferred together with the ability to excrete glutamic acid when an excreting strain was used as donor. The transconjugants showed a rapid spontaneous curing of both genetic markers. It was shown by two different methods that a band of covalently closed circular deoxyribonucleic acid is present in the cesium chloride gradients corresponding to the wild type and excretor mutants. Nonexcretor mutants described herein lacked such a band. Pro + transformants that were also excretors were obtained with plasmid deoxyribonucleic acid isolated either from wild type or from an excretor mutant. These data strongly indicate that glutamic acid excretion in C. intermedius C3 is related to the presence of extrachromosomal deoxyribonucleic acid. PMID:457593

  11. Deoxyribonucleic Acid Polymerase of Rous Sarcoma Virus: Reaction Conditions and Analysis of the Reaction Product Nucleic Acids

    PubMed Central

    Bishop, D. H. L.; Ruprecht, Ruth; Simpson, R. W.; Spiegelman, S.

    1971-01-01

    Reaction conditions for Rous sarcoma virus ribonucleic acid (RNA)-instructed deoxyribonucleic acid (DNA) polymerase activity are described whereby the viral RNA is relatively protected from endogenous or added nuclease activity. Three analyses of reaction product nucleic acids (3H-RNA, 32P-DNA) were compared, namely, gel electrophoresis, Cs2SO4 gradient centrifugation, and hydroxyapatite column chromatography. It was found that hydroxyapatite analysis could be misleading unless the state of the template RNA was monitored concomitantly with the DNA analysis. Gel electrophoresis and Cs2SO4 gradient centrifugation gave comparable results. It was concluded that analyses of the product of reverse transcriptase reactions should not only refer to the template RNA and product DNA species, but also be performed with virus or viral RNA which do not have or obtain nicks in the 60S RNA. Otherwise, interpretation of the results would have the ambiguity of potential artifacts caused by those degraded RNA molecules. PMID:4332143

  12. Four proteins synthesized in response to deoxyribonucleic acid damage in Micrococcus radiodurans.

    PubMed Central

    Hansen, M T

    1980-01-01

    Four proteins, alpha beta, gamma, and delta, preferentially synthesized in ultraviolet light-treated cells of Micrococcus radiodurans, were characterized in terms of their molecular weights and isoelectric points. Within the sublethal-dose range, the differential rate of synthesis for these proteins increased linearly with the inducing UV dose. The degree of induction reached 100-fold, and the most abundant protein beta, amounted to approximately 2% of the total newly synthesized protein after irradiation. Damage caused by ionizing radiation or by treatment with mitomycin C also provoked the synthesis of the four proteins. The proportions between the individual proteins, however, varied strikingly with the damaging agent. In contrast to treatments which introduced damage in the cellular deoxyribonucleic acid, the mere arrest of deoxyribonucleic acid replication, caused by nalidixic acid or by starvation for thymine, failed to elicit the synthesis of either protein. Repair of deoxyribonucleic acid damage requires that a number of versatile and efficient processes by employed. It is proposed that the induced proteins participate in deoxyribonucleic acid repair in M. radiodurans. Mechanisms are discussed which would allow a differentiated cellular response to damages of sufficiently distinctive nature. Images PMID:7354007

  13. Mapping of colicin E2 and colicin E3 plasmid deoxyribonucleic acid EcoR-1-sensitive sites.

    PubMed

    Inselburg, J; Johns, V

    1975-01-01

    Colicin plasmids E2 and E3 (Col E2 and Col E3) deoxyribonucleic acid (DNA) has been shown to contain, respectively, two and three EcoR1 restriction endonuclease-sensitive sites. This was determined by measuring the DNA fragments generated after EcoR1 endonuclease treatment by agarose gel electrophoresis and electron microscopy. The structure of heteroduplex Col E2-col E3 DNA molecules formed from EcoR1-generated fragments permitted a localization of the EcoR1-sensitive sites on the plasmid chromosomes.

  14. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... hircus) directing the expression of the human gene for antithrombin (which is intended for the treatment.... 528.1070 Section 528.1070 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... use. Five copies of a human Bc6 recombinant deoxyribonucleic acid (rDNA) construct located at the...

  15. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... hircus) directing the expression of the human gene for antithrombin (which is intended for the treatment.... 528.1070 Section 528.1070 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... use. Five copies of a human Bc6 recombinant deoxyribonucleic acid (rDNA) construct located at the...

  16. 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.

  17. Role of polyadenylic acid in a deoxyribonucleic acid-membrane fraction extracted from pneumococci.

    PubMed Central

    Firshein, W; Meyer, B; Epner, E; Viggiani, J

    1976-01-01

    After the addition of radioactive polyadenylic acid to cell suspensions of pneumocci, part of the radioactivity becomes associated with a deoxyribonucleic acid (DNA)-membrane fraction extracted from the cells. A variety of techniques show that a portion of this associated radioactivity may represent oligoadenylates complexed to DNA, probaby as part of a ribonucleic acid (RNA) component. Polyadenylic acid, which had previously been shown to enhance DNA synthesis in cell suspensions (Firshein and Benson, 1968), also enhances the extent of DNA synthesis by the DNA-membrane fraction in vitro under specific conditions of concentration and conformation. The mechanism of action of this enhancement may be related to the ability of oligoadenylates to increase the number of initiation sites for DNA replication by stimulating the production of an RNA primer, thus providing additional 3'-OH groups with which DNA polymerase can react. PMID:6428

  18. Fate of Donor Deoxyribonucleic Acid in a Highly Transformation-Deficient Strain of Haemophilus influenzae

    PubMed Central

    Kooistra, Jan; Venema, Gerard

    1974-01-01

    A transformation-deficient strain of Haemophilus influenzae (efficiency of transformation 104-fold less than that of the wild type), designated TD24, was isolated by selection for sensitivity to mitomycin C. In its properties the mutant was equivalent to recA type mutants of Escherichia coli. The TD24 mutation was linked with the str-r marker (about 30%) and only weakly linked with the nov-r2.5 marker. The uptake of donor deoxyribonucleic acid (DNA) was normal in the TD24 strain, but no molecules with recombinant-type activity (molecules carrying both the donor and the resident marker) were formed. In the mutant the intracellular presynaptic fate of the donor DNA was the same as that in the transformation-proficient (wild-type) strain, and the radioactive label of the donor DNA associated covalently with the recipient chromosome in about the same quantity as in the wild type. However, many fewer donor atoms were associated with segments of the mutant's recipient chromosome as compared with segments of the wild-type chromosome. In the mutant the association was accompanied by complete loss of donor marker activity. The lack of donor marker activity of the donor-recipient complex of DNA isolated from the mutant was not due to lack of uptake of the complex by the second recipient and its inability to associate with the second recipient's chromosome. Because the number of donor-atom-carrying resident molecules was higher than could be accounted for by the lengths of presynaptic donor molecules, we favor the idea that the association of donor DNA atoms with the mutant chromosome results from local DNA synthesis rather than from dispersive integration of donor DNA by recombination. PMID:4546806

  19. Contribution of light scattering to the circular dichroism of deoxyribonucleic acid films, deoxyribonucleic acid-polylysine complexes, and deoxyribonucleic acid particles in ethanolic buffers

    SciTech Connect

    Maestre, M.F.; Reich, C.

    1980-01-01

    The contribution of scattering to the circular dichroism (CD) of DNA films with twisted structures, DNA-polylysine complexes, and condensed DNA aggregates in ethanolic buffers of defined salt concentrations has been studied by the use of novel measuring techniques. These techniques include fluorscat cuvettes, fluorescence-detected circular dichroism (FDCD) methods, backscattering capturing devices, and beam-mounted goniometer detectors. The result of the experimental measurement is that DNA films can be made which have very large ellipticities or CD at sharp specific wavelengths. The sign of these ellipticities is related to the handedness of the twists, with a right-handed twist producing large positive rotations and a left-handed one producing negative rotations. The film shows nodal angles at which the interaction with light is minimal. The scattering patterns of both films, DNA-polylysine particles and DNA-EtOH condensates, show that the main interaction is light scattering produced by a resonance phenomenon similar to that produced in cholestric liquid crystals and twisted-nematic liquid crystals. It is proposed that the so-called psi-type CD spectrum is a manifestation of a side-by-side packing of DNA molecules with a long-range twisting order whose helical parameters match the helical parameter of circularly polarized light at specific resonance or critical wavelengths. Application of the Bragg law for cholesteric liquid crystals gives the periodicity of the long-range ordered structures. 9 figures.

  20. Deoxyribonucleic acid sequence of araBAD promoter mutants of Escherichia coli.

    PubMed

    Horwitz, A H; Morandi, C; Wilcox, G

    1980-05-01

    The controlling site region for the araBAD operon is defined, in part, by two classes of cis-acting constitutive mutations. The aralc mutations allow low-level constitutive expression of ara-BAD in the absence of the positive regulatory protein coded for by the araC gene, whereas the araXc mutations allow expression of araBAD in the absence of the cyclic adenosine monophosphate receptor protein. Six independently isolated aralc mutations and three independently isolated araXc mutations were cloned onto the plasmid pBR322 using in vitro recombinant deoxyribonucleic acid techniques and in vivo recombination between plasmid and chromosomal deoxyribonucleic acid. The location of these mutations was determined by deoxyribonucleic acid sequence analysis. All of the aralc mutations occurred at position -35 within the araBAD promoter (+1 = messenger ribonucleic acid start for araBAD) and resulted from an AT leads to GC transition. All of the araXc mutations occurred at position -10 within the araBAD promoter and resulted from a GC leads to AT transition. Models are presented to explain the mode of action of the aralc and araXc mutations.

  1. INCORPORATION OF DEOXYRIBONUCLEIC ACID IN THE BACILLUS SUBTILIS TRANSFORMATION SYSTEM1

    PubMed Central

    Young, F. E.; Spizizen, John

    1963-01-01

    Young, F. E. (Western Reserve University Cleveland, Ohio) and John Spizizen. Incorporation of deoxyribonucleic acid in the Bacillus subtilis transformation system. J. Bacteriol. 86:392–400. 1963.—The optimal conditions for the incorporation of deoxyribonucleic acid (DNA) were studied. In competent cells, the irreversible binding of DNA was influenced by temperature, hydrogen ion concentration, and aeration. Divalent cations, such as barium, strontium, calcium, or magnesium, were required. Under suboptimal environmental conditions and with metabolic inhibitors, the process of transformation was decreased to a greater extent than was incorporation of DNA. Under conditions of phosphate depletion, the incorporation of P32 increased. However, the frequency of transformation decreased. This inducible process was not related to competence. PMID:14066414

  2. Blood lymphocyte ultrastructure and deoxyribonucleic acid content in children with systemic lupus erythematosis.

    PubMed

    Ptasekas, R; Matulis, A; Urmonas, V; Graziene, V; Zukiene, G

    1980-01-01

    Two varieties of peripheral blood lymphocytes have been disclosed in systemic lupus erythematosus (SLE) cases: one showing signs of degradation and nuclear chromatine elimination and the other one manifesting a state of biological activation, possibly of an immunologic nature. This karyostructural lymphocyte heterogeneity in SLE may cause a great scattering of these cells on histograms in respect to their nuclear deoxyribonucleic acid content determined by cytophotometry. On the other hand, the expressiveness of the scattering and the degree of predominance of negative tendency towards proliferation (with a shift to the left from 2 n) may thereby serve as a very objective quantitative indication of nuclear structure degradation and of loss by lymphocytes of chromatine with deoxyribonucleic acid during SLE.

  3. KINETOPLAST DEOXYRIBONUCLEIC ACID OF THE HEMOFLAGELLATE TRYPANOSOMA LEWISI

    PubMed Central

    Renger, Hartmut C.; Wolstenholme, David R.

    1970-01-01

    Cesium chloride centrifugation of DNA extracted from cells of blood strain Trypanosoma lewisi revealed a main band, ρ = 1.707, a light satellite, ρ = 1.699, and a heavy satellite, ρ = 1.721. Culture strain T. lewisi DNA comprised only a main band, ρ = 1.711, and a light satellite, ρ = 1.699. DNA isolated from DNase-treated kinetoplast fractions of both the blood and culture strains consisted of only the light satellite DNA. Electron microscope examination of rotary shadowed preparations of lysates revealed that DNA from kinetoplast fractions was mainly in the form of single 0.4 µ circular molecules and large masses of 0.4 µ interlocked circles with which longer, often noncircular molecules were associated. The 0.4 µ circular molecules were mainly in the covalently closed form: they showed a high degree of resistance to thermal denaturation which was lost following sonication; and they banded at a greater density than linear DNA in cesium chloride-ethidium bromide gradients. Interpretation of the large masses of DNA as comprising interlocked covalently closed 0.4 µ circles was supported by the findings that they banded with single circular molecules in cesium chloride-ethidium bromide gradients, and following breakage of some circles by mild sonication, they disappeared and were replaced by molecules made up of low numbers of apparently interlocked 0.4 µ circles. When culture strain cells were grown in the presence of either ethidium bromide or acriflavin, there was a loss of stainable kinetoplast DNA in cytological preparations. There was a parallel loss of light satellite and of circular molecules from DNA extracted from these cells. PMID:5497546

  4. Studies on the sonic degradation of deoxyribonucleic acid.

    PubMed

    FREIFELDER, D; DAVISON, P F

    1962-05-01

    T7 DNA was partially degraded by x-rays, DNAase, and sonic irradiation. The molecular weight distributions were calculated from sedimentation velocity studies on the resulting preparations. Comparison with the theoretical curve derived by Montroll and Simha showed that the first two degradative methods act grossly at random, whereas sonication is a non-random process resulting in the preferential halving of the DNA molecules in solution.

  5. Studies on the Sonic Degradation of Deoxyribonucleic Acid

    PubMed Central

    Freifelder, David; Davison, Peter F.

    1962-01-01

    T7 DNA was partially degraded by x-rays, DNAase, and sonic irradiation. The molecular weight distributions were calculated from sedimentation velocity studies on the resulting preparations. Comparison with the theoretical curve derived by Montroll and Simha showed that the first two degradative methods act grossly at random, whereas sonication is a non-random process resulting in the preferential halving of the DNA molecules in solution. PMID:13894963

  6. Deoxyribonucleic acid-ribonucleic acid hybridization studies on the L-Arabinose operon of Escherichia coli B-r.

    PubMed

    Wilcox, G; Singer, J; Heffernan, L

    1971-10-01

    An increase in the rate of synthesis of ara-specific messenger ribonucleic acid as measured by deoxyribonucleic acid-ribonucleic acid hybridization has been detected in the induced wild-type (ara(+)) strain of Escherichia coli B/r as compared with the uninduced control, thus providing evidence that regulation of the positively controlled l-arabinose operon is at the level of transcription.

  7. Photodynamic Action on Native and Denatured Transforming Deoxyribonucleic Acid from Haemophilus influenzae

    PubMed Central

    León, Manuel Ponce-De; Cabrera-Juárez, Emiliano

    1970-01-01

    The photodynamic inactivation of native or denatured transforming deoxyribonucleic acid (DNA) from Haemophilus influenzae is described. The inactivation at the same pH was higher for denatured than native DNA. At acidic pH, the inactivation both for native and denatured DNA was faster than at alkaline pH. The guanine content of photoinactivated native DNA at neutral pH was less than untreated DNA. The inactivation of biological activity was more extensive than the alteration of guanine. The absorption spectrum of photoinactivated native or denatured DNA was only slightly different than the control DNA at the different experimental conditions. PMID:5309576

  8. 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

    2015-07-09

    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.

  9. Deoxyribonucleic acid polymerase III of Escherichia coli. Purification and properties.

    PubMed

    Livingston, D M; Hinkle, D C; Richardson, C C

    1975-01-25

    DNA polymerase III has been purified 4,500-fold from the Escherichis coli mutant, HMS83, which lacks DNA polymerases I and II. When subjected to disc gel electrophoresis, the most purified fraction exhibits a single major protein band from which enzymatic activity may be recovered. Polyacrylamide gel electrophoresis under denaturing conditions produces two protein bands with molecular weights of 140,000 and 40,000. The sedimentation coefficient of the enzyme is 7.0 S, and the Stokes radius is 62 A. Taken together these tow parameters indicate a native molecular weight of 180,000. Purified DNA polymerase III catalyzes the polymerization of nucleotides into DNA when provided with both a DNA template and a complementary primer strand. The newly synthesized DNA is covalently attached to the 3' terminus of the primer strand. Because the extent of polymerization is only 10 to 100 nucleotides, the best substrates are native DNA molecules with small single-stranded regions. The most purified enzyme preparation is devoid of endonuclease activities. In addition to the two exonuclease activities described in the accompanying paper, purified polymerase III also catalyzes pyrophosphorolysis and the exchange of pyrophosphate into deoxynucleoside triphosphates. DNA polymerase III has also been isolated from wild type E. coli containing the other two known DNA polymerases. Futhermore, the enzyme purified from three different polC mutants exhibits altered polymerase III activity, confirming that polC is the structural gene for DNA polymerase III (Gefter, M., Hirota, Y., Kornberb, T., Wechsler, J., and Barnoux, C. (1971) Proc. Natl. Acad. Sci. U. S. A. 68, 3150-3153).

  10. The complementary deoxyribonucleic acid sequence of guinea pig endometrial prorelaxin.

    PubMed

    Lee, Y A; Bryant-Greenwood, G D; Mandel, M; Greenwood, F C

    1992-03-01

    The nucleotide sequence of the relaxin gene transcript in the endometrium of the late pregnant guinea pig has been determined. The strategy used was a combination of polymerase chain reaction (PCR) with primers designed from the mRNA sequence of porcine preprorelaxin, rapid amplification of cDNA ends-PCR, and blunt end cloning in M13 mp18. With heterologous primers, a 226-basepair (bp) segment of the guinea pig relaxin gene sequence was obtained and was used to design a guinea pig-specific primer for use with the rapid amplification of cDNA ends-PCR method. The latter allowed completion of the sequence of 336 bp, with a 96-bp overlap. The sequence obtained shows greater homology at both the nucleotide and amino acid levels with porcine and human relaxins H1 and H2 than with rat relaxin, supporting the thesis that the guinea pig is not a rodent. The transcription of the guinea pig endometrial relaxin gene during pregnancy was confirmed by Northern analysis of guinea pig endometrial tissues with a species-specific cDNA probe. The endometrial relaxin gene is transcribed during pregnancy, but not in lactation, consistent with the observed immunostaining for relaxin.

  11. “BLACK LIGHT” INACTIVATION OF TRANSFORMING DEOXYRIBONUCLEIC ACID FROM HAEMOPHILUS INFLUENZAE

    PubMed Central

    Cabrera-Juárez, Emiliano

    1964-01-01

    Cabrera-Juárez, Emiliano (Instituto Politecnico Nacional, Mexico, D.F., Mexico). “Black light” inactivation of transforming deoxyribonucleic acid from Haemophilus influenzae. J. Bacteriol. 87:771–778. 1964.—The biological activity (intrinsic genetic markers or nitrous acid mutable regions) of transforming deoxyribonucleic acid (DNA) from Haemophilus influenzae has been inactivated by “black light” (BL) by two mechanisms: (i) photodynamic action (oxygen-dependent) and (ii) “BL inactivation” (oxygen-independent). The BL inactivation is greater in denatured than in native DNA, and it is dependent on the pH. It does not depend on the temperature, and the damage produced is stable. The effective wavelength of inactivation is between 330 and 360 mμ. The BL inactivation is not reactivated by photoreactivating enzyme or nitrous acid. The BL and ultraviolet inactivations are additive, suggesting that the changes produced by BL and ultraviolet irradiation on transforming DNA are different. T2 phage was also inactivated by BL. The nature of the photochemical changes produced in DNA by BL is not known. PMID:14139527

  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. Survival, Deoxyribonucleic Acid Breakdown, and Synthesis in Salmonella typhimurium as Compared with Escherichia coli B Strains

    PubMed Central

    Hudnik-Plevnik, Tamara A.; Djordjević, Nadežda

    1970-01-01

    Salmonella typhimurium LT-2 was compared with radioresistant (B/r) and radiosensitive (Bs−2) strains of Escherichia coli in respect to the survival, deoxyribonucleic acid (DNA) breakdown, and DNA synthesis after X irradiation. It is shown that S. typhimurium LT-2 is about four times more sensitive than E. coli B/r but less sensitive than Bs−2. The DNA breakdown is in S. typhimurium LT-2 lower than the postirradiation breakdown of DNA in both E. coli strains and DNA synthesis proceeds in this bacterium in spite of a much lower survival, as in the radioresistant E. coli B/r. PMID:4916313

  14. Influence of surfactant on dynamics of photoinduced motions in a dye-doped deoxyribonucleic acid

    NASA Astrophysics Data System (ADS)

    Mysliwiec, Jaroslaw; Parafiniuk, Kacper; Miniewicz, Andrzej; Rau, Ileana; Kajzar, Francois; Niziol, Jacek; Hebda, Edyta; Pielichowski, Jan; Sahraoui, Bouchta

    2012-10-01

    Pure deoxyribonucleic acid (DNA) is known to be soluble in water only and exhibits poor temperature stability. In contrary, it is well known that the complex of DNA - with cetyltrimethyl ammonium (CTMA) is soluble in alcohols and can be processed into very good optical quality thin films by solution casting and spin deposition. Despite the success of DNA-CTMA, there is still need for new cationic surfactants which would extend the range of available solvents for DNA complex. We test and present experimental results of influence of new surfactants based on benzalkonium chloride (BA), and didecyldimethylammonium chloride (DDCA) for applications in all optical switching.

  15. Genetic Control of the Secondary Modification of Deoxyribonucleic Acid in Escherichia coli1

    PubMed Central

    Mamelak, Linda; Boyer, Herbert W.

    1970-01-01

    The wild-type restriction and modification alleles of Escherichia coli K-12 and B were found to have no measurable effect on the patterns of methylated bases in the deoxyribonucleic acid (DNA) of these strains. The genetic region controlling the methylation of cytosine in E. coli K-12 was mapped close to his, and the presence or absence of this gene in E. coli B or E. coli K had no effect on the restriction and modification properties of these strains. Thus, only a few of the methylated bases in the DNA of these strains are involved in host modification, and the biological role of the remainder remains obscure. PMID:4919756

  16. Role of deoxyribonucleic acid ligase in a doxyribonucleic acid membrane fraction extracted from pneumococci.

    PubMed Central

    Greene, M; Firshein, W

    1976-01-01

    Deoxyribonucleic acid (DNA) ligase has been detected in a DNA membrane fraction extracted from Pneumococcus. The specific activity of the enzyme in this fraction is 10-fold greater than in the remaining cell extract. It remains firmly bound (with other enzymes) to the complex after a purification procedure in which a considerable percentage of the macromolecules are dissociated. The ligase acts in two ways in the DNA membrane fraction in vitro. One, it catalyzes the linkage of small-molecular-weight pieces of newly synthesized DNA into heavier-molecular-weight DNA strands as shown by others (M Gellert, 1976; R. Okazaki, A. Sugino, S. Hirose, T. Okazaki, Y. Imae, R. Kainuma-Kuroda, T. Ogawa, M. Arisawa, and Y. Kurosowa, 1973; B. Olivera and I. Lehman, 14; and A. Sugino, S. Hirose, and R. Okazaki, 1972) and, two, it protects DNA from degradation by deoxyribonucleases. This latter effect is due to a competition between the ability of the nucleases to degrade DNA and the ability of DNA ligase to seal the nicks produced by these degradative enzymes. The ligase acts cooperatively with other enzymes in the DNA membrane fraction to synthesize DNA. PMID:4433

  17. Influence of Bacteriophage PBS1 and φW-14 Deoxyribonucleic Acids on Homologous Deoxyribonucleic Acid Uptake and Transformation in Competent Bacillus subtilis

    PubMed Central

    López, Paloma; Espinosa, Manuel; Piechowska, Mirosława; Shugar, David

    1980-01-01

    Both bacteriophage PBS1 deoxyribonucleic acid (DNA) (in which all the thymine residues are replaced by uracil) and phage φW-14 DNA [in which half the thymine residues are replaced by 5-(aminobutylaminomethyl)uracil or 5-putrescinylthymine] exhibit comparable competing abilities for uptake of homologous DNA in a Bacillus subtilis competent system. But, whereas PBS1 DNA leads to a decrease in transformation frequencies compatible with its competing ability for DNA uptake, φW-14 DNA decreases transformation frequencies by a factor up to eightfold higher. The effect of φW-14 DNA on transformation frequencies is visible even at a concentration level that does not decrease transforming DNA uptake. No such effect was observed with heterologous DNA containing presumably ionically bound putrescine. Low concentrations of φW-14 DNA decreased the number of double (nonlinked) transformants more than single transformants. The influence on transformation was abolished when φW-14 DNA was added 20 min after addition of transforming DNA, i.e., when the recombination process was terminated. The putrescine-containing DNA also decreased retention of trichloroacetic acid-precipitable radioactivity of homologous DNA taken up. We conclude that φW-14 DNA inhibits some intracellular process(es) at the level of recombination. In addition, there is evidence that φW-14 DNA, but not heterologous DNA with ionically bound putrescine, binds also to site(s) on the cell surface other than receptors for homologous DNA. PMID:6772635

  18. Agreement Between Deoxyribonucleic Acid Base Composition and Taxometric Classification of Gram-Positive Cocci1

    PubMed Central

    Silvestri, L. G.; Hill, L. R.

    1965-01-01

    Silvestri, L. G. (Università Statale, Milan, Italy), and L. R. Hill. Agreement between deoxyribonucleic acid base composition and taxometric classification of gram-positive cocci. J. Bacteriol. 90:136–140. 1965.—It had been previously proposed, from taxometric analyses, that gram-positive, catalase-positive cocci be divided into two subgroups. Thirteen strains, representative of both subgroups, were examined for deoxyribonucleic acid (DNA) base composition, determined from melting temperatures. Per cent GC (guanine + cytosine/total bases) values fell into two groups: 30.8 to 36.5% GC and 69 to 75% GC. Strains with low per cent GC values belonged to the Staphylococcus aureus–S. saprophyticus–S. lactis taxometric subgroups, and those with high per cent GC values belonged to the S. roseus–S. afermentans subgroup. The hypothetical nature of any classification is emphasized, and, in the present work, the hypothesis derived from taxometric analyses of division into two subgroups is confirmed by the study of DNA base ratios. The two subgroups correspond, respectively, to the genera Staphylococcus and Micrococcus. PMID:16562008

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

    PubMed

    SIGAL, N; SENEZ, J C; LEGALL, J; SEBALD, M

    1963-06-01

    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 c(3) 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.

  20. Protein Synthesis and Deoxyribonucleic Acid-Membrane Attachment During Thymineless Death in Escherichia coli

    PubMed Central

    Dankberg, Frances; Cummings, Donald J.

    1973-01-01

    The proteins synthesized during thymineless death in Escherichia coli B and B/r were analyzed by polyacrylamide gel elctrophoresis. It was found that the amount of a protein of molecular weight 80,000 to 88,000 is greatly increased during thymineless death compared to the amounts of other cell proteins. A technique for the isolation of cell membrane-deoxyribonucleic acid (DNA)-nascent ribonucleic acid (RNA) complex on detergent crystals was used to determine whether DNA might be detached from the cell membrane as a result of thymineless death. It was found that under no conditions of thymineless death or immunity to thymineless death was there any change in the attachment of DNA or pulse-labeled RNA to cell membrane. Images PMID:4570604

  1. Fluorescence, spectroscopic and NLO properties of green tea extract in deoxyribonucleic acid

    NASA Astrophysics Data System (ADS)

    Manea, Ana-Maria; Rau, Ileana; Kajzar, Francois; Meghea, Aurelia

    2013-11-01

    Natural, purely biological deoxyribonucleic acid (DNA)-green tea extract (GTE) complexes at different concentrations were prepared and characterized for their spectroscopic, fluorescent, linear and nonlinear optical properties. The complexes can be processed into good optical quality thin films by solution casting. They fluoresce when excited in UV absorption band, with a significantly larger quantum yield for the DNA-GTE complex than for a pure GTE solution. The thin film refractive indices were determined by Fabry-Perot (FP) interference patterns. The third-order nonlinear optical (NLO) properties of thin films were determined by the optical third-harmonic generation technique at 1064.2 nm fundamental wavelength. The phase of THG susceptibility was determined from the concentration variation of THG susceptibility. It reveals presence of a two-photon resonance with a band lying in the optical gap.

  2. New Deoxyribonucleic Acid Polymerase Induced by Bacillus subtilis Bacteriophage PBS2

    PubMed Central

    Price, Alan R.; Cook, Sandra J.

    1972-01-01

    The deoxyribonucleic acid (DNA) of Bacillus subtilis phage PBS2 has been confirmed to contain uracil instead of thymine. PBS2 phage infection of wild-type cells or DNA polymerase-deficient cells results in an increase in the specific activity of DNA polymerase. This induction of DNA polymerase activity is prevented by actinomycin D and chloramphenicol. In contrast to the major B. subtilis DNA polymerase, which prefers deoxythymidine triphosphate (dTTP) to deoxyuridine triphosphate (dUTP), the DNA polymerase in crude extracts of PBS2-infected cells is equally active whether dTTP or dUTP is employed. This phage-induced polymerase may be responsible for the synthesis of uracil-containing DNA during PBS2 phage infection. PMID:4623224

  3. Performance of an electro-optic waveguide modulator fabricated using a deoxyribonucleic-acid-based biopolymer

    NASA Astrophysics Data System (ADS)

    Heckman, Emily M.; Grote, James G.; Hopkins, F. Kenneth; Yaney, Perry P.

    2006-10-01

    An electro-optic (EO) planar waveguide modulator using a deoxyribonucleic acid (DNA)-based biopolymer for both the waveguide core and cladding layers has been fabricated and its performance evaluated. A cross-linked DNA-surfactant biopolymer was used for the top and bottom cladding layers and the core layer was a cross-linked DNA-surfactant biopolymer with 3wt% Disperse Red 1. The EO coefficient r33 was induced through contact poling. The fabricated device was found to exhibit EO modulating behavior. Using an estimated value of r33=0.5pm/V, a sine-squared fit to the modulating data was obtained with Vπ=263V±10%.

  4. 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.

  5. Features of the damage produced by proflavine on transforming deoxyribonucleic acid.

    PubMed

    Cabrera-Juárez, E; Sánchez-Rincón, D A

    1979-03-01

    Proflavine formed a complex with transforming deoxyribonucleic acid (DNA) from Haemophilus influenzae, with optimal formation at a ratio of proflavine to DNA of 0.06. The rate of dissociation of the complex by dialysis increased in the order: native, denatured, renatured DNA. The transforming activity of the DNA was reduced by its interaction with proflavine. This inactivation was dependent on the physical state of the DNA, the proflavine concentration, and the temperature. DNA that had been denatured and renatured was most sensitive; native DNA was much less sensitive. The inactivation remained after dialysis and was stable to prolonged storage. It is concluded that the inactivation of transforming DNA by proflavine takes place by a mechanism different from that of DNA-proflavine complex formation.

  6. 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

  7. 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

  8. Synthesis and properties of novel 2'-C,4'-C-ethyleneoxy-bridged 2'-deoxyribonucleic acids with exocyclic methylene groups.

    PubMed

    Osawa, Takashi; Obika, Satoshi; Hari, Yoshiyuki

    2016-10-12

    Three 2'-C,4'-C-ethyleneoxy-bridged 2'-deoxyribonucleic acids possessing six-membered bridges with 6'-oxygen and 8'-exocyclic methylene groups (methylene-EoDNAs) were designed and synthesized in nine to ten steps from 5-methyluridine. The methylene-EoDNA-modified oligonucleotides showed excellent binding affinity with target ssRNA and extremely high nuclease resistance compared with natural oligonucleotides. These results proved the potential of methylene-EoDNAs for nucleic acid based technology.

  9. 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.

  10. Properties of the Deoxyribonucleic Acid Contained in the Defective Particle Coliphage 15 1

    PubMed Central

    Frampton, E. W.; Mandel, M.

    1970-01-01

    Escherichia coli strain 15 TAU, which requires thymine, arginine, and uracil for growth and harbors an apparently defective prophage, was induced by exposure to ultraviolet light (580 ergs/mm2) or to mitomycin C (5 μg/ml). Phage particles (coliphage 15) were recovered from the resulting lysate by treatment with deoxyribonuclease, filtration, and several cycles of differential centrifugation. Analysis of the phage particles obtained by using cesium chloride density gradient centrifugation in a preparative ultracentrifuge resulted in the resolution of three components. The major component had a peak density of 1.52 to 1.53 g/cm3 followed by components with densities of 1.5 and 1.49 g/cm3. The guanine plus cytosine content of coliphage 15 deoxyribonucleic acid (DNA) was determined by both analytical ultracentrifugation in cesium chloride and by thermal denaturation in standard saline citrate buffer. Respective values of 46.4 ± 1% and 46.6 ± 1% guanine plus cytosine content were obtained. Coliphage 15 DNA formed molecular hybrids with messenger ribonucleic acid (RNA) from both uninduced and ultraviolet-induced cultures of E. coli 15 TAU, but did not hybridize with E. coli ribosomal RNA. The molecular weight of coliphage 15 DNA was determined by constant velocity sucrose density gradient centrifugation to be about 33 × 106 daltons. PMID:4909911

  11. Integrity of nuclear genomic deoxyribonucleic acid in cooked meat: Implications for food traceability.

    PubMed

    Aslan, O; Hamill, R M; Sweeney, T; Reardon, W; Mullen, A M

    2009-01-01

    It is essential to isolate high-quality DNA from muscle tissue for PCR-based applications in traceability of animal origin. We wished to examine the impact of cooking meat to a range of core temperatures on the quality and quantity of subsequently isolated genomic (specifically, nuclear) DNA. Triplicate steak samples were cooked in a water bath (100 degrees C) until their final internal temperature was 75, 80, 85, 90, 95, or 100 degrees C, and DNA was extracted. Deoxyribonucleic acid quantity was significantly reduced in cooked meat samples compared with raw (6.5 vs. 56.6 ng/microL; P < 0.001), but there was no relationship with cooking temperature. Quality (A(260)/A(280), i.e., absorbance at 260 and 280 nm) was also affected by cooking (P < 0.001). For all 3 genes, large PCR amplicons (product size >800 bp) were observed only when using DNA from raw meat and steak cooked to lower core temperatures. Small amplicons (<200 bp) were present for all core temperatures. Cooking meat to high temperatures thus resulted in a reduced overall yield and probable fragmentation of DNA to sizes less than 800 bp. Although nuclear DNA is preferable to mitochondrial DNA for food authentication, it is less abundant, and results suggest that analyses should be designed to use small amplicon sizes for meat cooked to high core temperatures.

  12. Automated Quantification of the Impact of Defects on the Mechanical Behavior of Deoxyribonucleic acid Origami Nanoplates.

    PubMed

    Liang, Bowen; Nagarajan, Anand; Hudoba, Michael W; Alvarez, Ricardo; Castro, Carlos E; Soghrati, Soheil

    2017-04-01

    Deoxyribonucleic acid (DNA) origami is a method for the bottom-up self-assembly of complex nanostructures for applications, such as biosensing, drug delivery, nanopore technologies, and nanomechanical devices. Effective design of such nanostructures requires a good understanding of their mechanical behavior. While a number of studies have focused on the mechanical properties of DNA origami structures, considering defects arising from molecular self-assembly is largely unexplored. In this paper, we present an automated computational framework to analyze the impact of such defects on the structural integrity of a model DNA origami nanoplate. The proposed computational approach relies on a noniterative conforming to interface-structured adaptive mesh refinement (CISAMR) algorithm, which enables the automated transformation of a binary image of the nanoplate into a high fidelity finite element model. We implement this technique to quantify the impact of defects on the mechanical behavior of the nanoplate by performing multiple simulations taking into account varying numbers and spatial arrangements of missing DNA strands. The analyses are carried out for two types of loading: uniform tensile displacement applied on all the DNA strands and asymmetric tensile displacement applied to strands at diagonal corners of the nanoplate.

  13. Gating of single-layer graphene with single-stranded deoxyribonucleic acids.

    PubMed

    Lin, Jian; Teweldebrhan, Desalegne; Ashraf, Khalid; Liu, Guanxiong; Jing, Xiaoye; Yan, Zhong; Li, Rong; Ozkan, Mihri; Lake, Roger K; Balandin, Alexander A; Ozkan, Cengiz S

    2010-05-21

    Patterning of biomolecules on graphene layers could provide new avenues to modulate their electrical properties for novel electronic devices. Single-stranded deoxyribonucleic acids (ssDNAs) are found to act as negative-potential gating agents that increase the hole density in single-layer graphene. Current-voltage measurements of the hybrid ssDNA/graphene system indicate a shift in the Dirac point and "intrinsic" conductance after ssDNA is patterned. The effect of ssDNA is to increase the hole density in the graphene layer, which is calculated to be on the order of 1.8 x 10(12) cm(-2). This increased density is consistent with the Raman frequency shifts in the G-peak and 2D band positions and the corresponding changes in the G-peak full width at half maximum. Ab initio calculations using density functional theory rule out significant charge transfer or modification of the graphene band structure in the presence of ssDNA fragments.

  14. Effects of intradermally administered plasmid deoxyribonucleic acid on ovine popliteal lymph node morphology.

    PubMed

    Uwiera, R R; Rankin, R; Adams, G P; Pontarollo, R; van Drunen Littel-van den Hurk, S; Middleton, D M; Babiuk, L A; Griebel, P J

    2001-02-01

    In the last decade it has become apparent that bacterial deoxyribonucleic acid (DNA) is recognized as a "danger signal" by the mammalian immune system. To investigate this interaction, sheep were injected intradermally two centimeters distal to the lateral prominence of the fibular head with 400 microg of purified plasmid DNA. Over a 28-day period ultrasound measurements indicated a progressive increase in size of both plasmid and saline (controls) treated popliteal lymph nodes and at Day 30 macroscopic and histological measurements of the lymph nodes were determined. Compared with the contralateral control lymph nodes, plasmid exposed lymph nodes were heavier (2.8 +/- 0.1g vs. 2.0 +/- 0.6 g) and displayed prominent histological changes in the cortex and medulla. Average medullary cord thickness (114.2 +/- 25.2 microm) and the average distance across medullary sinuses (64.4 +/- 2.5 microm) were significantly greater after plasmid exposure relative to contralateral controls (62.7 +/- 14.9 microm and 36.5 +/- 1.0 microm, respectively). Total number of germinal centers (71.4 +/- 17.7) and the total area of germinal centers (4.0 +/- 1.3 mm(2)) within the cortex of popliteal lymph nodes exposed to plasmid were also significantly greater than the controls (40.4 +/- 11.4 and 1.6 +/- 0.5 mm(2), respectively). Our results demonstrate that a single exposure to plasmid DNA has long term effects on regional lymph node weight and morphology.

  15. Feasibility for quantitative determination of deoxyribonucleic acid by using near-infrared diffuse reflectance spectroscopy.

    PubMed

    Yang, Yafei; Tu, Jiarun; Cai, Wensheng; Shao, Xueguang

    2012-09-15

    A method for quantitative determination of fish sperm deoxyribonucleic acid (fsDNA) in solutions was developed by using adsorption preconcentration and near-infrared diffuse reflectance spectroscopy (NIRDRS). A high capacity adsorbent of amino-modified silica particle (AMSP) was prepared for preconcentration of fsDNA in solutions. Under the optimized conditions, the adsorption rate can be above 90% within 3 min. After adsorbing the DNA onto the adsorbent, near-infrared (NIR) spectra in diffuse reflectance mode were measured and partial least squares (PLS) model was established for fast quantitative prediction. The results show that the correlation coefficient (R) between the predicted and the reference concentration is 0.9894 and the recoveries are in the range of 92.9-123.4% for the validation samples in the concentration range of 3.00-29.38 mg L(-1). Therefore, the feasibility for quantitative analysis of DNA in solutions by NIRDRS is proved. This may provide an alternative way for fast determination of DNA in solutions.

  16. Formation of an 8-hydroxyguanine moiety in deoxyribonucleic acid on gamma-irradiation in aqueous solution

    SciTech Connect

    Dizdaroglu, M.

    1985-07-30

    Isolation and characterization of a novel radiation-induced product, i.e., the 8-hydroxyguanine residue, produced in deoxyribonucleic acid (DNA), 2'-deoxyguanosine, and 2'-deoxyguanosine 5'-monophosphate by gamma-irradiation in aqueous solution, are described. For this purpose, gamma-irradiated DNA was first hydrolyzed with a mixture of four enzymes, i.e., DNase I, spleen and snake venom exonucleases, and alkaline phosphatase. Analysis of the resulting mixture by capillary gas chromatography-mass spectrometry after trimethylsilylation revealed the presence of a product, which was identified as 8-hydroxy-2'-deoxyguanosine on the basis of the typical fragment ions of its trimethylsilyl (Me3Si) derivative. This product was then isolated by using reversed-phase high-performance liquid chromatography. The UV and proton nuclear magnetic resonance spectra taken from the isolated product confirmed the structure suggested by the mass spectrum of its Me3Si derivative. The yield of 8-hydroxyguanine was also measured. Its mechanism of formation is believed to involve OH radical addition to the C-8 position of guanine followed by oxidation of the radical adduct.

  17. Size, Composition, and Structure of the Deoxyribonucleic Acid of Herpes Simplex Virus Subtypes 1 and 2

    PubMed Central

    Kieff, Elliott D.; Bachenheimer, Steven L.; Roizman, Bernard

    1971-01-01

    Studies of the size, composition, and structure of the deoxyribonucleic acid (DNA) of the F and G prototypes of herpes simplex virus (HSV) subtypes 1 and 2 (HSV-1 and HSV-2) showed the following. (i) As previously reported by Good-heart et al. HSV-1 and HSV-2 DNA have a buoyant density of 1.726 and 1.728 g/cm3, corresponding to 67 and 69 guanine ± cytosine moles per cent, respectively. The difference in guanine plus cytosine content of the DNA species was confirmed by the finding of a 1 C difference in Tm. (ii) The DNA from purified virus on cocentrifugation with T4 DNA in neutral sucrose density gradients sedimented at 55S, corresponding to 99 ± 5 million daltons in molecular weight. HSV-1 and HSV-2 DNA could not be differentiated with respect to size. (iii) Cosedimentation of alkali-denatured DNA from purified virus with T4 DNA on alkaline sucrose density gradients consistently yielded several bands of single-stranded HSV DNA ranging from fragments 7 × 106 daltons to intact strands 48 × 106 daltons in molecular weight. PMID:4329966

  18. 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.

  19. Deoxyribonucleic acid modified poly(dimethylsiloxane) microfluidic channels for the enhancement of microchip electrophoresis.

    PubMed

    Liang, Ruping; Hu, Pengfei; Gan, Guihua; Qiu, Jianding

    2009-03-15

    In this paper, deoxyribonucleic acid (DNA) was employed to construct a functional film on the PDMS microfluidic channel surface and apply to perform electrophoresis coupled with electrochemical detection. The functional film was formed by sequentially immobilizing chitosan and DNA to the PDMS microfluidic channel surface using the layer-by-layer assembly. The polysaccharide backbone of chitosan can be strongly adsorbed onto the hydrophobic PDMS surface through electrostatic interaction in the acidic media, meanwhile, chitosan contains one protonatable functional moiety resulting in a strong electrostatic interactions between the surface amine group of chitosan and the charged phosphate backbone of DNA at low pH, which generates a hydrophilic microchannel surface and reveals perfect resistance to nonspecific adsorption of analytes. Aminophenol isomers (p-, o-, and m-aminophenol) served as a separation model to evaluate the effect of the functional PDMS microfluidic chips. The results clearly showed that these analytes were efficiently separated within 60s in a 3.7 cm long separation channel and successfully detected on the modified microchip coupled with in-channel amperometric detection mode at a single carbon fiber electrode. The theoretical plate numbers were 74,021, 92,658 and 60,552 Nm(-1) at the separation voltage of 900 V with the detection limits of 1.6, 4.7 and 2.5 microM (S/N=3) for p-, o-, and m-aminophenol, respectively. In addition, this report offered an effective means for preparing hydrophilic and biocompatible PDMS microchannel surface, which would facilitate the use of microfluidic devices for more widespread applications.

  20. 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

  1. Thymineless Death in Escherichia coli: Deoxyribonucleic Acid Replication and the Immune State

    PubMed Central

    Cummings, Donald J.; Kusy, Alvin R.

    1970-01-01

    Thymineless death (TLD) and nalidixic acid (NA) inactivation were studied in multiple auxotrophic strains of Escherichia coli B and B/r. As expected, it was found that both E. coli B and B/r exhibited an “immune state,” i.e., a fraction of the population survived inactivation to both TLD and NA. With glucose as a carbon source in minimal medium, 0.1 to 0.3% of strain B and 0.2 to 0.5% of strain B/r survived inactivation; with acetate as the carbon source, the surviving fractions were increased to 1 to 2% and 5 to 7%, respectively. These immune fractions could be increased in magnitude by preincubation in minimal media containing thymine. Systematic analysis of the particular supplements necessary for the immune state indicated that the absence of the required amino acids was essential for the maximal expression of immunity. However, immunity was not abolished in acetate medium even in the presence of the required supplements. Further studies on the replication of deoxyribonucleic acid (DNA) during preincubation indicated that the degree of immunity did not necessarily correlate with the completion of a round of DNA replication. This finding was supported by examining the immune state in synchronous populations. In both glucose and acetate medium, there was no significant change in the degree of immunity to inactivation within the cell cycles of E. coli B and B/r. We concluded that some other event, possibly inhibition of protein synthesis, was necessary in determining the degree of the immune state. DNA replication was investigated after TLD and NA inactivation, and, as expected, it was found that both events led to premature initiation of replication. The only differences observed in the effects of these two processes on DNA synthesis were the following. (i) NA-induced replication was less sensitive to chloramphenicol than was TLD. (ii) TLD-induced replication was unaffected by pretreatment of the cells with mitomycin C, but this pretreatment prevented the

  2. 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.

  3. 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

  4. 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

  5. Molecular hybridization between rat liver deoxyribonucleic acid and complementary ribonucleic acid

    PubMed Central

    Melli, Marialuisa; Bishop, J. O.

    1970-01-01

    RNA (cRNA) was synthesized in vitro on a template of rat liver DNA and its hybridization with rat liver DNA was studied by using the nitrocellulose-filter method. Sonication of the DNA diminished its apparent capacity to hybridize with RNA by about 50%. This is not due to cross-linkage of DNA molecules, because it could be shown that less than 2% of the sonicated DNA was cross-linked. The effect is due instead to the small size of the sonicated DNA molecules. Below a single-stranded molecular weight of 5×105 the DNA showed a progressive loss of capacity to hybridize with decrease in molecular weight. Evidence is presented suggesting that the apparently diminished capacity of the DNA to hybridize is due to loss of hybridized DNA from the membrane filters. When cRNA at concentrations of up to 25μg/ml is annealed with sonicated total DNA, an apparent hybridization saturation value is found at which about 2.5% of the DNA is hybridized with RNA. Increasing the cRNA concentration tenfold brought about the hybridization of a second component of the DNA approximately equal in amount to the first. The renaturation of rat liver DNA was studied by measuring the fall in the extinction at 260nm and two different components of renaturation were observed within the reiterated fraction of DNA. By hybridizing cRNA with different fractions of rat DNA the two components of the hybridization curve are shown to correspond to the two components of the renaturation curve. The conclusion is drawn that at a cRNA concentration of 250μg/ml most of the reiterated fraction of rat liver DNA is hybridized after annealing for 16h under standard conditions (0.30m-sodium chloride–30mm-sodium citrate at 65°C). Even with such a high cRNA concentration little or no hybridization of the slowly renaturing DNA fraction occurs. It is suggested that the most highly reiterated DNA component is poorly transcribed in vitro. PMID:5493851

  6. Alkylation by propylene oxide of deoxyribonucleic acid, adenine, guanosine and deoxyguanylic acid

    PubMed Central

    Lawley, P. D.; Jarman, M.

    1972-01-01

    1. Propylene oxide reacts with DNA in aqueous buffer solution at about neutral pH to yield two principal products, identified as 7-(2-hydroxypropyl)guanine and 3-(2-hydroxypropyl)adenine, which hydrolyse out of the alkylated DNA at neutral pH values at 37°C. 2. These products were obtained in quantity by reactions between propylene oxide and guanosine or adenine respectively. 3. The reactions between propylene oxide and adenine in acetic acid were parallel to those between dimethyl sulphate and adenine in neutral aqueous solution; the alkylated positions in adenine in order of decreasing reactivity were N-3, N-1 and N-9. A method for separating these alkyladenines is described. 4. Deoxyguanylic acid sodium salt was alkylated at N-7 by propylene oxide in neutral aqueous solution. 5. The nature of the side chain in the principal alkylation products was established by mass spectrometry, and the nature of the products is consistent with their formation by the bimolecular reaction mechanism. PMID:5073240

  7. Loss of Photoreversibility of Damage to Deoxyribonucleic Acid Replication in Ultraviolet-Irradiated Escherichia coli B/r thy trp

    PubMed Central

    Doudney, C. O.

    1974-01-01

    Loss of photoreversibility (LOP) of the ultraviolet (UV) damage which prevents reinitiation of deoxyribonucleic acid (DNA) replication occurred with incubation of Escherichia coli B/r thy trp cultures after UV doses of 240, 320, and 400 ergs/mm2. LOP occurred at the time of reinitiation of DNA replication in the cultures (i.e., after postirradiation lag periods of 45 min or more). Neither the absence of thymine nor the absence of tryptophan prevented LOP of the damage to DNA replication, suggesting that neither DNA replication nor protein synthesis is necessary for the process. These findings suggest that attempted initiation of DNA replication results in transformation of pyrimidine damage into permanent damage to chromosome structure at the reinitiation site. PMID:4607425

  8. 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.

  9. Influence of surfactant on dynamics of photoinduced motions and light emission of a dye-doped deoxyribonucleic acid

    NASA Astrophysics Data System (ADS)

    Sznitko, Lech; Parafiniuk, Kacper; Miniewicz, Andrzej; Rau, Ileana; Kajzar, Francois; Niziol, Jacek; Hebda, Edyta; Pielichowski, Jan; Sahraoui, Bouchta; Mysliwiec, Jaroslaw

    2013-10-01

    Pure deoxyribonucleic acid (DNA) is known to be soluble in water only and exhibits poor temperature stability. In contrary, it is well known that the complex of DNA - with cetyltrimethyl ammonium (CTMA) is insoluble in water but soluble in alcohols and can be processed into very good optical quality thin films by solution casting or spin deposition. Despite the success of DNA-CTMA, there is still need for new cationic surfactants which would extend the range of available solvents for DNA complex. We test and present experimental results of influence of new surfactants replacing CTMA in the DNA complex and based on benzalkonium chloride (BA) and didecyldimethylammonium chloride (DDCA) on their optical properties. Particularly, we were interested in all optical switching and light generation in amplified spontaneous emission process in these materials.

  10. 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.

  11. Properties of bacteriophage T4 mutants defective in gene 30 (deoxyribonucleic acid ligase) and the rII gene.

    PubMed

    Karam, J D; Barker, B

    1971-02-01

    In Escherichia coli K-12 strains infected with phage T4 which is defective in gene 30 [deoxyribonucleic acid (DNA) ligase] and in the rII gene (product unknown), near normal levels of DNA and viable phage were produced. Growth of such T4 ligase-rII double mutants was less efficient in E. coli B strains which show the "rapidlysis" phenotype of rII mutations. In pulse-chase experiments coupled with temperature shifts and with inhibition of DNA synthesis, it was observed that DNA synthesized by gene 30-defective phage is more susceptible to breakdown in vivo when the phage is carrying a wild-type rII gene. Breakdown was delayed or inhibited by continued DNA synthesis. Mutations of the rII gene decreased but did not completely abolish the breakdown. T4 ligase-rII double mutants had normal sensitivity to ultraviolet irradiation.

  12. Strong, but Age-Dependent, Protection Elicited by a Deoxyribonucleic Acid/Modified Vaccinia Ankara Simian Immunodeficiency Virus Vaccine.

    PubMed

    Chamcha, Venkateswarlu; Kannanganat, Sunil; Gangadhara, Sailaja; Nabi, Rafiq; Kozlowski, Pamela A; Montefiori, David C; LaBranche, Celia C; Wrammert, Jens; Keele, Brandon F; Balachandran, Harikrishnan; Sahu, Sujata; Lifton, Michelle; Santra, Sampa; Basu, Rahul; Moss, Bernard; Robinson, Harriet L; Amara, Rama Rao

    2016-01-01

    Background.  In this study, we analyzed the protective efficacy of a simian immunodeficiency virus (SIV) macaque 239 (SIVmac239) analogue of the clinically tested GOVX-B11 deoxyribonucleic acid (DNA)/modified vaccinia Ankara (MVA) human immunodeficiency virus vaccine. Methods.  The tested vaccine used a DNA immunogen mutated to mimic the human vaccine and a regimen with DNA deliveries at weeks 0 and 8 and MVA deliveries at weeks 16 and 32. Twelve weekly rectal challenges with 0.3 animal infectious doses of SIV sootey mangabey E660 (SIVsmE660) were administered starting at 6 months after the last immunization. Results.  Over the first 6 rectal exposures to SIVsmE660, <10-year-old tripartite motif-containing protein 5 (TRIM5)α-permissive rhesus macaques showed an 80% reduction in per-exposure risk of infection as opposed to a 46% reduction in animals over 10 years old; and, over the 12 challenges, they showed a 72% as opposed to a 10% reduction. Analyses of elicited immune responses suggested that higher antibody responses in the younger animals had played a role in protection. Conclusions.  The simian analogue of the GOVX-B11 HIV provided strong protection against repeated rectal challenges in young adult macaques.

  13. Inhibition of Thymidine Kinase Activity and Deoxyribonucleic Acid Synthesis in L Cells Infected with the Meningopneumonitis Agent

    PubMed Central

    Lin, Hsiu-San

    1968-01-01

    The activities of enzymes related to deoxyribonucleic acid (DNA) synthesis were studied in uninfected L cells and in L cells infected with Chlamydia psittaci (strain meningopneumonitis). The meningopneumonitis agent multiplied normally but failed to induce the synthesis of thymidine kinase in LM (TK−) cells which contain no thymidine kinase in the uninfected state. It was concluded that this microorganism has no thymidine kinase of its own and that it does not depend on the functioning of the host enzyme for synthesizing its DNA. Exposure of clone 5b L cells to the meningopneumonitis agent was followed by a decline in their thymidine kinase activity to nearly zero levels, whereas the levels of uridine kinase and thymidylate synthetase remained unchanged. Inhibition of thymidine kinase activity in L cells occurred soon after infection and required new protein synthesis by the meningopneumonitis agent. This inhibition occurred before inhibition of host DNA synthesis, but it was not an essential prelude to the latter inhibition. On the basis of this and previous investigations and in light of present knowledge of the mammalian cell cycle, it was postulated that the meningopneumonitis agent inhibits macromolecular synthesis in L cells by preventing the initiation of a new cell cycle. PMID:5724972

  14. Use of a Single-Strand Specific Nuclease for Analysis of Bacterial and Plasmid Deoxyribonucleic Acid Homo- and Heteroduplexes

    PubMed Central

    Crosa, Jorge H.; Brenner, Don J.; Falkow, Stanley

    1973-01-01

    Bacterial and plasmid homo- and heteroduplexes have been analyzed with a single-strand specific endonuclease, S1, of Aspergillus oryzae. Under appropriate assay conditions, there was a high degree of correlation between the degree of deoxyribonucleic acid (DNA)-DNA homoduplex formation assessed by the S1 endonuclease and by hydroxyapatite (HA). Heteroduplexes which contain extensive regions of polynucleotide sequences in common are similarly recognized by the S1 endonuclease and HA. In instances where there is little or imperfect complementarity between heterologous DNA strands, the S1 endonuclease and the HA method give slightly different estimates. From DNA duplex thermal stability experiments assayed with the S1 endonuclease, there is preliminary evidence that well-matched sequences identified by the enzyme are not similarly recognized by HA. The assay of homo- and heteroduplexes with the S1 endonuclease permits an accurate, reproducible and rapid determination of polynucleotide sequence relationships and may be seriously considered as a method of choice for survey work and for investigations which require a large number of DNA-DNA hybridization assays. PMID:4728274

  15. Greater Vulnerability of the Infecting Viral Strand of Replicative-Form Deoxyribonucleic Acid of Bacteriophage φX174

    PubMed Central

    Datta, B.; Poddar, R. K.

    1970-01-01

    Four types of φX-infected cells of Escherichia coli CR, a thymine-requiring strain of E. coli C, were prepared in which the parental replicative-form deoxyribonucleic acid (RF DNA) was labeled with same specific amounts of bromouracil in (i) both strands, (ii) only the infecting viral strand, (iii) only the complementary strand, and (iv) neither strand. The sensitivity of each type of infected cell toward irradiation by ultraviolet light, visible light, and X rays was measured. The results indicate that a certain amount of radiation damage in the infecting viral strand of the parental RF was more inhibitory to the production of progeny phage than when the damage was in the complementary strand. Similar conclusions were also drawn from “suicide” experiments of the phage-infected complexes containing 32P of the same specific activity on either strand of the parental RF DNA. The results suggest that the beta decay occurring in the infecting viral strand was more effective in inactivating the plaque-forming ability of the complex. PMID:4921725

  16. N-methylimidazolium modified magnetic particles as adsorbents for solid phase extraction of genomic deoxyribonucleic acid from genetically modified soybeans.

    PubMed

    Deng, Manchen; Jiang, Cheng; Jia, Li

    2013-04-10

    N-Methylimidazolium modified magnetic particles (MIm-MPs) were prepared and applied in the solid phase extraction of genomic deoxyribonucleic acid (DNA) from genetically modified soybeans. The adsorption of MIm-MPs for DNA mainly resulted from the strong electrostatic interaction between the positively charged MPs and the negatively charged DNA. The elution of DNA from MPs-DNA conjugates using phosphate buffer resulted from the stronger electrostatic interaction of phosphate ions with MPs than DNA. In the extraction procedure, no harmful reagents (e.g. phenol, chloroform and isopropanol, etc.) used, high yield (10.4 μg DNA per 30 mg sample) and high quality (A260/A280=1.82) of DNA can be realized. The as-prepared DNA was used as template for duplex-polymerase chain reaction (PCR) and the PCR products were analyzed by a sieving capillary electrophoresis method. Quick and high quality extraction of DNA template, and fast and high resolution detection of duplex PCR products can be realized using the developed method. No toxic reagents are used throughout the method.

  17. Initiation points for cellular deoxyribonucleic acid replication in human lymphoid cells converted by Epstein-Barr virus

    SciTech Connect

    Oppenheim, A.; Shlomai, Z.; Ben-Bassat, H.

    1981-08-01

    Replicon size was estimated in two Epstein-Barr virus (EBV)-negative human lymphoma lines, BJAB and Ramos, and four EBV-positive lines derived from the former ones by infection (conversion) with two viral strains, B95-8 and P3HR-1. Logarithmic cultures were pulse-labeled with (/sup -3/H)thymidine, and the deoxyribonucleic acid was spread on microscopic slides and autoradiographed by the method of Huberman and Riggs. Three of the four EBV-converted cell lines, BJAB/B95-8, Ra/B95-8, and Ra/HRIK, were found to have significantly shorter replicons (41, 21, 54% shorter, respectively), i.e., more initiation points, than their EBV-negative parents. BJAB/HRIK had replicons which were only slightly shorter (11%) than those of BJAB. However, analysis of track length demonstrated that extensive track fusion occurred during the labeling of BJAB/HRIK, implying that its true average replicon size is shorter than the observed value. The results indicate that in analogy to simian virus 40, EBV activates new initiation points for cellular DNA replication in EBV-transformed cells.

  18. Production of cells without deoxyribonucleic acid during thymidine starvation of lexA- cultures of Escherichia coli K-12.

    PubMed Central

    Howe, W E; Mount, D W

    1975-01-01

    When thymidine-requiring lexA- strains were starved for thymidine, the kinetics of survival were similar to those of a nearly isogenic lexA+ strain. The size distribution of cells in the lexA- and lexA+ cultures were, however, quite different. Whereas most of the cells in the starved lexA+ cultures grew into long filamentous forms (longer than 4.0 mum), many of the lexA- cells were found to have a normal rod shape (4.0 mum or shorter). It was shown that lexA- cells undergo more divisions during thymidine starvation than lexA+ cells. Furthermore, using an autoradiographic method to analyze deoxyribonucleic acid (DNA) distribution in the starved cells, we demonstrated that cells without DNA are produced in both normal and starved lexA- cultures at a much higher frequency than in lexA+ cultures. Some of these cells may be produced by breakdown of DNA, but we favor the hypothesis that they result from an abnormal cell division process. Since lexA mutations are dominant, we conclude that a diffusible product decreases the synthesis or activity of an inhibitor of cell division in lexA- strains when DNA synthesis is blocked by thymidine starvation. Images PMID:1104571

  19. Detection of Low Level Microwave Radiation Induced Deoxyribonucleic Acid Damage Vis-à-vis Genotoxicity in Brain of Fischer Rats

    PubMed Central

    Deshmukh, Pravin Suryakantrao; Megha, Kanu; Banerjee, Basu Dev; Ahmed, Rafat Sultana; Chandna, Sudhir; Abegaonkar, Mahesh Pandurang; Tripathi, Ashok Kumar

    2013-01-01

    Background: Non-ionizing radiofrequency radiation has been increasingly used in industry, commerce, medicine and especially in mobile phone technology and has become a matter of serious concern in present time. Objective: The present study was designed to investigate the possible deoxyribonucleic acid (DNA) damaging effects of low-level microwave radiation in brain of Fischer rats. Materials and Methods: Experiments were performed on male Fischer rats exposed to microwave radiation for 30 days at three different frequencies: 900, 1800 and 2450 MHz. Animals were divided into 4 groups: Group I (Sham exposed): Animals not exposed to microwave radiation but kept under same conditions as that of other groups, Group II: Animals exposed to microwave radiation at frequency 900 MHz at specific absorption rate (SAR) 5.953 × 10−4 W/kg, Group III: Animals exposed to 1800 MHz at SAR 5.835 × 10−4 W/kg and Group IV: Animals exposed to 2450 MHz at SAR 6.672 × 10−4 W/kg. At the end of the exposure period animals were sacrificed immediately and DNA damage in brain tissue was assessed using alkaline comet assay. Results: In the present study, we demonstrated DNA damaging effects of low level microwave radiation in brain. Conclusion: We concluded that low SAR microwave radiation exposure at these frequencies may induce DNA strand breaks in brain tissue. PMID:23833433

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

    PubMed

    Ge, Zhengwei; Wang, Wei; Yang, Chun

    2015-02-09

    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.

  1. Strong, but Age-Dependent, Protection Elicited by a Deoxyribonucleic Acid/Modified Vaccinia Ankara Simian Immunodeficiency Virus Vaccine

    PubMed Central

    Chamcha, Venkateswarlu; Kannanganat, Sunil; Gangadhara, Sailaja; Nabi, Rafiq; Kozlowski, Pamela A.; Montefiori, David C.; LaBranche, Celia C.; Wrammert, Jens; Keele, Brandon F.; Balachandran, Harikrishnan; Sahu, Sujata; Lifton, Michelle; Santra, Sampa; Basu, Rahul; Moss, Bernard; Robinson, Harriet L.; Amara, Rama Rao

    2016-01-01

    Background. In this study, we analyzed the protective efficacy of a simian immunodeficiency virus (SIV) macaque 239 (SIVmac239) analogue of the clinically tested GOVX-B11 deoxyribonucleic acid (DNA)/modified vaccinia Ankara (MVA) human immunodeficiency virus vaccine. Methods. The tested vaccine used a DNA immunogen mutated to mimic the human vaccine and a regimen with DNA deliveries at weeks 0 and 8 and MVA deliveries at weeks 16 and 32. Twelve weekly rectal challenges with 0.3 animal infectious doses of SIV sootey mangabey E660 (SIVsmE660) were administered starting at 6 months after the last immunization. Results. Over the first 6 rectal exposures to SIVsmE660, <10-year-old tripartite motif-containing protein 5 (TRIM5)α-permissive rhesus macaques showed an 80% reduction in per-exposure risk of infection as opposed to a 46% reduction in animals over 10 years old; and, over the 12 challenges, they showed a 72% as opposed to a 10% reduction. Analyses of elicited immune responses suggested that higher antibody responses in the younger animals had played a role in protection. Conclusions. The simian analogue of the GOVX-B11 HIV provided strong protection against repeated rectal challenges in young adult macaques. PMID:27006959

  2. Quantitation of pyrimidine dimer contents of nonradioactive deoxyribonucleic acid by electrophoresis in alkaline agarose gels

    SciTech Connect

    Sutherland, B.M.; Shih, A.G.

    1983-02-15

    We have developed a method of quantitating the pyrimidine dimer content of nonradioactive DNAs. DNA samples are treated with the UV-endonuclease from Micrococcus luteus and then separated according to molecular weight by electrophoresis on alkaline agarose gels. From their migration relative to known molecular weight standards, their median molecular weight and thus the number of dimers per DNA molecule in each sample can be calculated. Results of action spectra for dimer formation in T7 bacteriophage measured by this method agree well with action spectra for T7 killing. In addition, the method gives dimer yields in good agreement with those obtained by others using alkaline sucrose gradient sedimentation.

  3. Photoluminescence and Lasing from Deoxyribonucleic Acid Thin Films Doped With Sulforhodamine

    DTIC Science & Technology

    2007-03-20

    daltons. A sonication process16 was utilized to reduce the DNA MW to 150–200 kDa. For comparison to DNA, we have also used poly( methyl methacrylate ) (PMMA...29, 2729– (1990). 18. M. D. Rahn and T . A. King, “Comparison of laser performance of dye molecules in sol–gel, polycom, ormosil, and poly( methyl ...CTMA and PMMA thin films, solid DNA–CTMA and SRh powder were mixed and dissolved in butanol solution with different weight ratios. PMMA granules and

  4. Transformation of Bacillus subtilis in alpha-amylase productivity by deoxyribonucleic acid from B. subtilis var. amylosacchariticus.

    PubMed

    Yoneda, Y; Yamane, K; Yamaguchi, K; Nagata, Y; Maruo, B

    1974-12-01

    Deoxyribonucleic acid (DNA) of Bacillus subtilis var. amylosacchariticus showed almost the same ability as B. subtilis Marburg to induce transfer of several genetic markers in DNA-mediated transformation. DNA-DNA hybridization data also showed an intimate relationship between the two strains. Genetic elements involved in the production of extracellular alpha-amylase (EC 3.2.1.1.) in B. subtilis var. amylosacchariticus were studied by using DNA-mediated transformation. Two Marburg derivatives, NA20(amyR2) and NA20-22(amyR1), produced about 50 and 10 U of alpha-amylase per mg of cells, respectively, whereas B. subtilis var. amylosacchariticus produced as much as 150 U of the enzyme per mg of cells. When B. subtilis var. amylosacchariticus was crossed with strain NA20-22 as recipient, transformants that acquired high alpha-amylase productivity (about 50 U/mg of cells) were obtained. Genetic analysis revealed that a regulator gene (amyR) for alpha-amylase synthesis was found in B. subtilis var. amylosacchariticus, as in the case of B. natto 1212 (amyR2) and B. subtilis Marburg (amyR1). The allele was designated amyR3; it is phenotypically indistinguishable from amyR2, but is readily distinguishable from amyR1. The presence of amyR3 was not sufficient for an organism to render production of an exceptional amount of alpha-amylase. Extra-high alpha-amylase producers could be obtained by crossing B. subtilis var. amylosacchariticus as donor with strain NA20 as recipient. The transformants produced the same or even greater amounts of the enzyme than the donor strain. Results suggest the presence of another gene that is involved in the production of the exceptional amount of alpha-amylase.

  5. Structural studies of A-form sodium deoxyribonucleic acid: phosphorus-31 nuclear magnetic resonance of oriented fibers.

    PubMed

    Nall, B T; Rothwell, W P; Waugh, J S; Rupprecht, A

    1981-03-31

    A highly oriented sample of A-form sodium deoxyribonucleic acid (DNA) has been investigated by using proton-enhanced 31P nuclear magnetic resonance (NMR). Proton-decoupled spectra taken with different angles between the magnetic field direction and the fiber direction are compared to theoretical spectra which are calculated by assuming the following: (1) the orientation of the phosphate groups in the fiber is given by the A-form DNA coordinates suggested by Arnott & Hukins [Arnott, S., & Hukins, D. W. L. (1972) Biochem. Biophys. Res. Commun. 47, 1504-1509]; (2) the DNA phosphate groups may be considered stationary on the NMR time scale; (3) the relevant features of the spectra are determined solely by chemical shift anisotropy of the phosphorus atoms. The experimental and calculated spectra are in excellent agreement and support the validity of the above assumptions contrary to conclusions drawn in another investigation [Shindo, H., Wooton, J. B., Pheiffer, B. H., & Zimmerman, S. B. (1980) Biochemistry 19, 518-526]. In particular, we find no evidence to support the notion of a highly irregular phosphodiester backbone. Comparison of observed and simulated spectra allows the determination of the orientation of the 31P chemical shielding tensor relative to the bonding framework of the phosphodiester group. The orientation agrees with that expected from NMR studies of phosphodiester model compounds [Kohler, S. J., & Klein, M. P. (1976) Biochemistry 15, 967-973; Herzfeld, J., Griffin, R. G., & Haberkorn, R. A. (1978) Biochemistry 17, 2711-2718] and X-ray diffraction of oriented fibers [Arnott, S., & Hukins, D. W. L. (1972) Biochem. Biophys. Res. Commun. 47, 1504-1509].

  6. Molecular mechanisms of pyrimidine dimer excision in Saccharomyces cerevisiae: incision of ultraviolet-irradiated deoxyribonucleic acid in vivo

    SciTech Connect

    Reynolds, R.J.; Friedberg, E.C.

    1981-05-01

    A group of genetically related ultraviolet (uv)-sensitive mutants of Saccharomyces cerevisiae has been examined in terms of their survival after exposure to uv radiation, their ability to carry out excision repair or pyrimidine dimers as measured by the loss of sites (pyrimidine dimers) sensitive to a dimer-specific enzyme probe, and in terms of their ability to effect incision of their deoxyribonucleic acid (DNA) during post-uv incubation in vivo (as measured by the detection of single-strand breaks in nuclear DNA). In addition to a haploid RAD/sup +/ strain (S288C), 11 different mutants representing six RAD loci (RAD1, RAD2, RAD3, RAD4, RAD14, and RAD18) were examined. Quantitative analysis of excision repair capacity, as determined by the loss of sites in DNA sensitive to an enzyme preparation from M. luteus which is specific for pyrimidine dimers, revealed a profound defect in this parameter in all but three of the strains examined. The rad14-1 mutant showed reduced but significant residual capacity to remove enzyme-sensitive sites as did the rad2-4 mutant. The latter was the only one of three different rad2 alleles examined which was leaky in this respect. The uv-sensitive strain carrying the mutant allele rad18-1 exhibited normal loss of enzyme-sensitive sites consistent with its assignment to the RAD6 rather than the RAD3 epistatic group. All strains having mutant alleles of the RAD1, RAD2, RAD3, RAD4, and RAD14 loci showed no detectable incubation-dependent strand breaks in nuclear DNA after exposure to uv radiation. These experiments suggest that the RAD1, RAD2, RAD3, RAD4 (and probably RAD14) genes are all required for the incision of uv-irradiated DNA during pyrimidine dimer excision in vivo.

  7. 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.

  8. Determination of triadimenol based on the quenching effect on resonance light scattering from the triadimenol-deoxyribonucleic acid-hydrochloric acid system.

    PubMed

    Du, Fengpei; Luo, Xiaolin; Jiang, Guibin; Hou, Shicong; Liu, Gang; Ren, Liping; Zhang, Li; Huang, Qin; Jie, Nianqin

    2007-05-01

    Analysis of triadimenol was carried out using deoxyribonucleic acids (DNA) via the resonance light scattering (RLS) technique. After adding triadimenol into aqueous medium of pH 1.72, the RLS of DNA was remarkably quenched. A resonance light scattering peak at 310 nm was found, and the quenched intensity of RLS at this wavelength was proportional to the concentration of triadimenol. The linear range of the calibration curve was approximately 0-3 microg mL-1 with a detection limit (S/N=3) of 0.07 microg mL-1. The triadimenol in samples of water, cucumber and human serum was determined. The results were satisfactory, and the recovery rates were in the range of 96.3-106.0%, 94.8-105.9% and 92.3-100.5%, respectively. The interaction mechanism was also studied.

  9. Deoxyribonucleic acid repair in Bacillus subtilis: development of competent cells into a tester for carcinogens

    SciTech Connect

    Yasbin, R.E.; Miehl, R.

    1980-04-01

    The development of competent transformed Bacillus subtilis into a tester system for carcinogens is described. Precocious or noninduced activation of SOS functions occurs in competent cells. Thus, lower doses or concentrations of SOS inducing agents are needed to cause cell death due to indigenous prophage activation and lysis of bacteria. The two known defective prophages in B. subtilis enhance the sensitivity of competent cells to the carcinogens ultraviolet light, mitomycin C, and methyl methanesulfonate. However, these same cells have no enhanced sensitivity for the non-carcinogenic ethyl methanesulfonate or for nalidixic acid. Therefore, competent B. subtilis appears to be a sensitive tester for carcinogens.

  10. 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

  11. Transfecting deoxyribonucleic acid of Bacillus bacteriophage phi 29 that is protease sensitive.

    PubMed

    Hirokawa, H

    1972-06-01

    The transfecting activity of Bacillus phage varphi29 DNA, extracted either by sodium lauroyl sarcosine-phenol or by 2 M perchlorate, was destroyed by treatment with proteolytic enzymes, although these enzymes did not effect transfecting DNAs of SPP1, SPO1, and SP50. These facts suggest that a protein is associated with transfective varphi29 DNA. Stabilization of protease-resistance during transfection appeared earlier than that of DNaseresistance, indicating that the protein associated with varphi29 DNA is necessary for initiation of the incorporation of DNA molecules into competent cells. The physical nature of varphi29 DNA before and after the trypsin treatment was investigated by sucrose and CsCl density gradient centrifugations. The trypsin treatment did not alter the sedimentation rate of the unit varphi29 DNA; however, it did convert the sedimentation rate of the aggregated material in the untreated DNA to that of the unit varphi29 DNA. The density of the trypsinized DNA was 0.009 g/cm(3) greater than that of the untreated DNA. The possible location of the protein on the DNA is discussed.

  12. 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.

  13. Isolation and characterization of deoxyribonucleic acid from tissue of the woolly mammoth, Mammuthus primigenius.

    PubMed

    Johnson, P H; Olson, C B; Goodman, M

    1985-01-01

    DNA was isolated from tissue samples of several mammoth specimens, radiocarbon dated between 10,000 and 53,000 years old. The DNA was purified by chromatography on hydroxyapatite at 60 degrees C and was characterized as a heterogeneous population of fragments ranging in size from 3000 to 200 base pairs. Thermal denaturation analysis demonstrated that approximately 25% of the DNA had a base composition similar to Asian elephant DNA calculated as 36% G + C. Preliminary analysis by nucleic acid hybridization indicated that only a small fraction of DNA isolated from mammoth tissue (2-5%) was homologous to DNA of Asian elephant, a close living relative of the mammoth. Our results provide the first definitive isolation and characterization of DNA from ancient tissue and suggest a purification strategy that will lead to preparations of DNA from mammoth tissue significantly enriched in elephant-related DNA sequences.

  14. The Chinese hamster Alu-equivalent sequence: a conserved highly repetitious, interspersed deoxyribonucleic acid sequence in mammals has a structure suggestive of a transposable element.

    PubMed Central

    Haynes, S R; Toomey, T P; Leinwand, L; Jelinek, W R

    1981-01-01

    A consensus sequence has been determined for a major interspersed deoxyribonucleic acid repeat in the genome of Chinese hamster ovary cells (CHO cells). This sequence is extensively homologous to (i) the human Alu sequence (P. L. Deininger et al., J. Mol. Biol., in press), (ii) the mouse B1 interspersed repetitious sequence (Krayev et al., Nucleic Acids Res. 8:1201-1215, 1980) (iii) an interspersed repetitious sequence from African green monkey deoxyribonucleic acid (Dhruva et al., Proc. Natl. Acad. Sci. U.S.A. 77:4514-4518, 1980) and (iv) the CHO and mouse 4.5S ribonucleic acid (this report; F. Harada and N. Kato, Nucleic Acids Res. 8:1273-1285, 1980). Because the CHO consensus sequence shows significant homology to the human Alu sequence it is termed the CHO Alu-equivalent sequence. A conserved structure surrounding CHO Alu-equivalent family members can be recognized. It is similar to that surrounding the human Alu and the mouse B1 sequences, and is represented as follows: direct repeat-CHO-Alu-A-rich sequence-direct repeat. A composite interspersed repetitious sequence has been identified. Its structure is represented as follows: direct repeat-residue 47 to 107 of CHO-Alu-non-Alu repetitious sequence-A-rich sequence-direct repeat. Because the Alu flanking sequences resemble those that flank known transposable elements, we think it likely that the Alu sequence dispersed throughout the mammalian genome by transposition. Images PMID:9279371

  15. 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.

  16. No activation of new initiation points for deoxyribonucleic acid replication in BALB/c 3T3 cells transformed by Kirsten sarcoma virus

    SciTech Connect

    Oppenheim, A.; Horowitz, A.T.

    1981-08-01

    BALB/c 3T3 cells were transformed by Kirsten sarcoma virus, and five clones were isolated in soft agar. Average replicon sizes of the transformed cell lines were stimated by the method of fiber-autoradiography and found to be the same size as the nontransformed 3T3 cells, analyzed in parallel. The results indicate that, unlike simian virus 40 and Epstein-Barr virus, Kirsten sarcoma virus does not activate new initiation points for cellular deoxyribonucleic acid replication in murine sarcome virus-transformed BALB/c 3T3 cells.

  17. 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...

  18. Heritable and cancer risks of exposures to anticancer drugs: inter-species comparisons of covalent deoxyribonucleic acid-binding agents.

    PubMed

    Vogel, E W; Barbin, A; Nivard, M J; Stack, H F; Waters, M D; Lohman, P H

    1998-05-25

    In the past years, several methodologies were developed for potency ranking of genotoxic carcinogens and germ cell mutagens. In this paper, we analyzed six sub-classes of covalent deoxyribonucleic acid (DNA) binding antineoplastic drugs comprising a total of 37 chemicals and, in addition, four alkyl-epoxides, using four approaches for the ranking of genotoxic agents on a potency scale: the EPA/IARC genetic activity profile (GAP) database, the ICPEMC agent score system, and the analysis of qualitative and quantitative structure-activity and activity-activity relationships (SARs, AARs) between types of DNA modifications and genotoxic endpoints. Considerations of SARs and AARs focused entirely on in vivo data for mutagenicity in male germ cells (mouse, Drosophila), carcinogenicity (TD50s) and acute toxicity (LD50s) in rodents, whereas the former two approaches combined the entire database on in vivo and in vitro mutagenicity tests. The analysis shows that the understanding and prediction of rank positions of individual genotoxic agents requires information on their mechanism of action. Based on SARs and AARs, the covalent DNA binding antineoplastic drugs can be divided into three categories. Category 1 comprises mono-functional alkylating agents that primarily react with N7 and N3 moieties of purines in DNA. Efficient DNA repair is the major protective mechanism for their low and often not measurable genotoxic effects in repair-competent germ cells, and the need of high exposure doses for tumor induction in rodents. Due to cell type related differences in the efficiency of DNA repair, a strong target cell specificity in various species regarding the potency of these agents for adverse effects is found. Three of the four evaluation systems rank category 1 agents lower than those of the other two categories. Category 2 type mutagens produce O-alkyl adducts in DNA in addition to N-alkyl adducts. In general, certain O-alkyl DNA adducts appear to be slowly repaired, or

  19. 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.

  20. Babesia gibsoni: detection in blood smears and formalin-fixed, paraffin-embedded tissues using deoxyribonucleic acid in situ hybridization analysis.

    PubMed

    Yamasaki, Masahiro; Kobayashi, Yusuke; Nakamura, Kensuke; Sasaki, Noboru; Murakami, Masahiro; Rajapakshage, Bandula Kumara Wickramasekara; Ohta, Hiroshi; Yamato, Osamu; Maede, Yoshimitsu; Takiguchi, Mitsuyoshi

    2011-01-01

    In this study, we attempted to detect Babesia gibsoni in blood smears and formalin-fixed, paraffin-embedded tissues obtained from B. gibsoni-infected dogs using in situ hybridization. Using a digoxigenin-conjugated deoxyribonucleic acid (DNA) probe, both intraerythrocytic and exoerythrocytic parasites in the culture could be specifically stained in blood smears fixed with 4% phosphate-buffered paraformaldehyde. This indicated that genomic DNA extracted from the parasites could be detected using in situ hybridization. Moreover, the parasite could be specifically stained in paraffin-embedded spleen, lymph node, and kidney sections using in situ hybridization. Infected erythrocytes in blood vessels in the spleen and kidney, hemosiderin-laden macrophages in the spleen, and phagocytized erythrocytes, which seemed to be infected with the parasites, in lymph nodes were also specifically stained. This suggests that in situ hybridization can be utilized to investigate both the life cycle of B. gibsoni and the pathological condition of canine babesiosis.

  1. Evaluation of deoxyribonucleic acid toxicity induced by the radiopharmaceutical 99mTechnetium-Methylenediphosphonic acid and by stannous chloride in Wistar rats.

    PubMed

    Mattos, José Carlos Pelielo De; Matos, Vanessa Coutinho de; Rodrigues, Michelle Pinheiro; Oliveira, Marcia Betânia Nunes de; Dantas, Flavio José S; Santos-Filho, Sebastião David; Bernardo-Filho, Mario; Caldeira-de-Araujo, Adriano

    2012-11-01

    Radiopharmaceuticals are employed in patient diagnostics and disease treatments. Concerning the diagnosis aspect, technetium-99m (99mTc) is utilized to label radiopharmaceuticals for single photon computed emission tomography (SPECT) due to its physical and chemical characteristics. 99mTc fixation on pharmaceuticals depends on a reducing agent, stannous chloride (SnCl(2)) being the most widely-utilized. The genotoxic, clastogenic and anegenic properties of the 99mTc-MDP(methylene diphosphonate used for bone SPECT) and SnCl(2) were evaluated in Wistar rat blood cells using the Comet assay and micronucleus test. The experimental approach was to endovenously administer NaCl 0.9% (negative control), cyclophosphamide 50 mg/kg b.w. (positive control), SnCl(2) 500 μg/mL or 99mTc-MDP to animals and blood samples taken immediately before the injection, 3, and 24 h after (in the Comet assay) and 36 h after, for micronucleus test. The data showed that both SnCl(2) and 99mTc-MDP-induced deoxyribonucleic acid (DNA) strand breaks in rat total blood cells, suggesting genotoxic potential. The 99mTc-MDP was not able to induce a significant DNA strand breaks increase in in vivo assays. Taken together, the data presented here points to the formation of a complex between SnCl(2) in the radiopharmaceutical 99mTc-MDP, responsible for the decrease in cell damage, compared to both isolated chemical agents. These findings are important for the practice of nuclear medicine.

  2. Modification and restriction of T-even bacteriophages. In vitro degradation of deoxyribonucleic acid containing 5-hydroxymethylctosine.

    PubMed

    Fleischman, R A; Cambell, J L; Richardson, C C

    1976-03-25

    Using the single-stranded circular DNA of bacteriophage fd as template, double-stranded circular DNA has been prepared in vitro with either 5-hydroxymethylcytosine ([hmdC]DNA) or cytosine ([dC]DNA) in the product strand. Extracts prepared from Escherichia coli cells restrictive to T-even phage containing nonglucosylated DNA degrade [hmdC]DNA to acid-soluble material in vitro, but do not degrade [dC]dna. In contrast, extracts prepared from E. coli K12 rglA- rglB-, a strain permissive to T-even phage containing nonglucosylated DNA, do not degrade [hmdC]DNA or [dC]DNA. In addition, glucosylation of the [hmdC]DNA renders it resistant to degradation by extracts from restrictive strains. The conversion of [hmdC]DNA to acid-soluble material in vitro consists of an HmCyt-specific endonucleolytic cleavage requiring the presence of the RglB gene product to form a linear molecule, followed by a non-HmCyt-specific hydrolysis of the linear DNA to acid-soluble fragments, catalyzed in part by exonuclease V. The RglB protein present in extracts of E. coli K12 rglA- rglB+ has been purified 200-fold by complementation with extracts from E. coli K12 rglA- rglB-. The purified RglB protein does not contain detectable HmCyt-specific endonuclease or exonuclease activity. In vitro endonucleolytic cleavage of [hmdC]DNA thus requires additional factors present in cell extracts.

  3. Electrophoresis-Enhanced Detection of Deoxyribonucleic Acids on a Membrane-Based Lateral Flow Strip Using Avian Influenza H5 Genetic Sequence as the Model

    PubMed Central

    Wu, Jui-Chuang; Chen, Chih-Hung; Fu, Ja-Wei; Yang, Huan-Ching

    2014-01-01

    This study reports a simple strategy to detect a deoxyribonucleic acid (DNA) on a membrane-based lateral flow (MBLF) strip without tedious gel preparation, gel electrophoresis, and EtBr-staining processes. The method also enhances the detection signal of the genetic sample. A direct electric field was applied over two ends of the MBLF strips to induce an electrophoresis of DNAs through the strips. The signal enhancement was demonstrated by the detection of the H5 subtype of avian influenza virus (H5 AIV). This approach showed an excellent selectivity of H5 AIV from other two control species, Arabidopsis thaliana and human PSMA5. It also showed an effective signal repeatability and sensitivity over a series of analyte concentrations. Its detection limit could be enhanced, from 40 ng to 0.1 ng by applying 12 V. The nano-gold particles for the color development were labeled on the capture antibody, and UV-VIS and TEM were used to check if the labeling was successful. This detection strategy could be further developed to apply on the detection of drug-allergic genes at clinics or detection of infectious substances at incident sites by a simple manipulation with an aid of a mini-PCR machine and auxiliary kits. PMID:24603637

  4. 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)

  5. 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.

  6. 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.

  7. Aminosulfhydryl and Aminodisulfide Compounds Enhance Binding of the Glucocorticoid Receptor Complex to Deoxyribonucleic Acid-Coated Cellulose and to Chromatin

    DTIC Science & Technology

    1993-01-01

    glucocorticoid receptor [21]. Diaminosulfhydryl chloroacetic acid was obtained from the Fisher compounds are more active at enhancing GRC Scientific...phase consisting of 0. I M BASE containing 25mM KCI and 3 mM chloroacetic acid and 5mM d/-10-camphorsul- MgCI2, pH 7.6 at 0 0C) was added to each tube...Enhance Binding of the Glucocorticoid Receptor Complex to Deoxy- ribonucleic Acid -Coated Cellulose and to Chromatin 4. AUThOR(S)’ J.M. Karle, R. Olmeda and

  8. 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

  9. Effects of retinoids on iodine metabolism, thyroid peroxidase gene expression, and deoxyribonucleic acid synthesis in porcine thyroid cells in culture.

    PubMed

    Arai, M; Tsushima, T; Isozaki, O; Shizume, K; Emoto, N; Demura, H; Miyakawa, M; Onoda, N

    1991-12-01

    Effects of retinoids on DNA synthesis, iodine metabolism, and thyroid peroxidase messenger RNA levels were studied in cultured porcine thyroid cells. Retinol (10(-8)-10(-5) M) alone did not affect DNA synthesis but potentiated that induced by epidermal growth factor or insulin-like growth factor-I without changes in the number or affinity of receptors for the growth factors, suggesting that retinol stimulates postreceptor events responsible for DNA synthesis. Retinol was an inhibitor of TSH-stimulated iodine metabolism. Iodide uptake and release of organified iodine stimulated by TSH or forskolin were inhibited dose dependently by treatment with retinol. The inhibition was detected at 10(-8) M and was approximately 50% at 10(-6) M. The potency of retinoic acid was comparable to that of retinol. The inhibitory effect of retinol was detected after treatments of thyroid cells for 24 h, and the maximal effect occurred after 48 h incubation. The cAMP accumulation in cultures treated with TSH plus retinol was lower than that of control cultures treated with TSH alone. However, iodide uptake stimulated by 8-bromo-cAMP was also inhibited by retinoids. Retinol reduced TSH- or 8-bromo-cAMP-stimulated gene expression of thyroid peroxidase. Thus, the data suggest that retinoids inhibit TSH-stimulated iodine metabolism by reducing cAMP accumulation and also by acting on the steps subsequent to cAMP production.

  10. The effect of feeding with a tryptophan-free amino acid mixture on rat liver magnesium ion-activated deoxyribonucleic acid-dependent ribonucleic acid polymerase

    PubMed Central

    Henderson, A. R.

    1970-01-01

    1. The Widnell & Tata (1966) assay method for Mg2+-activated DNA-dependent RNA polymerase was used for initial-velocity determinations of rat liver nuclear RNA polymerase. One unit (U) of RNA polymerase was defined as that amount of enzyme required for 1 mmol of [3H]GMP incorporation/min at 37°C. 2. Colony fed rats were found to have a mean RNA polymerase activity of 65.9μU/mg of DNA and 18h-starved rats had a mean activity of 53.2μU/mg of DNA. Longer periods of starvation did not significantly decrease RNA polymerase activity further. 3. Rats that had been starved for 18h were used for all feeding experiments. Complete and tryptophan-deficient amino acid mixtures were given by stomach tube and the animals were killed 15–120min later. The response of RNA polymerase to the feeding with the complete amino acid mixture was rapid and almost linear over the first hour of feeding, resulting in a doubling of activity. The activity was still elevated above the starvation value at 120min after feeding. The tryptophan-deficient amino acid mixture produced a much less vigorous response about 45min after the feeding, and the activity had returned to the starvation value by 120min after the feeding. 4. The response of RNA polymerase to the feeding with the complete amino acid mixture was shown to occur within a period of less than 5min to about 10min after the feeding. 5. Pretreatment of the animals with puromycin or cycloheximide was found to abolish the 15min RNA polymerase response to the feeding with the complete amino acid mixture, but the activity of the controls was unaffected. 6. The characteristics of the RNA polymerase from 18h-starved animals and animals fed with the complete or incomplete amino acid mixtures for 1h were examined. The effects of Mg2+ ions, pH, actinomycin D and nucleoside triphosphate omissions were determined. The [Mg2+]– and pH–activity profiles of the RNA polymerase from the animal fed with the complete mixture appeared to differ from

  11. 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.

  12. 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.

  13. 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.

  14. Early effects of oestradiol-17β on the chromatin and activity of the deoxyribonucleic acid-dependent ribonucleic acid polymerases (I and II) of the rat uterus

    PubMed Central

    Glasser, S. R.; Chytil, F.; Spelsberg, T. C.

    1972-01-01

    Oestradiol-17β (1.0μg) was injected intravenously into ovariectomized rats. The earliest detectable hormonal response in isolated uterine nuclei was an increase (10–15min) in RNA polymerase II activity (DNA-like RNA synthesis), which reached a peak at 30min and then decreased to control values (by 1–2h) before displaying a second increase over control activity from 2 to 12h. The next response to oestradiol-17β was an increase (30–60min) in polymerase I activity (rRNA synthesis) and template capacity of the chromatin. The concentrations of acidic chromatin proteins did not begin to increase until 1h after injection of oestradiol-17β and histone concentrations showed no significant changes during the 8h period after administration. The early (15min) increase in RNA synthesis in `high-salt conditions' can be completely eliminated by α-amanitin, an inhibitor of the RNA polymerase II. The exact nature of this early increase in endogenous polymerase II activity remains to be determined, e.g. whether it is caused by the increased availability of transcribable DNA of the chromatin or via direct hormonal activation of the enzyme per se. PMID:4656807

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Detection of a New Interstellar Molecule: Thiocyanic Acid HSCN

    NASA Astrophysics Data System (ADS)

    Halfen, D. T.; Ziurys, L. M.; Brünken, S.; Gottlieb, C. A.; McCarthy, M. C.; Thaddeus, P.

    2009-09-01

    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 Ka = 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 × 1013 cm-2 in Sgr B2(N) is only three times lower than that of HNCS. The fractional abundances of HSCN and HNCS relative to H2 are 4.5 × 10-12 and 1.1 × 10-11. By analogy with the isomeric pair HCN and HNC, these two sulfur-bearing isomers are plausibly formed from a common cation precursor.

  2. Hard and soft acids and bases: small molecules.

    PubMed

    Reed, James L

    2009-08-03

    The operational chemical hardness has been determined for the hydride, chloride, and fluoride derivatives of the anionic atomic bases of the second period. Of interest is the identification of the structure and associated processes that give rise to hard-soft behavior in small molecules. The Pearson Principle of Hard and Soft Acids and Bases has been taken to be the defining statement about hard-soft behavior and as a definition of chemical hardness. Similar to the case for atoms, the molecule's responding electrons have been identified as the structure giving rise to hard-soft behavior, and a relaxation described by a modified Slater model has been identified as the associated process. The responding electrons are the molecule's valence electrons that are not undergoing electron transfer in an acid-base interaction. However, it has been demonstrated that chemical hardness is a local property, and only those responding electrons that are associated with the base's binding atom directly impact chemical hardness.

  3. Magnetic Resonance Imaging-Detected Tumor Residue after Intensity-Modulated Radiation Therapy and its Association with Post-Radiation Plasma Epstein-Barr Virus Deoxyribonucleic Acid in Nasopharyngeal Carcinoma

    PubMed Central

    Lv, Jia-Wei; Zhou, Guan-Qun; Li, Jia-Xiang; Tang, Ling-Long; Mao, Yan-Ping; Lin, Ai-Hua; Ma, Jun; Sun, Ying

    2017-01-01

    Purpose: To evaluate the prognostic value of magnetic resonance imaging (MRI)-detected tumor residue after intensity-modulated radiation therapy (IMRT) and its association with post-treatment plasma Epstein-Barr virus deoxyribonucleic acid (EBV DNA) in nasopharyngeal carcinoma (NPC). Methods and materials: A prospective database of patients with histologically-proven NPC was used to retrospectively analyze 664 cases. Pre- and post-treatment MRI scans were independently reviewed by two senior radiologists who were blinded to clinical findings. Factors significantly associated with MRI-detected tumor residue were identified and included in the following multivariate logistic regression model. Residual risk model were established. Receiver operating characteristic (ROC) identify the optimal cut-off risk score for tumor residue. Results: MRI-detected residual tumor at three months after IMRT was associated with poor prognosis. The 5-year survival rates for the non-residual and residual groups were: OS (93.8% vs. 76.6%, P<0.001), PFS (84.7% vs. 67.9%, P=0.006), LRFS (93.4% vs. 80.4%, P=0.002), and DMFS (90.3% vs. 87.9%, P=0.305), respectively. Three-month post-treatment EBV DNA was significantly associated with tumor residue (P<0.001). A residual risk score model was established, consisting of T and N categories and post-treatment EBV DNA. ROC identified 22.74 as the optimal cut-off risk score for tumor residue. High-risk score was independently associated with poor treatment outcomes. Conclusions: MRI-detected tumor residue was an independent adverse prognostic factor in NPC; and significantly associated with three-month post-treatment EBV DNA. As limited resources in some endemic areas prevent patients from undergoing routine post-treatment imaging, our study identifies a selection risk-model, providing a cost-effective reference for the selection of follow-up strategies and clinical decision-making. PMID:28382149

  4. [Microspeciation of amphoteric molecules of unusual acid-base properties].

    PubMed

    Kóczián, Kristóf

    2007-01-01

    The phisico-chemical properties of bio- and drug molecules greatly influence their interactions in the body and strongly effect the mechanism of drug action. Among these properties, macroscopic and site-specific protonation constants are of crucial importance. Latter one is the tool to calculate the relative concentration of the various microspecies in the compartments of the body at different pH values, and also, it is the versatile parameter to improve the pharmacokinetic properties of a new molecule in a particular family of drugs. In the present thesis work, the microspeciation of three molecules of great pharmaceutical importance and unusual acid-base properties, were carried out. The microconstants of tenoxicam, the non-steroidal anti-inflammatory drug, were described, introducing a novel deductive method using Hammett constants. For this purpose, a total of 8 tenoxicam and piroxicam derivatives were synthesised. To the best of our knowledge, the log k(N)O microconstant of tenoxicam obtained thus is the lowest enolate basicity value, which, however, can be well explained by the effects of the intramolecular environment. The developed evaluation procedure is suitable for microconstant determination of compounds in other molecule families. Besides, prodrug-type compounds and analogues similar to the structures of selective COX-2 isoenzyme inhibitors were synthesised. The other two molecules studied, the 6-aminopenicillanic acid and 7-cephalosporanic acid, the core molecules of the two most important beta-lactam antibiotic-types were derivatised and investigated by 1D and 2D NMR techniques. The NMR-pH titration on the parent compounds and their ester derivatives, combined with in situ pH-measurements allowed the microspeciation of these easily decomposing molecules. One of the protonation constant of 7-ACA (log kN(O) = 4.12), to the best of our knowledge, is the least non-aromatic basic amino-site among the natural compounds.

  5. Interactions of carcinogens with DNA (deoxyribonucleic acid)

    SciTech Connect

    Broyde, S.; Shapiro, R.

    1989-10-01

    The principal goal of this research has been the determination of the conformational changes produced in DNA by the covalent binding of a carcinogenic aromatic amine, and the correlation of these changes with the mutations and carcinogenic effects initiated by the same substances. To this end, we have devised new synthetic methods for the preparation of oligonucleotides modified by derivatives af 4-aminobiphenyl and aniline. We have also performed potential energy minimization studies on the above substances and on single and double stranded DNA fragments bearing the above amines as well as acetylaminofluorene, aminofluorene, aminopyrene and the antibiotic mitomycin. Our computations have been carried out on DOE supercomputers using our program, DUPLEX. We have defined a number of novel structures for these modified DNAs, including Hoogsteen, wedge'' (see below) denatured, cross-linked and intercalated forms. Some suggestions have been made about the relation of these forms to mutagenesis. 7 refs.

  6. 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.

  7. Exporters for Production of Amino Acids and Other Small Molecules.

    PubMed

    Eggeling, Lothar

    2016-11-11

    Microbes are talented catalysts to synthesize valuable small molecules in their cytosol. However, to make full use of their skills - and that of metabolic engineers - the export of intracellularly synthesized molecules to the culture medium has to be considered. This step is as essential as is each step for the synthesis of the favorite molecule of the metabolic engineer, but is frequently not taken into account. To export small molecules via the microbial cell envelope, a range of different types of carrier proteins is recognized to be involved, which are primary active carriers, secondary active carriers, or proteins increasing diffusion. Relevant export may require just one carrier as is the case with L-lysine export by Corynebacterium glutamicum or involve up to four carriers as known for L-cysteine excretion by Escherichia coli. Meanwhile carriers for a number of small molecules of biotechnological interest are recognized, like for production of peptides, nucleosides, diamines, organic acids, or biofuels. In addition to carriers involved in amino acid excretion, such carriers and their impact on product formation are described, as well as the relatedness of export carriers which may serve as a hint to identify further carriers required to improve product formation by engineering export.

  8. History of gymnemic acid, a molecule that does not exist. .

    PubMed

    Zarrelli, Armando; Romanucci, Valeria; Gravante, Raffaele; Di Marino, Cinzia; Di Fabio, Giovanni

    2014-10-01

    In the literature there are hundreds of articles, the first dating back to 1866 and the last to 2014, on gymnemic acid, isolated from Gymnnema sylvestre, from its isolation to the determination of its biological activities. Gymnemic acid has a CAS number but its structure is not specified. Studies during the second half of the 1970s clearly demonstrated that what was being referred to as gymnemic acid is actually a very complex mixture of dozens of substances, belonging to different classes of natural compounds. This plant, whose infusions or complex mixtures of its metabolites are the basis for many formulas sold in pharmacies and by herbalists, has anti-diabetic and slimming effects. It is certainly misleading to talk about gymnemic acid as a specific molecule. There may be doubts about the exact composition of the products, and consequently about their origin and the claimed effects.

  9. Endogenous molecules stimulating N-acylethanolamine-hydrolyzing acid amidase (NAAA).

    PubMed

    Tai, Tatsuya; Tsuboi, Kazuhito; Uyama, Toru; Masuda, Kim; Cravatt, Benjamin F; Houchi, Hitoshi; Ueda, Natsuo

    2012-05-16

    Fatty acid amide hydrolase (FAAH) plays the central role in the degradation of bioactive N-acylethanolamines such as the endocannabinoid arachidonoylethanolamide (anandamide) in brain and peripheral tissues. A lysosomal enzyme referred to as N-acylethanolamine-hydrolyzing acid amidase (NAAA) catalyzes the same reaction with preference to palmitoylethanolamide, an endogenous analgesic and neuroprotective substance, and is therefore expected as a potential target of therapeutic drugs. In the in vitro assays thus far performed, the maximal activity of NAAA was achieved in the presence of both nonionic detergent (Triton X-100 or Nonidet P-40) and the SH reagent dithiothreitol. However, endogenous molecules that might substitute for these synthetic compounds remain poorly understood. Here, we examined stimulatory effects of endogenous phospholipids and thiol compounds on recombinant NAAA. Among different phospholipids tested, choline- or ethanolamine-containing phospholipids showed potent effects, and 1 mM phosphatidylcholine increased NAAA activity by 6.6-fold. Concerning endogenous thiol compounds, dihydrolipoic acid at 0.1-1 mM was the most active, causing 8.5-9.0-fold stimulation. These results suggest that endogenous phospholipids and dihydrolipoic acid may contribute in keeping NAAA active in lysosomes. Even in the presence of phosphatidylcholine and dihydrolipoic acid, however, the preferential hydrolysis of palmitoylethanolamide was unaltered. We also investigated a possible compensatory induction of NAAA mRNA in brain and other tissues of FAAH-deficient mice. However, NAAA expression levels in all the tissues examined were not significantly altered from those in wild-type mice.

  10. Ultrasensitive nucleic acid sequence detection by single-molecule electrophoresis

    SciTech Connect

    Castro, A; Shera, E.B.

    1996-09-01

    This is the final report of a one-year laboratory-directed research and development project at Los Alamos National Laboratory. There has been considerable interest in the development of very sensitive clinical diagnostic techniques over the last few years. Many pathogenic agents are often present in extremely small concentrations in clinical samples, especially at the initial stages of infection, making their detection very difficult. This project sought to develop a new technique for the detection and accurate quantification of specific bacterial and viral nucleic acid sequences in clinical samples. The scheme involved the use of novel hybridization probes for the detection of nucleic acids combined with our recently developed technique of single-molecule electrophoresis. This project is directly relevant to the DOE`s Defense Programs strategic directions in the area of biological warfare counter-proliferation.

  11. Endogenous Molecules Stimulating N-Acylethanolamine-Hydrolyzing Acid Amidase (NAAA)

    PubMed Central

    2012-01-01

    Fatty acid amide hydrolase (FAAH) plays the central role in the degradation of bioactive N-acylethanolamines such as the endocannabinoid arachidonoylethanolamide (anandamide) in brain and peripheral tissues. A lysosomal enzyme referred to as N-acylethanolamine-hydrolyzing acid amidase (NAAA) catalyzes the same reaction with preference to palmitoylethanolamide, an endogenous analgesic and neuroprotective substance, and is therefore expected as a potential target of therapeutic drugs. In the in vitro assays thus far performed, the maximal activity of NAAA was achieved in the presence of both nonionic detergent (Triton X-100 or Nonidet P-40) and the SH reagent dithiothreitol. However, endogenous molecules that might substitute for these synthetic compounds remain poorly understood. Here, we examined stimulatory effects of endogenous phospholipids and thiol compounds on recombinant NAAA. Among different phospholipids tested, choline- or ethanolamine-containing phospholipids showed potent effects, and 1 mM phosphatidylcholine increased NAAA activity by 6.6-fold. Concerning endogenous thiol compounds, dihydrolipoic acid at 0.1–1 mM was the most active, causing 8.5–9.0-fold stimulation. These results suggest that endogenous phospholipids and dihydrolipoic acid may contribute in keeping NAAA active in lysosomes. Even in the presence of phosphatidylcholine and dihydrolipoic acid, however, the preferential hydrolysis of palmitoylethanolamide was unaltered. We also investigated a possible compensatory induction of NAAA mRNA in brain and other tissues of FAAH-deficient mice. However, NAAA expression levels in all the tissues examined were not significantly altered from those in wild-type mice. PMID:22860206

  12. Characterization of the chicken follicle-stimulating hormone receptor (cFSH-R) complementary deoxyribonucleic acid, and expression of cFSH-R messenger ribonucleic acid in the ovary.

    PubMed

    You, S; Bridgham, J T; Foster, D N; Johnson, A L

    1996-11-01

    Studies were conducted to characterize the chicken (c) FSH receptor (R) cDNA, and to evaluate expression of cFSH-R mRNA in the hen ovary at known stages during follicle development. A total of 2.5 kb of nucleic acid sequence including the complete cFSH-R coding region was isolated by a combination of the reverse-transcription polymerase chain reaction and 5'- and 3'-rapid amplification of cDNA ends techniques. Overall, the nucleic acid sequence homology of the cFSH-R cDNA coding region is 71.8% and 72.2% compared to the rat and bovine FSH-R, respectively, while the deduced amino acid sequence identity for the receptor protein (693 amino acids) is 71.9% and 72.4%, respectively. By comparison, the cFSH-R nucleic acid and amino acid sequences are 60.1% and 49.4% identical to the respective cLH-R sequences. Northern blot analysis detected a single 4.3-kb cFSH-R mRNA transcript, which was selectively expressed in ovarian (granulosa, theca, and stromal) tissues, but not the oviduct, adrenal, liver, muscle, or brain. As the follicle developed from the prehierarchical (6- to 8-mm diameter) to the largest preovulatory (F1 follicle) stage, cFSH-R mRNA levels progressively declined within both the granulosa and theca layers (p < 0.05). Moreover, cFSH-R mRNA levels were lower in whole atretic than in morphologically normal 3- to 5-mm follicles (p = 0.0015). The pattern of cFSH-R mRNA expression within the granulosa layer during follicle development was notably different from that of the recently reported cLH-R, in that cLH-R mRNA levels increase to become readily detectable coincident with dramatically increased steroidogenic capacity during the last few days before ovulation of the follicle. On the other hand, highest levels of cFSH-R mRNA in 6- to 8-mm (prehierarchical) follicles were consistent with a role for the cFSH-R in maintaining the viability of prehierarchical follicles and in initiating granulosa cell differentiation at the time when follicles are selected into the

  13. Variationally optimized basis orbitals for biological molecules

    NASA Astrophysics Data System (ADS)

    Ozaki, T.; Kino, H.

    2004-12-01

    Numerical atomic basis orbitals are variationally optimized for biological molecules such as proteins, polysaccharides, and deoxyribonucleic acid within a density functional theory. Based on a statistical treatment of results of a fully variational optimization of basis orbitals ( full optimized basis orbitals) for 43 biological model molecules, simple sets of preoptimized basis orbitals classified under the local chemical environment (simple preoptimized basis orbitals) are constructed for hydrogen, carbon, nitrogen, oxygen, phosphorous, and sulfur atoms, each of which contains double valence plus polarization basis function. For a wide variety of molecules we show that the simple preoptimized orbitals provide well convergent energy and physical quantities comparable to those calculated by the full optimized orbitals, which demonstrates that the simple preoptimized orbitals possess substantial transferability for biological molecules.

  14. 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.

  15. 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

  16. Hydroxamic acid – A novel molecule for anticancer therapy

    PubMed Central

    Pal, Dilipkumar; Saha, Supriyo

    2012-01-01

    Hydroxamic acid is a potent moiety not only in the field of cancer therapy but also as a mutagenic agent. Among the various derivatives of hydroxamic acid, SAHA (Suberoylanilide Hydroxamic Acid) is considered as a potent anticancer agent. Scientists from the different corner synthesized different hydroxamic acid moieties with some straight chain oxazole, thiadiazole, biphenyl moieties in the terminal position. Acetylation and deacetylation of histones of the core proteins of nucleosomes in chromatin play an important role in the regulation of gene expression. The level of acetylation of histones is established and maintained by two classes of enzymes, histone acetyltransferase and histone deacetylases, which have been identified as transcriptional coactivators and transcriptional corepressors, respectively. There is increasing evidence that aberrant histone acetylation has been linked to various malignant diseases. Great efforts are currently underway for the design of more potent and less toxic candidates for the treatment of cancer. In recent years, hydroxamic acid derivatives have attracted increasing attention for their potential as highly efficacious in combating various etiological factors associated with cancer. Our main intention to draw an attention is that this single functional moiety has not only fit in the receptor but also create a diversified activity. PMID:22837956

  17. RESTORATION OF NORMAL GLUTAMIC ACID TRANSPORT IN VITAMIN B6-DEFICIENT LACTOBACILLUS PLANTARUM BY ACETATE, AMMONIUM, AND VITAMIN B6,

    DTIC Science & Technology

    GLUTAMIC ACID, * LACTOBACILLUS , VITAMIN B COMPLEX, METABOLIC DISEASES, VITAMIN B COMPLEX, ACETATES, AMMONIUM COMPOUNDS, CHLORAMPHENICOL, DEOXYRIBONUCLEIC ACIDS, AMINO ACIDS, PENICILLINS, CELL WALL, SYNTHESIS, OSMOSIS.

  18. 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 ...

  19. 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.

  20. 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.

  1. 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.

  2. Possible involvement of undissociated acid molecules in the acid response of the chorda tympani nerve of the rat.

    PubMed

    Ogiso, K; Shimizu, Y; Watanabe, K; Tonosaki, K

    2000-05-01

    To test whether undissociated acid is capable of exciting the chorda tympani nerves in rats, we have used buffered acid solutions as taste stimuli. These solutions were prepared by adding alkali to weak acids, such as acetic acid, so that the proportion of undissociated and dissociated acids was varied whereas keeping the total acid concentration constant. When acetic acid solutions, adjusted to wide ranges of pH by NaOH, were applied to the tongue, the response magnitude of the chorda tympani nerves was not varied systematically with pH changes. However, if the sodium effect was eliminated by amiloride or replacement of cation by potassium or Tris[hydroxymethyl]aminomethane; NH(2)C(CH(2)OH)(3) (Tris-base), the chorda tympani response was reduced systematically as pH increased. Similar results were obtained with citric acid and ascorbic acid. This pH-dependent change in taste nerve response to acid cannot be solely attributed to the proton gradient because the response magnitude induced by hydrogen itself, which was estimated from responses to strong acids, was much smaller than that by equi-pH acetic acid ( approximately 85%). Thus we cannot explain the pH-dependent responses of the chorda tympani nerves to weak acids unless effects of undissociated acid molecules are postulated. It is therefore concluded that undissociated acids in weak acid solutions can be a stimulant to taste receptor cells.

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

    PubMed

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

    2016-03-07

    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.

  4. Methylation of deoxyribonucleic acid in cultured mammalian cells by N-methyl-N′-nitro-N-nitrosoguanidine. The influence of cellular thiol concentrations on the extent of methylation and the 6-oxygen atom of guanine as a site of methylation

    PubMed Central

    Lawley, P. D.; Thatcher, Carolyn J.

    1970-01-01

    1. In neutral aqueous solution N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) yields salts of nitrocyanamide as u.v.-absorbing products. With cysteine, as found independently by Schulz & McCalla (1969), the principal product is 2-nitràminothiazoline-4-carboxylic acid. Both these reactions liberate the methylating species; thiols enhance the rate markedly at neutral pH values. An alternative reaction with thiols gives cystine, presumably via the unstable S-nitrosocysteine. 2. Thiols (glutathione or N-acetylcysteine) in vitro at about the concentration found in mammalian cells enhance the rate of methylation of DNA markedly over that in neutral solution. 3. Treatment of cultured mammalian cells with MNNG results in rapid methylation of nucleic acids, the extent being greater the higher the thiol content of the cells. Rodent embryo cells are more extensively methylated than mouse L-cells of the same thiol content. Cellular thiol concentrations are decreased by MNNG. Proteins are less methylated by MNNG than are nucleic acids. 4. Methylation of cells by dimethyl sulphate does not depend on cellular thiol content and protein is not less methylated than nucleic acids. Methylation by MNNG may therefore be thiol-stimulated in cells. 5. Both in vitro and in cells about 7% of the methylation of DNA by MNNG occurs at the 6-oxygen atom of guanine. The major products 7-methylguanine and 3-methyladenine are given by both MNNG and dimethyl sulphate, but dimethyl sulphate does not yield O6-methylguanine. Possible reaction mechanisms to account for this difference between these methylating agents and its possible significance as a determinant of their biological effects are discussed. PMID:5435496

  5. Single-Molecule Studies of Nucleic Acid Interactions Using Nanopores

    NASA Astrophysics Data System (ADS)

    Wanunu, Meni; Soni, Gautam V.; Meller, Amit

    This chapter presents biophysical studies of single biopolymers using nanopores. Starting from the fundamental process of voltage-driven biopolymer translocation, the understanding of which is a prerequisite for virtually all nanopore applications, the chapter describes recent experiments that resolve nucleic acid structure and its interaction with enzymes, such as exonucleases and polymerases. It then outlines progress made with solid-state nanopores fabricated in ultrathin membranes and discusses experiments describing biopolymer dynamics in synthetic pores. The chapter concludes with a discussion on some of the main challenges facing nanopore technology, as well as on some of the future prospects associated with nanopore-based tools.

  6. Competitive Adsorption of Naphthenic Acids and Polyaromatic Molecules at a Toluene-Water Interface.

    PubMed

    Teklebrhan, Robel B; Jian, Cuiying; Choi, Phillip; Xu, Zhenghe; Sjöblom, Johan

    2016-12-22

    The early-stage competitive co-adsorption of interfacially active naphthenic acids (NAs) and polyaromatic (PA) molecules to a toluene-water interface from the bulk toluene phase was studied using molecular dynamics (MD) simulation. The NA molecules studied had the same polar functional group but different cycloaliphatic nonpolar tails, and a perylene bisimide (PBI)-based molecule was used as a representative PA compound. The results from our simulations suggest that the size and structural features of NA molecules greatly influence the interfacial activity of PA molecules and partitioning of NA molecules at the toluene-water interface. At low concentrations of PA (∼2.3 wt %) and NA (∼0.4 wt %) molecules, NA molecules containing large cycloaliphatic rings (e.g., four rings) or with a very long aliphatic tail (e.g., carbon chain length of 14) were observed to impede the migration of PA molecules to the interface, whereas small NA molecules containing two cycloaliphatic rings had little effect on the adsorption of PA molecules at the toluene-water interface. At high NA concentrations, the adsorption of PA molecules (∼5.75-17.25 wt %) was greatly hindered by the presence of small NA molecules (∼1.6-4.8 wt %) due to the solvation of PA nanoaggregates in the bulk. Adsorption mechanisms of PA and NA molecules at toluene-water interfaces were clarified through a detailed analysis on the interactions among different species in the system. The results obtained from this work provide insights into designing appropriate chemical demulsifiers or co-demulsifiers for breaking water-in-oil emulsions of great industrial applications.

  7. 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.

  8. 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.

  9. Laser-triggered release of encapsulated molecules from polylactic-co-glycolic acid microcapsules

    NASA Astrophysics Data System (ADS)

    Ariyasu, Kazumasa; Ishii, Atsuhiro; Umemoto, Taiga; Terakawa, Mitsuhiro

    2016-08-01

    The controlled release of encapsulated molecules from a microcapsule is a promising method of targeted drug delivery. Laser-triggered methods for the release of encapsulated molecules have the advantage of spatial and temporal controllability. In this study, we demonstrated the release of encapsulated molecules from biodegradable polymer-based microcapsules using near-infrared femtosecond laser pulses. The polylactic-co-glycolic acid microcapsules encapsulating fluorescein isothiocyanate-dextran molecules were fabricated using a dual-coaxial nozzle system. Irradiation of femtosecond laser pulses enhanced the release of the molecules from the microcapsules, which was accompanied by a decrease in the residual ratio of the microcapsules. The laser-induced modification of the surface of the shell of the microcapsules indicated the potential for sustained release as well as burst release.

  10. Phenolic acids act as signaling molecules in plant-microbe symbioses

    PubMed Central

    Mandal, Santi M; Chakraborty, Dipjyoti

    2010-01-01

    Phenolic acids are the main polyphenols made by plants. These compounds have diverse functions and are immensely important in plant-microbe interactions/symbiosis. Phenolic compounds act as signaling molecules in the initiation of legumerhizobia symbioses, establishment of arbuscular mycorrhizal symbioses and can act as agents in plant defense. Flavonoids are a diverse class of polyphenolic compounds that have received considerable attention as signaling molecules involved in plant-microbe interactions compared to the more widely distributed, simple phenolic acids; hydroxybenzoic and hydroxycinnamic acids, which are both derived from the general phenylpropanoid pathway. This review describes the well-known roles attributed to phenolic compounds as nod gene inducers of legume-rhizobia symbioses, their roles in induction of the GmGin1 gene in fungus for establishment of arbuscular mycorrhizal symbiosis, their roles in inducing vir gene expression in Agrobacterium, and their roles as defense molecules operating against soil borne pathogens that could have great implications for rhizospheric microbial ecology. Amongst plant phenolics we have a lack of knowledge concerning the roles of phenolic acids as signaling molecules beyond the relatively well-defined roles of flavonoids. This may be addressed through the use of plant mutants defective in phenolic acids biosynthesis or knock down target genes in future investigations. PMID:20400851

  11. 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

  12. 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.

  13. Trimethylamine as a probe molecule to differentiate acid sites in Y-FAU zeolite: FTIR study.

    PubMed

    Sarria, Francisca Romero; Blasin-Aubé, Vanessa; Saussey, Jacques; Marie, Olivier; Daturi, Marco

    2006-07-06

    In heterogeneous catalysis acidity has a very important influence on activity and selectivity: correct determination of acidic properties is a base to improve industrial processes. The aim of this work was to study trimethylamine (TMA) as a probe molecule able to distinguish between the different Brønsted acid sites in zeolitic frameworks. Our work mainly focused on faujasite-type zeolites because the HY zeolite is one of the most used acidic catalysts in industrial processes. In this paper, typical IR bands assigned to TMA-protonated species (formed in supercages) are detected in the HY zeolite. TMA interacting by hydrogen bonding with the acid sites located in the sodalite units is also observed. The wavenumbers of some typical IR bands assigned to TMA-protonated species appear to depend on the acidic strength, and a complementary study with ZSM-5 and X-FAU samples confirms this proposition.

  14. Practical Calculation of Molecular Acidity with the Aid of a Reference Molecule

    SciTech Connect

    Burger, Steven K; Liu, Shubin; Ayers, Paul W

    2011-02-24

    A set of linear free energy models are presented for determining the pK{sub a} values of amines, alcohols, and carboxylic acids. Models are determined from a series of pK{sub a} predictors, taken both from traditional natural atomic orbital analysis (NAO) and from a novel approach introduced here of using a reference molecule: an ammonium ion for amines and a hydrogen sulfide molecule for alcohols and carboxylic acids. Using these reference molecules, we calculate the barrier to proton transfer and show that a number of properties associated with the transition state are correlated with the pK{sub a}. By considering 38 predictors, we obtain a four-variable model for amines and a three-variable model for oxygen-containing compounds. The model for amines is based on 145 compounds and has a root mean squared error (RMSE) of 0.45 and R{sup 2} = 0.98. The oxygen set has 48 molecules: RMSE = 0.26, and R{sup 2} = 0.993. Similar, linear, and multilinear models are constructed after separating the sets into chemically similar categories: alcohols, carboxylic acids, and primary, secondary, tertiary, and aromatic amines. This separation gives simpler models with relatively low RMSE values, where the most important predictor of the pK{sub a} is the difference in energy between transferring the proton from the reference molecular base to the conjugate acid from the data set.

  15. 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

  16. Kinetic and spectrophotometric studies on the renaturation of deoxyribonucleic acid.

    PubMed

    Thrower, K J; Peacocke, A R

    1968-10-01

    The kinetics of the renaturation of Escherichia coli DNA in 0.4-1.0m-sodium chloride at temperatures from 60 degrees to 90 degrees have been studied. The extent of renaturation was a maximum at 65 degrees to 75 degrees and increased with ionic strength, and the rate constant increased with both ionic strength and temperature. The energy and entropy of activation of renaturation were calculated to be 6-7kcal.mole(-1) and -40cal.deg.(-1)mole(-1) respectively. It has been shown that renaturation is a second-order process for 5hr. under most conditions. The results are consistent with a reaction in which the rate-controlling step is the diffusion together of two separated complementary DNA strands and the formation of a nucleus of base pairs between them. The kinetics of the renaturation of T7-phage DNA and Bordetella pertussis DNA have also been studied, and their rates of renaturation related quantitatively to the relative heterogeneity of the DNA samples. By analysis of the spectra of DNA at different stages during renaturation it was shown that initially the renatured DNA was rich in guanine-cytosine base pairs and non-random in base sequence, but that, as equilibrium was approached, the renatured DNA gradually resembled native DNA more closely. The rate constant for the renaturation of guanine-cytosine base pairs was slightly higher than for adenine-thymine base pairs.

  17. Deoxyribonucleic acid (DNA)-Ni-nanostrands composites for EMI shielding

    NASA Astrophysics Data System (ADS)

    Ouchen, Fahima; Wilson, Benjamin G.; Yaney, Perry P.; Salour, Michael M.; Grote, James G.

    2016-09-01

    In this study, we demonstrated the use of DNA-CTMA (DC) in combination with Nickel Nanostrands (NiNs) for application in Electromagnetic Interference (EMI) shielding. The addition of NiNs fillers to DC led to films with higher shielding effectiveness (SE) than when Silver nanoparticles were used. An enhanced EMI shielding effectiveness (SE) was also achieved by the fabrication of the DC-NiNs shielding film structure in a layered architecture. Very thin layer of Guanine ( 60 nm) were inserted between layers of DNA-NiNs ( 100um each) to total a thickness of 500um of the shielding film. An increase of the SE by 6-8 dB for the layered structure as compared to the bulk thick film with NiNs loadings up to 10 wt%. At higher loadings (>10 wt. %), a significant physical degradation of the films was observed for all films regardless of the thickness or the process of fabrication.

  18. Method Optimization of Deoxyribonucleic Acid (DNA) Thin Films for Biotronics

    DTIC Science & Technology

    2011-09-01

    Added to the Spin-coater ......................................................................4 3.3 Comparison of Spin - Coating Speed and Sample...precipitate after centrifugation. ..............................3 Figure 3. Diagram of spin - coating method. First, the DNA-CTMA solution was pipetted onto... spin - coating speeds. ...................................................................................................................6 Figure 5

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. Photodissociation of organic molecules in star-forming regions. II. Acetic acid

    NASA Astrophysics Data System (ADS)

    Pilling, S.; Santos, A. C. F.; Boechat-Roberty, H. M.

    2006-04-01

    Fragments from organic molecule dissociation (such as reactive ions and radicals) can form interstellar complex molecules like amino acids. The goal of this work is to experimentally study photoionization and photodissociation processes of acetic acid (CH3COOH), a glycine (NH2CH2COOH) precursor molecule, by soft X-ray photons. The measurements were taken at the Brazilian Synchrotron Light Laboratory (LNLS), employing soft X-ray photons from a toroidal grating monochromator (TGM) beamline (100-310 eV). Mass spectra were obtained using the photoelectron photoion coincidence (PEPICO) method. Kinetic energy distribution and abundances for each ionic fragment have been obtained from the analysis of the corresponding peak shapes in the mass spectra. Absolute photoionization and photodissociation cross sections were also determined. We have found, among the channels leading to ionization, that only 4-6% of CH3COOH survive the strong ionization field. CH3CO^+, COOH+ and CH3+ ions are the main fragments, and the presence of the former may indicate that the production-destruction process of acetic acid in hot molecular cores (HMCs) could decrease the H2O abundance since the net result of this process converts H2O into OH + H^+. The COOH+ ion plays an important role in ion-molecule reactions to form large biomolecules like glycine.

  5. 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.

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

    PubMed

    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.

  7. A density functional and ab initio investigation of the p-aminobenzoic acid molecule

    NASA Astrophysics Data System (ADS)

    Lago, A. F.; Dávalos, J. Z.; de Brito, A. Naves

    2007-08-01

    The p-aminobenzoic acid (C 7H 7NO 2) molecule has been investigated at different levels of theory. DFT methods (B3LYP and PBE1PBE), second order Møller-Plesset perturbation theory (MP2) and composite ab initio methods (G3MP2 and CBS) have been employed, in conjunction with large basis sets. Important informations on the electronic structure and thermochemistry of this molecule have been extracted, and the performance of the density functional and ab initio methods has been evaluated, based on the comparison of the calculated and the available experimental data.

  8. Dynamics and mass accommodation of HCl molecules on sulfuric acid-water surfaces.

    PubMed

    Behr, P; Scharfenort, U; Ataya, K; Zellner, R

    2009-09-28

    A molecular beam technique has been used to study the dynamics and mass accommodation of HCl molecules in collision with sulfuric acid-water surfaces. The experiments were performed by directing a nearly mono-energetic beam of HCl molecules onto a continuously renewed liquid film of 54-76 wt% sulfuric acid at temperatures between 213 K and 243 K. Deuterated sulfuric acid was used to separate sticking but non-reactive collisions from those that involved penetration through the phase boundary followed by dissociation and recombination with D+. The results indicate that the mass accommodation of HCl on sulfuric acid-water surfaces decreases sharply with increasing acidity over the concentration range 54-76 wt%. Using the capillary wave theory of mass accommodation this effect is explained by a change of the surface dynamics. Regarding the temperature dependence it is found that the mass accommodation of HCl increases with increasing temperature and is limited by the bulk phase viscosity and driven by the restoring forces of the surface tension. These findings imply that under atmospheric conditions the uptake of HCl from the gas phase depends crucially on the bulk phase parameters of the sulfuric acid aerosol.

  9. [The effect of spermine on acid-base equilibrium in DNA molecule].

    PubMed

    Slonitskiĭ, S V; Kuptsov, V Iu

    1990-01-01

    The influence of spermine (Sp) on the acid-induced predenaturational and denaturational transitions in the DNA molecule structure has been studied by means of circular dichroism, spectrophotometric and viscometric titration at supporting electrolyte concentration 10 mM NaCl. The data available indicate that at [N]/[P] less than or equal to 0.60 (here [N] and [P] are molar concentrations of Sp nitrogen and DNA phosphours, respectively) the cooperative structural B----B(+)----S transitions are accompanied by the DNA double-helice winding. No competition for proton acceptor sites in the DNA molecule between H+ and Sp4+ cations has been observed when binding to neutral macromolecule. At 0.60 less than or equal to [N]/[P] less than or equal to 0.75 the displacement of the B----B(+)----S transitions midpoints to acidic pH region has been established. This is accompanied by DNA condensation and the appearance of differential scattering of circularly polarized light. The calculations carried out in the framework of the two-variable Manning theory have shown that the acid-induced reduction of the effective polyion charge density facilitates the Sp-induced DNA condensation. It has been shown that the acid-base equilibrium in the DNA molecule is determined by local [H+] in the 2-3 A hydrated monolayer of the macromolecule. An adequate estimation of [H+] can be obtained on the basis of the Poisson-Boltzman approach. The data obtained are consistent with recently proposed hypothesis of polyelectrolyte invariance of the acid-base equilibrium in the DNA molecule.

  10. Identification of antisense nucleic acid hybridization sites in mRNA molecules with self-quenching fluorescent reporter molecules.

    PubMed

    Gifford, Lida K; Opalinska, Joanna B; Jordan, David; Pattanayak, Vikram; Greenham, Paul; Kalota, Anna; Robbins, Michelle; Vernovsky, Kathy; Rodriguez, Lesbeth C; Do, Bao T; Lu, Ponzy; Gewirtz, Alan M

    2005-02-17

    We describe a physical mRNA mapping strategy employing fluorescent self-quenching reporter molecules (SQRMs) that facilitates the identification of mRNA sequence accessible for hybridization with antisense nucleic acids in vitro and in vivo, real time. SQRMs are 20-30 base oligodeoxynucleotides with 5-6 bp complementary ends to which a 5' fluorophore and 3' quenching group are attached. Alone, the SQRM complementary ends form a stem that holds the fluorophore and quencher in contact. When the SQRM forms base pairs with its target, the structure separates the fluorophore from the quencher. This event can be reported by fluorescence emission when the fluorophore is excited. The stem-loop of the SQRM suggests that SQRM be made to target natural stem-loop structures formed during mRNA synthesis. The general utility of this method is demonstrated by SQRM identification of targetable sequence within c-myb and bcl-6 mRNA. Corresponding antisense oligonucleotides reduce these gene products in cells.

  11. Sugar-assisted kinetic resolution of amino acids and amplification of enantiomeric excess of organic molecules.

    PubMed

    Córdova, Armando; Sundén, Henrik; Xu, Yongmei; Ibrahem, Ismail; Zou, Weibiao; Engqvist, Magnus

    2006-07-17

    The origins of biological homochirality have intrigued researchers since Pasteur's discovery of the optical activity of biomolecules. Herein, we propose and demonstrate a novel alternative for the evolution of homochirality that is not based on autocatalysis and forges a direct relationship between the chirality of sugars and amino acids. This process provides a mechanism in which a racemic mixture of an amino acid can catalyze the formation of an optically active organic molecule in the presence of a sugar product of low enantiomeric excess.

  12. 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.

  13. 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.

  14. 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.

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

    DOEpatents

    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.

  16. 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).

  17. Amino Acid Specific Effects on RNA Tertiary Interactions: Single-Molecule Kinetic and Thermodynamic Studies.

    PubMed

    Sengupta, Abhigyan; Sung, Hsuan-Lei; Nesbitt, David J

    2016-10-10

    In light of the current models for an early RNA-based universe, the potential influence of simple amino acids on tertiary folding of ribozymal RNA into biochemically competent structures is speculated to be of significant evolutionary importance. In the present work, the folding-unfolding kinetics of a ubiquitous tertiary interaction motif, the GAAA tetraloop-tetraloop receptor (TL-TLR), is investigated by single-molecule fluorescence resonance energy transfer spectroscopy in the presence of natural amino acids both with (e.g., lysine, arginine) and without (e.g., glycine) protonated side chain residues. By way of control, we also investigate the effects of a special amino acid (e.g., proline) and amino acid mimetic (e.g., betaine) that contain secondary or quaternary amine groups rather than a primary amine group. This combination permits systematic study of amino acid induced (or amino acid like) RNA folding dynamics as a function of side chain complexity, pKa, charge state, and amine group content. Most importantly, each of the naturally occurring amino acids is found to destabilize the TL-TLR tertiary folding equilibrium, the kinetic origin of which is dominated by a decrease in the folding rate constant (kdock), also affected by a strongly amino acid selective increase in the unfolding rate constant (kundock). To further elucidate the underlying thermodynamics, single-molecule equilibrium constants (Keq) for TL-TLR folding have been probed as a function of temperature, which reveal an amino acid dependent decrease in both overall exothermicity (ΔΔH° > 0) and entropic cost (-TΔΔS° < 0) for the overall folding process. Temperature-dependent studies on the folding/unfolding kinetic rate constants reveal analogous amino acid specific changes in both enthalpy (ΔΔH(⧧)) and entropy (ΔΔS(⧧)) for accessing the transition state barrier. The maximum destabilization of the TL-TLR tertiary interaction is observed for arginine, which is consistent with early

  18. Synthesis and anti-tumor activity evaluation of gallic acid-mangiferin hybrid molecule.

    PubMed

    Hu, Xiang-yu; Deng, Jia-gang; Wang, Lin; Yuan, Ye-fei

    2013-12-01

    To improve the anti-tumor effects of gallic acid and mangiferin, a gallic acid-mangiferin hybrid molecule (GAMA) was synthesized from gallic acid with mangiferin in the presence of ionic liquid ChC1(choline chloride)·2SnC12. Chemical and spectroscopic methods, such as (1)H and (13)C NMR spectroscopy, and HR-ESIMS were used for the structure identification of GA-MA. Using the cell counting kit-8 (CCK-8) assay, the in vitro anti-tumor effects were compared between GA-MA, gallic acid and mangiferin on human hepatoma HepG2, human nasopharyngeal carcinoma CNE, human lung cancer NCI-H460, human ovarian cancer SK-OV-3, and human cervical cancer Hela cells. The results showed that the half inhibitory concentration (IC50) of GA-MA on HepG2, CNE, NCI-H460, SK-OV-3, and Hela cells was significantly lower than that of gallic acid or mangiferin. This showed that GA-MA has a better in vitro anti-tumor effect than gallic acid and mangi-ferin.

  19. Oxalic acid: a signal molecule for fungus-feeding bacteria of the genus Collimonas?

    PubMed

    Rudnick, M B; van Veen, J A; de Boer, W

    2015-10-01

    Mycophagous (=fungus feeding) soil bacteria of the genus Collimonas have been shown to colonize and grow on hyphae of different fungal hosts as the only source of energy and carbon. The ability to exploit fungal nutrient resources might require a strategy for collimonads to sense fungi in the soil matrix. Oxalic acid is ubiquitously secreted by soil fungi, serving different purposes. In this study, we investigated the possibility that collimonads might use oxalic acid secretion to localize a fungal host and move towards it. We first confirmed earlier indications that collimonads have a very limited ability to use oxalic acid as growth substrate. In a second step, with using different assays, we show that oxalic acid triggers bacterial movement in such a way that accumulation of cells can be expected at micro-sites with high free oxalic acid concentrations. Based on these observations we propose that oxalic acid functions as a signal molecule to guide collimonads to hyphal tips, the mycelial zones that are most sensitive for mycophagous bacterial attack.

  20. 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.

  1. 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

  2. Hydrothermal reactions of pyruvic acid: synthesis, selection, and self-assembly of amphiphilic molecules.

    PubMed

    Hazen, Robert M; Deamer, David W

    2007-04-01

    Selection and self-assembly of organic compounds in aqueous phases must have been a primary process leading to emergent molecular complexity and ultimately to the origin of life. Facile reactions of pyruvic acid under hydrothermal conditions produce a complex mixture of larger organic molecules, some of which are amphiphiles that readily self-assemble into cell-sized vesicular structures. Chemical characterization of major components of this mixture reveals similarities to the suite of organic compounds present in the Murchison carbonaceous chondrite, some of whose molecules also self-assemble into membranous vesicles. Physical properties of the products are thus relevant to understanding the prebiotic emergence of molecular complexity. These results suggest that a robust family of prebiotic reaction pathways produces similar products over a range of geochemical and astrochemical environments.

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

    PubMed Central

    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.

    2013-01-01

    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. PMID:24101502

  4. 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.

  5. Polysialic acid of the neural cell adhesion molecule distinguishes small cell lung carcinoma from carcinoids.

    PubMed Central

    Komminoth, P.; Roth, J.; Lackie, P. M.; Bitter-Suermann, D.; Heitz, P. U.

    1991-01-01

    The neural cell adhesion molecule (NCAM) exists in various types of neuroendocrine cells and their tumors. A typical feature of NCAM is polysialic acid, of which the chain length is developmentally regulated. The authors have performed a comparative immunohistochemical study on small cell lung carcinomas and bronchial as well as gastrointestinal carcinoids with the monoclonal antibody (MAb) 735 reactive with the long-chain form of polysialic acid. The small cell lung carcinomas, irrespective of their histological type, were positive for polysialic acid. Metastatic tumor cell complexes also exhibited immunostaining. The tumor cell-surface-associated immunostaining for polysialic acid was sensitive to endoneuraminidase. The mature and atypical bronchial and gastrointestinal carcinoids were not immunoreactive for polysialic acid. Cytoplasmic staining in groups of cells of carcinoids (2 of 28 cases) was due to nonspecific antibody binding, which could be prevented by increased ion strength. These data indicate that neuroendocrine tumors of the lung can be distinguished by their content of highly sialylated NCAM. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:1651057

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

    PubMed

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

    2016-07-05

    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.

  7. Experimental and theoretical investigation of the parabanic acid molecule following VUV excitation and photodissociation

    NASA Astrophysics Data System (ADS)

    Lago, A. F.; Oliva, J. M.; Dávalos, J. Z.

    2012-01-01

    Photodissociation experiments have been performed for the parabanic acid (C 3H 2N 2O 3) molecule in vapor phase using time-of-flight mass spectrometry and synchrotron radiation in the VUV photon energy range. Electron ion coincidence (PEPICO) spectra and partial ion yields have been recorded as a function of the photon energy covering the 11-21 eV valence range region. The resulting photoionization products as well as proposed fragmentation pathways leading to those species are presented and discussed. Electronic structure computations for the neutral and ionic species were also carried out at the B3LYP/ aug-cc-pVTZ level of theory.

  8. 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.

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

    PubMed

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

    2016-09-08

    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.

  10. 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

  11. Oleamide: a fatty acid amide signaling molecule in the cardiovascular system?

    PubMed

    Hiley, C Robin; Hoi, Pui Man

    2007-01-01

    Oleamide (cis-9,10-octadecenoamide), a fatty acid primary amide discovered in the cerebrospinal fluid of sleep-deprived cats, has a variety of actions that give it potential as a signaling molecule, although these actions have not been extensively investigated in the cardiovascular system. The synthetic pathway probably involves synthesis of oleoylglycine and then conversion to oleamide by peptidylglycine alpha-amidating monooxygenase (PAM); breakdown of oleamide is by fatty acid amide hydrolase (FAAH). Oleamide interacts with voltage-gated Na(+) channels and allosterically with GABA(A) and 5-HT(7) receptors as well as having cannabinoid-like actions. The latter have been suggested to be due to potentiation of the effects of endocannabinoids such as anandamide by inhibiting FAAH-mediated hydrolysis. This might underlie an "entourage effect" whereby co-released endogenous nonagonist congeners of endocannabinoids protect the active molecule from hydrolysis by FAAH. However, oleamide has direct agonist actions at CB(1) cannabinoid receptors and also activates the TRPV1 vanilloid receptor. Other actions include inhibition of gap-junctional communication, and this might give oleamide a role in myocardial development. Many of these actions are absent from the trans isomer of 9,10-octadecenoamide. One of the most potent actions of oleamide is vasodilation. In rat small mesenteric artery the response does not involve CB(1) cannabinoid receptors but another pertussis toxin-sensitive, G protein-coupled receptor, as yet unidentified. This receptor is sensitive to rimonabant and O-1918, an antagonist at the putative "abnormal-cannabidiol" or endothelial "anandamide" receptors. Vasodilation is mediated by endothelium-derived nitric oxide, endothelium-dependent hyperpolarization, and also through activation of TRPV1 receptors. A physiological role for oleamide in the heart and circulation has yet to be demonstrated, as has production by cells of the cardiovascular system, but

  12. 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

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

    PubMed Central

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

    2016-01-01

    Secondary metabolites synthesized by nonribosomal peptide synthetases (NRPSs) display diverse and complex topologies and possess an impressive range of biological activities1,2 Much of this diversity derives from a synthetic strategy that entails the oxidation of both the chiral amino acid building blocks and the assembled peptide scaffolds pre-3 and post-assembly2. 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.4 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 outside of nature.5 In this manuscript, 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-center 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 (UAAs) representing seven distinct functional group arrays; late-stage C—H functionalizations of a single proline-containing tripeptide furnish eight tripeptides, each having different UAAs. Additionally, a macrocyclic peptide containing a proline turn element is transformed via late-stage C—H oxidation to one containing a linear UAA. PMID:27479323

  14. Structural and vibrational spectroscopy investigation of the 5-[(diphenyl) amino] isophthalic acid molecule

    NASA Astrophysics Data System (ADS)

    Kurt, M.; Şaş, E. Babur; Can, M.; Okur, S.; Icli, S.; Demic, S.

    2014-10-01

    The molecular structure and vibrations of 5-(diphenyl) amino] isophthalic acid (DPIFA) were investigated by different spectroscopic techniques (such as infrared and Raman). FT-IR, FT-Raman and dispersive Raman spectra were recorded in the solid phase. HOMO-LUMO analyses were performed. The theoretical calculations for the molecular structure and spectroscopic studies were performed with DFT (B3LYP) and 6-311G(d,p) basis set calculations using the Gaussian 09 program. After optimizing the geometry of the molecule, vibration wavenumbers and fundamental vibrations wavenumbers were assigned on the basis of the potential energy distribution (PED) of the vibrational modes calculated with VEDA 4 program. The results of theoretical calculations for the spectra of the title compound were compared with the observed spectra.

  15. 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.

  16. 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.

  17. Cyclic diguanylic acid behaves as a host molecule for planar intercalators.

    PubMed

    Liaw, Y C; Gao, Y G; Robinson, H; Sheldrick, G M; Sliedregt, L A; van der Marel, G A; van Boom, J H; Wang, A H

    1990-05-21

    Cyclic ribodiguanylic acid, c-(GpGp), is the endogenous effector regulator of cellulose synthase. Its three-dimensional structure from two different crystal forms (tetragonal and trigonal) has been determined by X-ray diffraction analysis at 1 A resolution. In both crystal forms, two independent c-(GpGp) molecules associate with each other to form a self-intercalated dimer. A hydrated cobalt ion is found to coordinate to two N7 atoms of adjacent guanines, forcing these two guanines to destack with a large dihedral angle (32 degrees), in the dimer of the tetragonal form. This metal coordination mechanism may be relevant to that of the anticancer drug cisplatin. Moreover, c-(GpGp) exhibits unusual spectral properties not seen in any other cyclic dinucleotide. It interacts with planar organic intercalator molecules in ways similar to double helical DNA. We propose a cage-like model consisting of a tetrameric c-(GpGp) aggregate in which a large cavity ('host') is generated to afford a binding site for certain planar intercalators ('guests').

  18. Changes in aggregation behavior of collagen molecules in solution with varying concentrations of acetic acid.

    PubMed

    Yang, Huan; Xu, Songcheng; Shen, Lirui; Liu, Wentao; Li, Guoying

    2016-11-01

    A critical aggregation concentration of 0.30-0.50mg/mL was previously obtained for type I collagen at 0.1M acetic acid (AA). In the present study, the aggregation behavior of collagen in solution (0.5mg/mL) in the presence of 0.1-2.0M AA was investigated. Circular dichroism showed that the three helix structure was maintained across the whole AA concentration range. However, the ratio of positive peak intensity over negative peak intensity varied depending on the conformational state of collagen aggregates. Ultra-sensitive differential scanning calorimetry revealed that transition temperatures Tm1 and Tm2 decreased by 8.35°C and 7.80°C, respectively, between 0.1M and 2.0M, indicating a possible relationship between the aggregation state and the thermal effect. The surrounding polarity of collagen molecules in solution containing pyrene was investigated by fluorescence spectroscopy, which demonstrated that disaggregation of collagen aggregates was enhanced with increasing AA concentration. This observation was correlated with changes in collagen fiber size observed by atomic force microscopy. Furthermore, collagen tyrosine residues were blue-shifted in an intrinsic fluorescence spectra, further indicating changes in aggregation behavior with increasing AA concentration. Finally, the dynamic response of collagen molecules to AA was analyzed by two-dimensional correlation fluorescence spectra.

  19. Intramolecular cyclization of aspartic acid residues assisted by three water molecules: a density functional theory study

    NASA Astrophysics Data System (ADS)

    Takahashi, Ohgi; Kirikoshi, Ryota

    2014-01-01

    Aspartic acid (Asp) residues in peptides and proteins (l-Asp) are known to undergo spontaneous nonenzymatic reactions to form l-β-Asp, d-Asp, and d-β-Asp residues. The formation of these abnormal Asp residues in proteins may affect their three-dimensional structures and hence their properties and functions. Indeed, the reactions have been thought to contribute to aging and pathologies. Most of the above reactions of the l-Asp residues proceed via a cyclic succinimide intermediate. In this paper, a novel three-water-assisted mechanism is proposed for cyclization of an Asp residue (forming a gem-diol precursor of the succinimide) by the B3LYP/6-31 + G(d,p) density functional theory calculations carried out for an Asp-containing model compound (Ace-Asp-Nme, where Ace = acetyl and Nme = NHCH3). The three water molecules act as catalysts by mediating ‘long-range’ 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 (iminolization). Then, reorientation of a water molecule and a conformational change occur successively, followed by the nucleophilic attack of the iminol nitrogen on the carboxyl carbon of the Asp side chain to form the gem-diol species. A satisfactory agreement was obtained between the calculated and experimental energetics.

  20. 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.

  1. 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

    2015-08-03

    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.

  2. Ketogenic essential amino acids replacement diet ameliorated hepatosteatosis with altering autophagy-associated molecules.

    PubMed

    Xu, Ling; Kanasaki, Megumi; He, Jianhua; Kitada, Munehiro; Nagao, Kenji; Jinzu, Hiroko; Noguchi, Yasushi; Maegawa, Hiroshi; Kanasaki, Keizo; Koya, Daisuke

    2013-10-01

    Ketogenic amino acid (KAA) replacement diet has been shown to cure hepatic steatosis, a serious liver disease associated with diverse metabolic defects. In this study, we investigated the effects of KAA replacement diet on nutrition sensing signaling pathway and analyzed whether induction of hepatic autophagy was involved. Mice are fed with high fat diet (HFD) or KAA replacement in high-fat diet (30% fat in food; HFD)-fed (HFD(KAAR)) and sacrificed at 8, 12, 16 weeks after initiation of experimental food. Hepatic autophagy was analyzed in protein expression of several autophagy-associated molecules and in light chain-3 green fluorescent protein (LC-3 GFP) transgenic mice. HFD(KAAR) showed increased AMP-activated protein kinase (AMPK) phosphorylation and enhanced liver kinase B1 (LKB1) expression compared to control HFD-fed mice. The KAA-HFD-induced activation of AMPK was associated with an increased protein expression of sirtuin 1 (Sirt1), decreased forkhead box protein O3a (Foxo3a) level, and suppression of mammalian target of rapamycin (mTOR) phosphorylation compared with the HFD-fed mice. The intervention study revealed that a KAA-replacement diet also ameliorated all the established metabolic and autophagy defects in the HFD-fed mice, suggesting that a KAA-replacement diet can be used therapeutically in established diseases. These results indicate that KAA replacement in food could be a novel strategy to combat hepatic steatosis and metabolic abnormalities likely involvement of an induction of autophagy.

  3. Microfluidic integrated acoustic waving for manipulation of cells and molecules.

    PubMed

    Barani, Alireza; Paktinat, Hossein; Janmaleki, Mohsen; Mohammadi, Aminollah; Mosaddegh, Peiman; Fadaei-Tehrani, Alireza; Sanati-Nezhad, Amir

    2016-11-15

    Acoustophoresis with its simple and low-cost fabrication, rapid and localized fluid actuation, compatibility with microfluidic components, and biocompatibility for cellular studies, has been extensively integrated into microfluidics to provide on-chip microdevices for a variety of applications in biology, bioengineering and chemistry. Among different applications, noninvasive manipulation of cells and biomolecules are significantly important, which are addressed by acoustic-based microfluidics. Here in this paper, we briefly explain the principles and different configurations of acoustic wave and acoustic streaming for the manipulation of cells and molecules and overview its applications for single cell isolation, cell focusing and sorting, cell washing and patterning, cell-cell fusion and communication, and tissue engineering. We further discuss the application of acoustic-based microfluidic systems for the mixing and transport of liquids, manipulation of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) molecules, followed by explanation on the present challenges of acoustic-based microfluidics for the handling of cells and molecules, and highlighting the future directions.

  4. Acidity Constant (pKa ) Calculation of Large Solvated Dye Molecules: Evaluation of Two Advanced Molecular Dynamics Methods.

    PubMed

    De Meyer, Thierry; Ensing, Bernd; Rogge, Sven M J; De Clerck, Karen; Meijer, Evert Jan; Van Speybroeck, Veronique

    2016-11-04

    pH-Sensitive dyes are increasingly applied on polymer substrates for the creation of novel sensor materials. Recently, these dye molecules were modified to form a covalent bond with the polymer host. This had a large influence on the pH-sensitive properties, in particular on the acidity constant (pKa ). Obtaining molecular control over the factors that influence the pKa value is mandatory for the future intelligent design of sensor materials. Herein, we show that advanced molecular dynamics (MD) methods have reached the level at which the pKa values of large solvated dye molecules can be predicted with high accuracy. Two MD methods were used in this work: steered or restrained MD and the insertion/deletion scheme. Both were first calibrated on a set of phenol derivatives and afterwards applied to the dye molecule bromothymol blue. Excellent agreement with experimental values was obtained, which opens perspectives for using these methods for designing dye molecules.

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

    PubMed

    Huschka, Ryan; Neumann, Oara; Barhoumi, Aoune; Halas, Naomi J

    2010-10-13

    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.

  6. 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

  7. Isomerization of HNO to HON in the singlet state assisted by amino acid residues and/or water molecules

    NASA Astrophysics Data System (ADS)

    Shi, Junyou; Li, Ping; Bu, Yuxiang; Wang, Weihua; Mou, Zhaoxia; Song, Rui

    The effects of amino acid residues in the presence or absence of water molecules on the isomerization of the singlet state of HNO/HON have been systematically investigated at the B3LYP/6-311++G** level of theory. The structural characteristics, proton transfer (PT) mechanisms, and the corresponding thermodynamic and kinetic parameters, have been discussed, respectively. All the optimized complexes have been characterized by the ring structures through the intermolecular H-bonds. The origin of the increase in N bond H stretching frequency (blue shifts) occurring in the reactants has also been investigated using the natural bonding orbital (NBO) analyses, which is mainly attributed to the decrease of the electron densities in the antibonding orbital of the N bond H bonds as well as the increase of the polarization of the N bond H bond. All the PTs proceed with the concerted mechanisms since no ionic intermediates have been located during PT processes. At the same time, the cooperative effects of amino acid residues and water molecules on the selected PT processes have been observed, where the PTs assisted solely by the selected residues cannot occur without the participation of the water molecule. Overall, the introductions of one or two water molecules are more favorable for the isomerization of HNO assisted by the amino acid residues.

  8. Nanostructured lipid carrier-loaded hyaluronic acid microneedles for controlled dermal delivery of a lipophilic molecule.

    PubMed

    Lee, Sang Gon; Jeong, Jae Han; Lee, Kyung Min; Jeong, Kyu Ho; Yang, Huisuk; Kim, Miroo; Jung, Hyungil; Lee, Sangkil; Choi, Young Wook

    2014-01-01

    Nanostructured lipid carriers (NLCs) were employed to formulate a lipophilic drug into hydrophilic polymeric microneedles (MNs). Hyaluronic acid (HA) was selected as a hydrophilic and bioerodible polymer to fabricate MNs, and nile red (NR) was used as a model lipophilic molecule. NR-loaded NLCs were consolidated into the HA-based MNs to prepare NLC-loaded MNs (NLC-MNs). A dispersion of NLCs was prepared by high-pressure homogenization after dissolving NR in Labrafil and mixing with melted Compritol, resulting in 268 nm NLCs with a polydispersity index of 0.273. The NLC dispersion showed a controlled release of NR over 24 hours, following Hixson-Crowell's cube root law. After mixing the NLC dispersion with the HA solution, the drawing lithography method was used to fabricate NLC-MNs. The length, base diameter, and tip diameter of the NLC-MNs were approximately 350, 380, and 30 μm, respectively. Fluorescence microscopic imaging of the NLC-MNs helped confirm that the NR-loaded NLCs were distributed evenly throughout the MNs. In a skin permeation study performed using a Franz diffusion cell with minipig dorsal skin, approximately 70% of NR was localized in the skin after 24-hour application of NLC-MNs. Confocal laser scanning microscopy (z-series) of the skin at different depths showed strong fluorescence intensity in the epidermal layer, which appeared to spread out radially with the passage of time. This study indicated that incorporation of drug-loaded NLCs into MNs could represent a promising strategy for controlled dermal delivery of lipophilic drugs.

  9. 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.

  10. Quantitative Structure of an Acetate Dye Molecule Analogue at the TiO2-Acetic Acid Interface.

    PubMed

    Hussain, Hadeel; Torrelles, Xavier; Cabailh, Gregory; Rajput, Parasmani; Lindsay, Robert; Bikondoa, Oier; Tillotson, Marcus; Grau-Crespo, Ricardo; Zegenhagen, Jörg; Thornton, Geoff

    2016-04-14

    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.

  11. 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

  12. Hyaluronic Acid--an "Old" Molecule with "New" Functions: Biosynthesis and Depolymerization of Hyaluronic Acid in Bacteria and Vertebrate Tissues Including during Carcinogenesis.

    PubMed

    Tsepilov, R N; Beloded, A V

    2015-09-01

    Hyaluronic acid is an evolutionarily ancient molecule commonly found in vertebrate tissues and capsules of some bacteria. Here we review modern data regarding structure, properties, and biological functions of hyaluronic acid in mammals and Streptococcus spp. bacteria. Various aspects of biogenesis and degradation of hyaluronic acid are discussed, biosynthesis and degradation metabolic pathways for glycosaminoglycan together with involved enzymes are described, and vertebrate and bacterial hyaluronan synthase genes are characterized. Special attention is given to the mechanisms underlying the biological action of hyaluronic acid as well as the interaction between polysaccharide and various proteins. In addition, all known signaling pathways involving hyaluronic acid are outlined. Impaired hyaluronic acid metabolism, changes in biopolymer molecular weight, hyaluronidase activity, and enzyme isoforms often accompany carcinogenesis. The interaction between cells and hyaluronic acid from extracellular matrix that may be important during malignant change is discussed. An expected role for high molecular weight hyaluronic acid in resistance of naked mole rat to oncologic diseases and the protective role of hyaluronic acid in bacteria are discussed.

  13. Theoretical study of the NLO responses of some natural and unnatural amino acids used as probe molecules.

    PubMed

    Derrar, S N; Sekkal-Rahal, M; Derreumaux, P; Springborg, M

    2014-08-01

    The first hyperpolarizabilities β of the natural aromatic amino acids tryptophan and tyrosine have been investigated using several methods and basis sets. Some of the theoretical results obtained were compared to the only experimental hyper-Rayleigh scattering data available. The sensitivity of tryptophan to its local environment was analyzed by constructing two-dimensional potential energy plots around the dipeptide tryptophan-lysine. Static hyperpolarizabilities β(0) of the found minima were calculated by a second-order Møller-Plesset (MP2) method in combination with the 6-31+G(d) basis set. Moreover, the efficiency of tryptophan and those of a series of unnatural amino acids as endogenous probe molecules were tested by calculating the nonlinear responses of some peptides. Impressive results were obtained for the amino acid ALADAN, which shows significantly improved nonlinear performance compared to other amino acids with weak nonlinear responses.

  14. Kojic acid--a new leading molecule for a preparation of compounds with an anti-neoplastic potential.

    PubMed

    Novotný, L; Rauko, P; Abdel-Hamid, M; Váchalková, A

    1999-01-01

    Kojic acid as a molecule of natural origin may serve as template for the synthesis of new biologically active compounds. The synthetic KA (pyranone) derivatives possess various kinds of biological activities which are related by their similarity to flavonoids. The most important property is the antifungal and antineoplastic activity and capability of chelating metals. It is shown that the antineoplastic activity of kojic acid derivatives is based on various mechanisms of action on different levels of cellular metabolism and functions what makes this compound interesting for future investigation as cytotoxic agent.

  15. How to determine local stretching and tension in a flow-stretched DNA molecule

    NASA Astrophysics Data System (ADS)

    Pedersen, Jonas N.; Marie, Rodolphe; Kristensen, Anders; Flyvbjerg, Henrik

    2016-04-01

    We determine the nonuniform stretching of and tension in a mega base pairs-long fragment of deoxyribonucleic acid (DNA) that is flow stretched in a nanofluidic chip. We use no markers, do not know the contour length of the DNA, and do not have the full DNA molecule inside our field of view. Instead, we analyze the transverse thermal motion of the DNA. Tension at the center of the DNA adds up to 16 pN, giving almost fully stretched DNA. This method was devised for optical mapping of DNA, specifically, DNA denaturation patterns. It may be useful also for other studies, e.g., DNA-protein interactions, specifically, their tension dependence. Generally, wherever long strands of DNA—e.g., native DNA extracted from human cells or bacteria—must be stretched with ease for inspection, this method applies.

  16. In silico Screening and Evaluation of the Anticonvulsant Activity of Docosahexaenoic Acid-Like Molecules in Experimental Models of Seizures

    PubMed Central

    Loron, Ali Gharibi; Sardari, Soroush; Narenjkar, Jamshid; Sayyah, Mohammad

    2017-01-01

    Background: Resistance to antiepileptic drugs and the intolerability in 20-30% of the patients raises demand for developing new drugs with improved efficacy and safety. Acceptable anticonvulsant activity, good tolerability, and inexpensiveness of docosahexaenoic acid (DHA) make it as a good candidate for designing and development of the new anticonvulsant medications. Methods: Ten DHA-based molecules were screened based on in silico screening of DHA-like molecules by root-mean-square deviation of atomic positions, the biological activity score of Professional Association for SQL Server, and structural requirements suggested by pharmacophore design. Anticonvulsant activity was tested against clonic seizures induced by pentylenetetrazole (PTZ, 60 mg/kg, i.p.) and tonic seizures induced by maximal electroshock (MES, 50 mA, 50 Hz, 1 ms duration) by intracerebroventricular (i.c.v.) injection of the screened compounds to mice. Results: Among screened compounds, 4-Phenylbutyric acid, 4-Biphenylacetic acid, phenylacetic acid, and 2-Phenylbutyric acid showed significant protective activity in pentylenetetrazole test with ED50 values of 4, 5, 78, and 70 mM, respectively. In MES test, shikimic acid and 4-tert-Butylcyclo-hexanecarboxylic acid showed significant activity with ED50 values 29 and 637 mM, respectively. Effective compounds had no mortality in mice up to the maximum i.c.v. injectable dose of 1 mM. Conclusion: Common electrochemical features and three-dimensional spatial structures of the effective compounds suggest the involvement of the anticonvulsant mechanisms similar to the parent compound DHA. PMID:27592363

  17. Small molecule-mediated duplex formation of nucleic acids with 'incompatible' backbones.

    PubMed

    Cafferty, Brian J; Musetti, Caterina; Kim, Keunsoo; Horowitz, Eric D; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

    2016-04-07

    Proflavine, a known intercalator of DNA and RNA, promotes duplex formation by nucleic acids with natural and non-natural backbones that otherwise form duplexes with low thermal stability, and even some that show no sign of duplex formation in the absence of proflavine. These findings demonstrate the potential for intercalators to be used as cofactors for the assembly of rationally designed nucleic acid structures, and could provide fundamental insights regarding intercalation of natural nucleic acid duplexes.

  18. Acidity Constant (pK a) Calculation of Large Solvated Dye Molecules: Evaluation of Two Advanced Molecular Dynamics Methods

    PubMed Central

    De Meyer, Thierry; Ensing, Bernd; Rogge, Sven M. J.; De Clerck, Karen

    2016-01-01

    Abstract pH‐Sensitive dyes are increasingly applied on polymer substrates for the creation of novel sensor materials. Recently, these dye molecules were modified to form a covalent bond with the polymer host. This had a large influence on the pH‐sensitive properties, in particular on the acidity constant (pK a). Obtaining molecular control over the factors that influence the pK a value is mandatory for the future intelligent design of sensor materials. Herein, we show that advanced molecular dynamics (MD) methods have reached the level at which the pK a values of large solvated dye molecules can be predicted with high accuracy. Two MD methods were used in this work: steered or restrained MD and the insertion/deletion scheme. Both were first calibrated on a set of phenol derivatives and afterwards applied to the dye molecule bromothymol blue. Excellent agreement with experimental values was obtained, which opens perspectives for using these methods for designing dye molecules. PMID:27570194

  19. Statistical model for self-assembly of trimesic acid molecules into homologous series of flower phases

    NASA Astrophysics Data System (ADS)

    Ibenskas, A.; Tornau, E. E.

    2012-11-01

    The statistical three-state model is proposed to describe the ordering of triangular TMA molecules into flower phases. The model is solved on a rescaled triangular lattice, assuming following intermolecular interactions: exclusion of any molecules on nearest neighbor sites, triangular trio H-bonding interactions for molecules of the same orientation on next-nearest neighbor sites, and dimeric H-bonding interactions for molecules of different (“tip-to-tip”) orientations on third-nearest neighbor sites. The model allows us to obtain the analytical solution for the ground state phase diagram with all homologous series of flower phases included, starting with the honeycomb phase (n=1) and ending with the superflower structure (n=∞). Monte Carlo simulations are used to obtain the thermodynamical properties of this model. It is found that phase transitions from disordered to any of the flower phases (except n=1) undergo via intermediate correlated triangular domains structure. The transition from the disordered phase to the intermediate phase is, most likely, of the first order, while the transition from the intermediate to the flower phase is definitely first order phase transition. The phase diagrams including low-temperature flower phases are obtained. The origin of the intermediate phase, phase separation, and metastable structures are discussed.

  20. Fatty acid bile acid conjugates (FABACs)—New molecules for the prevention of cholesterol crystallisation in bile

    PubMed Central

    Gilat, T; Somjen, G; Mazur, Y; Leikin-Frenkel, A; Rosenberg, R; Halpern, Z; Konikoff, F.

    2001-01-01

    BACKGROUND—Cholesterol gall stones are a frequent disease for which at present surgery is the usual therapy. Despite the importance of bile acids it has become evident that phospholipids are the main cholesterol solubilisers in bile. Even phospholipid components, such as fatty acids, have anticrystallising activity.
AIM—To synthesise fatty acid bile acid conjugates (FABACs) and study their effects on cholesterol crystallisation in bile in vitro and in vivo.
METHODS—FABACs were prepared by conjugation of cholic acid at position 3 with saturated fatty acids of variable chain length using an amide bond. Cholesterol crystallisation and its kinetics (crystal observation time, crystal mass) were studied in model bile, pooled enriched human bile, and fresh human bile using FABACs with saturated fatty acids of varying chain length (C-6 to C-22). Absorption of FABACs into blood and bile was tested in hamsters. Prevention of biliary cholesterol crystallisation in vivo was tested in hamsters and inbred mice.
RESULTS—FABACs strongly inhibited cholesterol crystallisation in model as well as native bile. The FABACs with longer acyl chains (C-16 to C-22) were more effective. At a concentration of 5 mM, FABACs almost completely inhibited cholesterol crystallisation in fresh human bile for 21 days. FABACs were absorbed and found in both portal and heart blood of hamsters. Levels in bile were 2-3 times higher than in blood, indicating active secretion. Appreciable levels were found in the systemic circulation 24-48 hours after a single administration. Ingested FABACs completely prevented the formation of cholesterol crystals in the gall bladders of hamsters and mice fed a lithogenic diet.
CONCLUSIONS—FABACs are potent inhibitors of cholesterol crystallisation in bile. They are absorbed and secreted into bile and prevent the earliest step of cholesterol gall stone formation in animals. These compounds may be of potential use in cholesterol gall stone disease in

  1. Single-chain structure of human ceruloplasmin: the complete amino acid sequence of the whole molecule.

    PubMed Central

    Takahashi, N; Ortel, T L; Putnam, F W

    1984-01-01

    We have determined the amino acid sequence of the amino-terminal 67,000-dalton (67-kDa) fragment of human ceruloplasmin and have established overlapping sequences between the 67-kDa and 50-kDa fragments and between the 50-kDa and 19-kDa fragments. The 67-kDa fragment contains 480 amino acid residues and three glucosamine oligosaccharides. These results together with our previous sequence data for the 50-kDa and 19-kDa fragments complete the amino acid sequence of human ceruloplasmin. The polypeptide chain has a total of 1,046 amino acid residues (Mr 120,085) and has attachment sites for four glucosamine oligosaccharides; together these account for the total molecular mass of human ceruloplasmin (132 kDa). The sequence analysis of the peptides overlapping the fragments showed that one additional amino acid, arginine, is present between the 67-kDa and 50-kDa fragments, and another, lysine, is between the 50-kDa and 19-kDa fragments. Only two apparent sites of amino acid interchange have been identified in the polypeptide chain. Both involve a single-point interchange of glycine and lysine that would result in a difference in charge. The results of the complete sequence analysis verified that human ceruloplasmin is composed of a single polypeptide chain and that the subunit-like fragments are produced by proteolytic cleavage during purification (and possibly also in vivo). PMID:6582496

  2. 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.

  3. Modeling and spectral simulation of matrix-isolated molecules by density functional calculations: A case study on formic acid dimer

    NASA Astrophysics Data System (ADS)

    Ito, Fumiyuki

    2010-12-01

    The supermolecule approach has been used to model molecules embedded in solid argon matrix, wherein interaction between the guest and the host atoms in the first solvation shell is evaluated with the use of density functional calculations. Structural stability and simulated spectra have been obtained for formic acid dimer (FAD)-Arn (n = 21-26) clusters. The calculations at the B971/6-31++G(3df,3pd) level have shown that the tetrasubstitutional site on Ar(111) plane is likely to incorporate FAD most stably, in view of consistency with the matrix shifts available experimentally.

  4. 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.

  5. Identification and characterization of the motion of water molecules in normal and deuterated pyromellitic acid dihydrate

    NASA Astrophysics Data System (ADS)

    Schajor, W.; Haeberlen, U.; Tegenfeldt, T.

    Proton wide-line, multiple-pulse, T1 and T1 ϱ measurements on single crystals of PMADH, and deuteron EFG measurements and bandshape analyses of spectra recorded from deuterated crystals of PMADH are reported. The wide-line and multiple-pulse proton results indicate that the water molecules in PMADH are flipping about their twofold symmetry axes. Both T1 and T1 ϱ were measured as a function of crystal orientation and temperature. Comparison of the experimental data with model calculations for T1 ϱ based on the established flipping motions of the water molecules shows that {1}/{T 1ϱ} is dominated by this process whereas {1}/{T 1} is not. The T1 ϱ data thus enable determination of the rate of the H 2O flips as a function of temperature. EFGs of the water deuterons in deuterated PMADH, measured at low and high temperatures, confirm the occurrence of the flips for D 2O in PMADH. The flips constitute an exchange process for the water deuterons. Bandshape analyses of single-crystal deuteron spectra recorded at temperatures covering the full range of exchange rates allowed determination of the flip rates of the D 2O molecules. The activation energies for the H 2O and D 2O flips are the same, Ea = 10 kcal/mol, within the limits of accuracy of the experiments. The frequency factors in the Arrhenius relation are 8.3 X 10 13 sec -1 (H 2O) and 2.6 X 10 13 sec -1 (D 2O).

  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

    2016-02-04

    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.

  7. 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.

  8. 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.

  9. Electrical characteristics and doping mechanism of DNA molecules doped with iodine solutions.

    PubMed

    Kim, Nam-Hoon; Lee, Woo Cheol; Roh, Yonghan

    2010-05-01

    This study examined the electrical characteristics of deoxyribonucleic acid (DNA) molecules doped with iodine solution and their chemical state changes before and after doping. The experiments were progressed in each lambda (A), poly(dA)-poly(dT) and poly(dG)-poly(dC) DNA under the same conditions. The authors prepared 20 nm gap Au/Ti electrodes fabricated by e-beam lithography. DNA solutions were dropped on the nano gap of the electrodes and DNA films were formed by drying in a vacuum. DNA films were doped with an iodine solution dissolved in methanol. The authors measured the electrical conductivity of DNA molecules as the number of iodine doping times in 10(-2) torr vacuum. As increase of the iodine solution doping number, the electrical conductivity of three sorts of DNA molecules was remarkably improved respectively. X-ray photoelectron spectroscopy (XPS) was performed to inspect the electrical conduction mechanism that holes on DNA nitrogen region were generated by transferring electrons to iodine molecules.

  10. Monte Carlo computer simulation of spreading pressure-area isotherms of Langmuir monolayers of fatty-acid molecules

    NASA Astrophysics Data System (ADS)

    Polimeno, Antonino; Ros, J. Marijin; Levine, Yehudi K.

    2001-10-01

    We describe an off-lattice model with chemical group resolution for investigating the spreading pressure-area isotherms of Langmuir monolayers of fatty-acid molecules at air-water interfaces. It is shown that a balance of the attractive interactions between the methylene chains and longer-range repulsive interactions between the headgroups determines the form of the isotherms. The model reproduces the experimentally observed dependence of the isotherms on the chain length and unsaturation. At 300 K model palmitic acid chains (C16:0) are shown to form liquid-condensed monolayers at all spreading pressures, while the isotherms of monolayers of myristic acid (C14:0) exhibit a liquid-condensed to liquid-expanded transition in agreement with experiments. Moreover, the simulations show that the introduction of cis-unsaturated segments into the 7-8 positions of the C14 chains depresses the phase transition temperature, so that the monolayers undertake a liquid-expanded structure.

  11. 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

  12. Gallic acid-based small-molecule inhibitors of JC and BK polyomaviral infection.

    PubMed

    O'Hara, Bethany A; Rupasinghe, Chamila; Yatawara, Achani; Gaidos, Gabriel; Mierke, Dale F; Atwood, Walter J

    2014-08-30

    JCPyV and BKPyV are common human polyomaviruses that cause lifelong asymptomatic persistent infections in their hosts. In immunosuppressed individuals, increased replication of JCPyV and BKPyV cause significant disease. JCPyV causes a fatal and rapidly progressing demyelinating disease known as progressive multifocal leukoencephalopathy. BKPyV causes hemorrhagic cystitis and polyomavirus associated nephropathy in bone marrow transplant recipients and in renal transplant recipients respectively. There are no specific anti-viral therapies to treat polyomavirus induced diseases. Based on detailed studies of the structures of these viruses bound to their receptors we screened several compounds that possessed similar chemical space as sialic acid for their ability to bind the virus. Positive hits in the assay were restricted to gallic acid based compounds that mimic the viruses known cellular glycan receptors. Pre-treatment of virions with these inhibitors reduced virus infection in cell culture and as such may form the basis for the development of virion specific antagonists to treat these infections.

  13. 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

  14. A Nanosensor for Trans-membrane Capture and Identification of Single Nucleic Acid Molecules.

    NASA Astrophysics Data System (ADS)

    Nakane, Jonathan; Wiggin, Matthew; Marziali, Andre

    2004-03-01

    We present the construction and operation of a self-assembling nanosensor for sequence-specific detection of nucleotides across a membrane. The probe is constructed of two main components: a single alpha-hemolysin nanopore self-assembled into a lipid bilayer, and a DNA probe tethered to avidin at one end and complementary to the analyte nucleotide at the other end. The sensor is assembled by electrophoretic insertion of the probe into the cis-side of the nanopore (observable as an increase in electrical impedance). Hybridization of the probe to analyte on the trans- side of the pore traps the probe in place, and increases the time constant for probe exit on subsequent voltage reversal. Using this sensor, we can uncover the energy landscape of binding interactions between single DNA molecules on the trans side of the membrane and the probe strand. This allows us to detect and identify single base mutations in short oligonucleotide strands specifically targeted based on the sensor probe sequence. The nanosensor shows promise for applications such as single nucleotide polymorphism detection, and potentially, for in vivo detection of specific RNA sequences.

  15. Self-assembly into soft materials of molecules derived from naturallyoccurring fatty-acids

    NASA Astrophysics Data System (ADS)

    Zhang, Mohan

    The self-assembly of molecular gelators has provided an attractive route for the construction of nanostructured materials with desired functionalities. A well-defined paradigm for the design of molecular gels is needed, but none has yet been established. One of the important challenges to defining this paradigm is the creation of structure-property correlations for gelators at different distance scales. This dissertation centers on gaining additional insights in the relationship between small changes in gelator structures derived from long-chain, naturally-occurring fatty acids and the properties of the corresponding gels. This approach offers a reasonable method to probe the rational design of molecular gelators. (Abstract shortened by ProQuest.).

  16. The origins of life -- the 'protein interaction world' hypothesis: protein interactions were the first form of self-reproducing life and nucleic acids evolved later as memory molecules.

    PubMed

    Andras, Peter; Andras, Csaba

    2005-01-01

    The 'protein interaction world' (PIW) hypothesis of the origins of life assumes that life emerged as a self-reproducing and expanding system of protein interactions. In mainstream molecular biology, 'replication' refers to the material copying of molecules such as nucleic acids. However, PIW is conceptualized as an abstract communication system constituted by the interactions between proteins, in which 'replication' happens at the level of self-reproduction of these interactions between proteins. Densely concentrated peptide interaction systems may have reproduced and expanded as 'protocell' vesicles surrounded by lipid bi-layer membranes. Protocells led to the emergence of proto-RNA molecules of greater chemical stability which served as chemically differentiated 'memories' of peptide interaction states, thereby facilitating the reproduction and expansion of protocells. Simplification-driven expansion led to the selection of biotic amino acids and the reduction of the typical RNA alphabet to the four usual bases (A, C, G and U). Dense interactions between RNA molecules led to the emergence of the RNA interaction subsystem of the cell, and to the emergence of 'memories' of RNA interactions in the form of DNA molecules with greater chemical stability. The expansion of DNA molecule interactions led to the dense clustering and encapsulation of DNA molecules within the cell nucleus. RNA molecules therefore serve as memories of protein interactions and DNA molecules are memories of RNA interactions. We believe that the PIW hypothesis is more evolutionarily plausible than the mainstream RNA world hypothesis, and has greater explanatory power.

  17. Small Molecule Positive Allosteric Modulation of TRPV1 Activation by Vanilloids and Acidic pHS⃞

    PubMed Central

    Kaszas, Krisztian; Keller, Jason M.; Coddou, Claudio; Mishra, Santosh K.; Hoon, Mark A.; Stojilkovic, Stanko; Jacobson, Kenneth A.

    2012-01-01

    Transient receptor potential cation channel subfamily V member 1 (TRPV1) is a high-conductance, nonselective cation channel strongly expressed in nociceptive primary afferent neurons of the peripheral nervous system and functions as a multimodal nociceptor gated by temperatures greater than 43°C, protons, and small-molecule vanilloid ligands such as capsaicin. The ability to respond to heat, low pH, vanilloids, and endovanilloids and altered sensitivity and expression in experimental inflammatory and neuropathic pain models made TRPV1 a major target for the development of novel, nonopioid analgesics and resulted in the discovery of potent antagonists. In human clinical trials, observations of hyperthermia and the potential for thermal damage by suppressing the ability to sense noxious heat suggested that full-scale blockade of TRPV1 function can be counterproductive and subtler pharmacological approaches are necessary. Here we show that the dihydropyridine derivative 4,5-diethyl-3-(2-methoxyethylthio)-2-methyl-6-phenyl-1,4-(±)-dihydropyridine-3,5-dicarboxylate (MRS1477) behaves as a positive allosteric modulator of both proton and vanilloid activation of TRPV1. Under inflammatory-mimetic conditions of low pH (6.0) and protein kinase C phosphorylation, addition of MRS1477 further increased sensitivity of already sensitized TPRV1 toward capsaicin. MRS1477 does not affect inhibition by capsazepine or ruthenium red and remains effective in potentiating activation by pH in the presence of an orthosteric vanilloid antagonist. These results indicate a distinct site on TRPV1 for positive allosteric modulation that may bind endogenous compounds or novel pharmacological agents. Positive modulation of TRPV1 sensitivity suggests that it may be possible to produce a selective analgesia through calcium overload restricted to highly active nociceptive nerve endings at sites of tissue damage and inflammation. PMID:22005042

  18. 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

    2009-11-03

    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.

  19. Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy.

    PubMed

    Das, Priyadip; Duanias-Assaf, Tal; Reches, Meital

    2017-03-06

    The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals leads to the formation of composite materials with unique properties. In addition, the undesirable process of biofouling is initiated by the adsorption of biomolecules, mainly proteins, on surfaces. This organic layer is an adhesion layer for bacteria and allows them to interact with the surface. Understanding the fundamental forces that govern the interactions at the organic-inorganic interface is therefore important for many areas of research and could lead to the design of new materials for optical, mechanical and biomedical applications. This paper demonstrates a single-molecule force spectroscopy technique that utilizes an AFM to measure the adhesion force between either peptides or amino acids and well-defined inorganic surfaces. This technique involves a protocol for attaching the biomolecule to the AFM tip through a covalent flexible linker and single-molecule force spectroscopy measurements by atomic force microscope. In addition, an analysis of these measurements is included.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

    2013-05-07

    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.

  6. 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

  7. 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.

  8. 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

  9. 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.

    2016-10-01

    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.

  10. 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.

  11. Niflumic acid renders dendritic cells tolerogenic and up-regulates inhibitory molecules ILT3 and ILT4.

    PubMed

    Svajger, Urban; Vidmar, Alenka; Jeras, Matjaz

    2008-07-01

    Niflumic acid is a member of non-steroidal anti-inflammatory agents, from which aspirin was recently shown to inhibit maturation of human-monocyte derived dendritic cells (DCs). DCs are crucial regulators of the immune response, capable of inducing immunity as well as tolerance. In our in vitro study we showed a tolerogenic effect of NFA on phenotype and function of LPS-matured monocyte-derived DCs. Different drug concentrations dose-dependently down-regulated the expression of co-stimulatory molecules, particularly CD80 and lowered the expression of dendritic cell marker CD1a. Opposingly, the expressions of two inhibitory surface molecules, associated with tolerogenic DCs, immunoglobulin-like transcripts (ILT)3 and ILT4 were induced in treated DCs. The levels of TNFalpha production by NFA-treated DCs did not change significantly compared to controls, whereas the IL-12p70 and IL-10 production was completely abrogated at higher drug concentrations. However, at lower drug concentrations, the production of IL-12p70 was increased. There were no significant differences in the uptake of FITC labeled dextran by treated DCs compared to untreated cells. In allogeneic cultures with whole CD4+ T cells, dendritic cells differentiated in the presence of NFA appeared poor stimulators of CD4+ T-cell proliferation, even compared to immature DCs (iDCs). These results indicate the immunosuppressive properties of NFA, which may be therapeutically useful in controlling chronic immune and/or inflammatory diseases, by modulating DC characteristics towards tolerogenic DCs.

  12. 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.

  13. Amino Acid Sequences Mediating Vascular Cell Adhesion Molecule 1 Binding to Integrin Alpha 4: Homologous DSP Sequence Found for JC Polyoma VP1 Coat Protein

    PubMed Central

    Meyer, Michael Andrew

    2013-01-01

    The JC polyoma viral coat protein VP1 was analyzed for amino acid sequences homologies to the IDSP sequence which mediates binding of VLA-4 (integrin alpha 4) to vascular cell adhesion molecule 1. Although the full sequence was not found, a DSP sequence was located near the critical arginine residue linked to infectivity of the virus and binding to sialic acid containing molecules such as integrins (3). For the JC polyoma virus, a DSP sequence was found at residues 70, 71 and 72 with homology also noted for the mouse polyoma virus and SV40 virus. Three dimensional modeling of the VP1 molecule suggests that the DSP loop has an accessible site for interaction from the external side of the assembled viral capsid pentamer. PMID:24147211

  14. Amino Acid Sequences Mediating Vascular Cell Adhesion Molecule 1 Binding to Integrin Alpha 4: Homologous DSP Sequence Found for JC Polyoma VP1 Coat Protein.

    PubMed

    Meyer, Michael Andrew

    2013-01-01

    The JC polyoma viral coat protein VP1 was analyzed for amino acid sequences homologies to the IDSP sequence which mediates binding of VLA-4 (integrin alpha 4) to vascular cell adhesion molecule 1. Although the full sequence was not found, a DSP sequence was located near the critical arginine residue linked to infectivity of the virus and binding to sialic acid containing molecules such as integrins (3). For the JC polyoma virus, a DSP sequence was found at residues 70, 71 and 72 with homology also noted for the mouse polyoma virus and SV40 virus. Three dimensional modeling of the VP1 molecule suggests that the DSP loop has an accessible site for interaction from the external side of the assembled viral capsid pentamer.

  15. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET

    PubMed Central

    Perdios, Louis; Lowe, Alan R.; Saladino, Giorgio; Bunney, Tom D.; Thiyagarajan, Nethaji; Alexandrov, Yuriy; Dunsby, Christopher; French, Paul M. W.; Chin, Jason W.; Gervasio, Francesco Luigi; Tate, Edward W.; Katan, Matilda

    2017-01-01

    Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo. PMID:28045057

  16. 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.

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

    PubMed Central

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

    2015-01-01

    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

  18. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET

    NASA Astrophysics Data System (ADS)

    Perdios, Louis; Lowe, Alan R.; Saladino, Giorgio; Bunney, Tom D.; Thiyagarajan, Nethaji; Alexandrov, Yuriy; Dunsby, Christopher; French, Paul M. W.; Chin, Jason W.; Gervasio, Francesco Luigi; Tate, Edward W.; Katan, Matilda

    2017-01-01

    Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo.

  19. 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.

  20. 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

  1. Enzymatic Depletion of the Polysialic Acid Moiety Associated with the Neural Cell Adhesion Molecule Inhibits Antidepressant Efficacy.

    PubMed

    Wainwright, Steven R; Barha, Cindy K; Hamson, Dwayne K; Epp, Jonathan R; Chow, Carmen; Lieblich, Stephanie E; Rutishauser, Urs; Galea, Liisa Am

    2016-05-01

    Antidepressant drugs are too often ineffective, the exact mechanism of efficacy is still ambiguous, and there has been a paucity of novel targets for pharmacotherapy. In an attempt to understand the pathogenesis of depression and subsequently develop more efficacious antidepressant drugs, multiple theories have been proposed, including the modulation of neurotransmission, the upregulation of neurogenesis and neurotrophic factors, normalizing hypothalamic-pituitary-adrenal reactivity, and the reduction of neuroinflammation; all of which have supporting lines of evidence. Therefore, an ideal molecular target for novel pharmaceutical intervention would function at the confluence of these theories. The polysialylated form of the neural cell adhesion molecule (PSA-NCAM) functions broadly, serving to mediate synaptic plasticity, neurogenesis, neurotrophic factor signaling, and inflammatory signaling throughout the brain; all of which are associated with the pathophysiology and treatment of depression. Moreover, the expression of PSA-NCAM is reduced by depression, and conversely enhanced by antidepressant treatment, particularly within the hippocampus. Here we demonstrate that selectively cleaving the polysialic acid moiety, using the bacteriophage-derived enzyme endoneuraminidase N, completely inhibits the antidepressant efficacy of the selective-serotonin reuptake inhibitor fluoxetine (FLX) in a chronic unpredictable stress model of depression. We also observe a corresponding attenuation of FLX-induced hippocampal neuroplasticity, including decreased hippocampal neurogenesis, synaptic density, and neural activation. These data indicate that PSA-NCAM-mediated neuroplasticity is necessary for antidepressant action; therefore PSA-NCAM represents an interesting, and novel, target for pharmacotherapy.

  2. New molecular motif for recognizing sialic acid using emissive lanthanide-macrocyclic polyazacarboxylate complexes: deprotonation of a coordinated water molecule controls specific binding.

    PubMed

    Ouchi, Kazuki; Saito, Shingo; Shibukawa, Masami

    2013-06-03

    A new molecular motif--lanthanide-macrocyclic polyazacarboxylate hexadentate complexes, Ln(3+)-ABNOTA--was found to specifically bind to sialic acid with strong emission enhancement and high affinity. The selectivity toward sialic acid over other monosaccharides was one of the highest among artificial receptors. Also, the novel binding mechanism was investigated in detail; binding selectivity is controlled by interactions between sialic acid and both the central metal and a hydroxyl group produced by deprotonation of a coordinated water molecule in the Ln(3+) complex.

  3. Subnucleosomes and their relationships to the arrangement of histone binding sites along nucleosome deoxyribonucleic acid

    SciTech Connect

    Nelson, D.A.; Mencke, A.J.; Chambers, S.A.; Oosterhof, D.K.; Rill, R.L.

    1982-01-01

    Micrococcal nuclease cleaves within nucleosomes at sites spaced about 10.4 base pairs (bp) apart. Cleavages at sites equivalent to 30-35 bp from the ends of 146-bp cores cause spontaneous loss of an H2a-H2b pair associated with 30-40 bp length DNA. Cleavages at certain other sites do not affect the nucleosome integrity unless a solvent perturbant such as urea is added. Chromatin moderately digested with micrococcal nuclease, when fractionated by sedimentation or electrophoresis in the presence of 3 M urea, yielded four previously unobserved subnucleosomes with the following histone/DNA compositions: (H3)/sub 2/(H4)/sub 2/(H2a)(H2b)/95-115 bp; (H3)(H4)/70-80 bp DNA; (H2a)(H2b)/50-60 bp DNA; and (H1)/60-70 bp DNA. All but the latter subnucleosome were also obtained upon DNase I digestion of purified nucleosome cores labeled on the 5' ends with /sup 32/P. Only subnucleosomes that retained H2a and H2b also retained labeled ends. These results show that H2a and H2b are paired on the terminal 30-40 bp of core DNA, as suggested from analyses of histone-DNA cross-link products by Mirzabekov and coworkers. Considerations of the orgins and compositions of subnucleosomes and of cross-linking data suggest an expanded model for the locations of histone binding sites along nucleosome core DNA. The principal features of this model are (i) strong electrostatic binding sites of H2a and H2b occur at positions approximately 20-30 bp from the core ends, (ii) strong electrostatic binding sites of H3 and H4 occur primarily on the central 40 bp of core DNA, (iii) strong nonelectrostatic, urea-sensitive binding sites of H3 and H4 occur at positions approximately 30-50 bp from the core ends, and (iv) urea-sensitive binding sites of H2a or H2b may occur on the terminal 10-20 bp of core DNA.

  4. Deoxyribonucleic acid base composition and taxonomy of Moniliella and allied genera.

    PubMed

    de Hoog, G S; Guého, E

    1984-01-01

    DNA base compositions of representative (type) strains of Moniliella, Trichosporonoides and Hyalodendron were determined. Within Trichosporonoides over 16% variance was found. Most species separated well, but M. suaveolens showed considerable heterogeneity. The standard 2% G + C differences for species distinction is probably not applicable to these yeasts. The new combination M. pollinis is proposed for M. tomentosa var. pollinis on the basis of slight ecological, morphological and physiological differences, supported by a marked difference in % G + C.

  5. Chromatographic isolation of the functionally active MutS protein covalently linked to deoxyribonucleic acid.

    PubMed

    Monakhova, Mayya; Ryazanova, Alexandra; Hentschel, Andreas; Viryasov, Mikhail; Oretskaya, Tatiana; Friedhoff, Peter; Kubareva, Elena

    2015-04-10

    DNA metabolism is based on formation of different DNA-protein complexes which can adopt various conformations. To characterize functioning of such complexes, one needs a solution-based technique which allows fixing a complex in a certain transient conformation. The crosslinking approach is a popular tool for such studies. However, it is under debate if the protein components retain their natural activities in the resulting crosslinked complexes. In the present work we demonstrate the possibility of obtaining pure DNA conjugate with functionally active protein using as example MutS protein from Escherichia coli mismatch repair system. A conjugate of a chemically modified mismatch-containing DNA duplex with MutS is fixed by thiol-disulfide exchange reaction. To perform a reliable test of the protein activity in the conjugate, such conjugate must be thoroughly separated from the uncrosslinked protein and DNA prior to the test. In the present work, we employ anion exchange chromatography for this purpose for the first time and demonstrate this technique to be optimal for the conjugate purification. The activity test is a FRET-based detection of DNA unbending. We show experimentally that MutS in the conjugate retains its ability to unbend DNA in response to ATP addition and find out for the first time that the DNA unbending rate increases with increasing ATP concentration. Since the crosslinked complexes contain active MutS protein, they can be used in further experiments to investigate MutS interactions with other proteins of the mismatch repair system.

  6. 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.

  7. Partial Characterization of Small Plasmid Deoxyribonucleic Acid Present in ’ Neisseria Meningitidis’,

    DTIC Science & Technology

    1981-05-01

    could account for the patterns of recent epidemics of meningococcal meningitis in Brazil and Finland. In those outbreaks, there was a rapid increase...strains of this organism. Such studies will further help in the diagnosis, treatment and control of meningococcal meningitis. UNCLASSIFIED ._7 7--Li;A...been pre- viously shown to be highly virulent in a mouse model of meningococcal septicemia (Holbein, B.E., Infect. Immun., in press). As some virulence

  8. The Simulation and Analysis of an Evolutionary Model of Deoxyribonucleic Acid (DNA).

    DTIC Science & Technology

    1983-09-01

    Armstrong, Robert A. and Michael E. Gilpin. "Evolution in a Time-Varying Environment," Scienge: 591-592, 11 February 1977. 6. Arnheim, Normal and Charles...Hecht, and William C. Steere. New York NY: Appleton Century-Crofts, 1970. 62. and Etan Markowitz. "An Improved Method for Determining Codon...Methods," Markoy Chains and Monte Carla Calclations in 2olvmer Science, Edited by George G. Lowry. New York NY: Marcel Dekker, Inc., 1970. 64. Fogel

  9. [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.

  10. Pellet pestle homogenization of agarose gel slices at 45 degrees C for deoxyribonucleic acid extraction.

    PubMed

    Kurien, B T; Kaufman, K M; Harley, J B; Scofield, R H

    2001-09-15

    A simple method for extracting DNA from agarose gel slices is described. The extraction is rapid and does not involve harsh chemicals or sophisticated equipment. The method involves homogenization of the excised gel slice (in Tris-EDTA buffer), containing the DNA fragment of interest, at 45 degrees C in a microcentrifuge tube with a Kontes pellet pestle for 1 min. The "homogenate" is then centrifuged for 30 s and the supernatant is saved. The "homogenized" agarose is extracted one more time and the supernatant obtained is combined with the previous supernatant. The DNA extracted using this method lent itself to restriction enzyme analysis, ligation, transformation, and expression of functional protein in bacteria. This method was found to be applicable with 0.8, 1.0, and 2.0% agarose gels. DNA fragments varying from 23 to 0.4 kb were extracted using this procedure and a yield ranging from 40 to 90% was obtained. The yield was higher for fragments 2.0 kb and higher (70-90%). This range of efficiency was maintained when the starting material was kept between 10 and 300 ng. The heat step was found to be critical since homogenization at room temperature failed to yield any DNA. Extracting DNA with our method elicited an increased yield (up to twofold) compared with that extracted with a commercial kit. Also, the number of transformants obtained using the DNA extracted with our method was at least twice that obtained using the DNA extracted with the commercial kit.

  11. Conservation of Salmonella typhimurium deoxyribonucleic acid by chromosomal insertion in a partially diploid Escherichia coli hybrid.

    PubMed Central

    Johnson, E M; Placek, B P; Snellings, N J; Baron, L S

    1975-01-01

    A partially diploid Escherichia coli hybrid recovered from mating with a Salmonella typhimurium donor was converted to an Hfr strain, designated WR2080, as a means to examine the manner in which the added Salmonella genetic material was conserved in it. The Salmonella argH-+, metB-+, and RHA-+ alleles contained as supernumerary genes in WR2080 were transferred together to E. coli recipients in interrupted mating experiments approximately 25 min after initial parental contact; transfer of the allelic E. coli genes by a haploid Hfr of the same transfer orientation occurred between 23.5 min (argH-+) and 25 min (rha-+) after initial contact. Entry of the E. coli ilv-+ marker of WR2080 in these experiments occurred at 29.5 min, 1.5 min later than the entry time of this marker from the haploid E. coli Hfr. When unselected inheritance of the recessive E. coli argH-minus and rha-minus alleles of WR2080 was examined among ilv-+ selected E. coli recipients in which unselected inheritance of the Salmonella donor genes was shown to be low (8%), inheritance of argH-minus was only 7%, whereas 51% inherited the neighboring rha-minus gene. In a comparative cross employing a haploid E. coli Hfr, in which rha inheritance was similar at 56%, argH inheritance was 41%. It was concluded that the Salmonella genes contained in WR2080 were conserved on a genetic segment about 1.5 min in length chromosomally inserted near the allelic E. coli genes, thus creating a duplication on that region within the hybrid chromosome. PMID:1095545

  12. Studies on the interaction of the food colorant tartrazine with double stranded deoxyribonucleic acid.

    PubMed

    Basu, Anirban; Suresh Kumar, Gopinatha

    2016-05-01

    Interaction of the food additive tartrazine with double-stranded DNA was studied by spectroscopic and calorimetric techniques. Absorbance studies revealed that tartrazine exhibited hypochromism in the presence of DNA without any bathochromic effects. Minor groove displacement assay of DAPI and Hoechst 33258 suggested that tartrazine binds in the minor groove of DNA. The complexation was predominantly entropy driven with a smaller but favorable enthalpic contribution to the standard molar Gibbs energy. The equilibrium constant was evaluated to be (3.68 ± .08) × 10(4) M(-1) at 298.15 K. The negative standard molar heat capacity value along with an enthalpy-entropy compensation phenomenon proposed the involvement of dominant hydrophobic forces in the binding process. Tartrazine enhanced the thermal stability of DNA by 7.53 K under saturation conditions.

  13. 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...

  14. 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...

  15. Validation and application of an assay for deoxyribonucleic acid to estimate concentrations of bull sperm.

    PubMed

    Fenton, S E; Ax, R L; Cowan, C M; Coyle, T; Gilbert, G R; Lenz, R W

    1990-11-01

    Spectrophotometers are used for estimating sperm concentrations from raw ejaculates in semen processing laboratories. Unfortunately, these instruments have a limited detection spectrum and do not permit accurate quantification of sperm numbers in highly diluted or concentrated samples. The objectives of this study were to validate a DNA assay for quantification of sperm numbers in extended or undiluted semen samples and to determine precision of the assay. The principle of the assay is based upon a fluorescent dye that binds to adenine-thymine base pairs in double-stranded DNA. Semen samples and calf thymus DNA standards were sonicated in 2 M NaCl buffer with 1 mM EDTA. The DNA content of samples was compared to standards of calf thymus DNA using fluorometry. Sensitivity of the assay was determined to be 1.4 x 10(5) sperm cells. Concentrations of sperm estimated from DNA assay values did not differ from flow cytometric cell counts. Assays were performed in three different laboratories, using different equipment, to assess the assay's repeatability. Estimates of sperm concentrations determined by the DNA assay were similar, regardless of location and source of equipment used to perform the assays. This assay fulfills statistical criteria for being sensitive, accurate, and repeatable, and it can be employed in laboratories processing semen for artificial insemination as a tool for spectrophotometer calibration, a check for straw filling accuracy, or to quantify sperm numbers in extended, packaged semen.

  16. Superimposed Code Theoretic Analysis of Deoxyribonucleic Acid (DNA) Codes and DNA Computing

    DTIC Science & Technology

    2010-01-01

    hybridization that occurs between a DNA strand and its Watson - Crick complement can be used to perform mathematical computation. This research addresses how the...are 5′→3′ and strands with strikethrough are 3′→5′. A dsDNA duplex formed between a strand and its reverse complement is called a Watson - Crick (WC...3’ 5’ 3’ 5’TACGCGACTTTC3’ 5’GAAAGTCGCGTA3’ ATCAAACGATGC GCATCGTTTGAT Watson Crick (WC) Duplexes TACGCGACTTTC

  17. A modular microfluidic system for deoxyribonucleic acid identification by short tandem repeat analysis.

    PubMed

    Reedy, Carmen R; Hagan, Kristin A; Marchiarullo, Daniel J; Dewald, Alison H; Barron, Annalise; Bienvenue, Joan M; Landers, James P

    2011-02-21

    Microfluidic technology has been utilized in the development of a modular system for DNA identification through STR (short tandem repeat) analysis, reducing the total analysis time from the ∼6 h required with conventional approaches to less than 3h. Results demonstrate the utilization of microfluidic devices for the purification, amplification, separation and detection of 9 loci associated with a commercially-available miniSTR amplification kit commonly used in the forensic community. First, DNA from buccal swabs purified in a microdevice was proven amplifiable for the 9 miniSTR loci via infrared (IR)-mediated PCR (polymerase chain reaction) on a microdevice. Microchip electrophoresis (ME) was then demonstrated as an effective method for the separation and detection of the chip-purified and chip-amplified DNA with results equivalent to those obtained using conventional separation methods on an ABI 310 Genetic Analyzer. The 3-chip system presented here demonstrates development of a modular, microfluidic system for STR analysis, allowing for user-discretion as to how to proceed after each process during the analysis of forensic casework samples.

  18. 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.

  19. Dynamical features of deoxyribonucleic acid and configuration transition in the transcription process

    NASA Astrophysics Data System (ADS)

    Pang, Xiao-feng; Feng, Yuan Ping; Zhang, Huai-wu; Assad, S. M.

    2006-10-01

    Biological functions and genetic features of DNA, such as duplication, transcription and gene expression, are mainly determined by its structure, but depend also on the temperature and features of solution, such as salt concentration. We study the influence of temperature and salt concentration on the conformation changes and transcription of DNA by using a new dynamical model. This new model admits three degrees of freedom per base-pair: two displacement variables related to the vibrations of hydrogen atom in the hydrogen bonds and base (nucleotide), respectively, and an angular variable related to the rotation of base. The important role of motion of hydrogen atom in the hydrogen bonds is specially stressed in this model. This is helpful to reveal the mechanism of transcription of DNA. According to their properties of motion, we first give the Hamiltonian of the system, corresponding equations of motion and their soliton-solutions. The solitons are the excitation states formed by the displacements of hydrogen atoms and bases and the rotations of bases, arising from the energy absorbed by DNA, in the systems, respectively. By applying the transfer integral method we obtain the thermodynamic properties (e.g. free energy and entropy) of the thermal excitation state of DNA at the biological temperature in this model. According to the properties of these thermodynamic functions obtained we study the mechanism and processes of melting and transcription of DNA with the aid of the transforms of energy carried by the soliton in such a case. We further give the properties of the transcription of DNA with the help of the average value of the mean square of displacement of hydrogen atom, and the values of subcritical temperature and force of the phase transition are also found. Finally, we conclude that the transcription of DNA not only depends directly on the properties of its structure and of energy absorbed by it, but also is influenced by the temperature and salt concentration in the solution of DNA, which is consistent with experimental data. Therefore this new model not only can predict the transcription of DNA, but also can give the relationship among the conformation changes and the temperature and salt concentration. Finally we discuss in simple terms the influences of water or solution around DNA on its dynamics and further point out the defects and limitations of the new model of the dynamics of DNA and its direction of development.

  20. Identification of Biological Warfare (BW) Threat Agents Using Deoxyribonucleic Acid (DNA) Microarrays

    DTIC Science & Technology

    2005-02-01

    Escherichia coli 0157:H7 and the non-virulent K-12 strain. By assaying for the presence of: 1) unique sequences at various levels of the phylogenetic tree , 2...the phylogenetic tree , 2) virulence genes, 3) antibiotic resistance genes, 4) virulence plasmid sequences and 5) ribosomal genes, we are in a unique...demonstrating species-level discrimination between Bacillus anthracis, vaccinia virus and Yersinia pestis and strain-level discrimination between

  1. Determination of mammalian deoxyribonucleic acid (DNA) in commercial vegetarian and vegan diets for dogs and cats.

    PubMed

    Kanakubo, K; Fascetti, A J; Larsen, J A

    2017-02-01

    The determination of undeclared ingredients in pet food using different analytical methods has been reported in recent years, raising concerns regarding adequate quality control, dietary efficacy and the potential for purposeful adulteration. The objective of this study was to determine the presence or absence of mammalian DNA using multiplex polymerase chain reaction (PCR) on diets marketed as vegetarian or vegan for dogs and cats. The diets were tested in duplicate; two samples were purchased approximately 3 to 4 months apart with different lot numbers. Multiplex PCR-targeted mitochondrial DNA with two species-specific primers was used to amplify and sequence two sections of the cytochrome b gene for each of the 11 mammalian species. Half of the diets assessed (7/14) were positive for one or more undeclared mammalian DNA source (bovine, porcine, or ovine), and the result was repeatable for one or more species in six diets. While most of the detected DNA was found at both time points, in some cases, the result was positive only at one time point, suggesting the presence may have been due to unintentional cross-contact with animal-sourced ingredients. DNA from feline, cervine, canine, caprine, equine, murine (mouse and rat) and leporine was not identified in any samples. However, evidence of mammalian DNA does not confirm adulteration by the manufacturer nor elucidate its clinical significance when consumed by animals that may benefit from a vegetarian or vegan diet.

  2. Assisted reproductive technology alters deoxyribonucleic acid methylation profiles in bloodspots of newborn infants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To evaluate the effect of infertility and intracytoplasmic sperm injection (ICSI) on DNA methylation of offspring. Microarray analysis of DNA methylation in archived neonatal bloodspots of in vitro fertilization (IVF)/ICSI-conceived children compared with controls born to fertile and infertile paren...

  3. Deoxyribonuclease I generates single-stranded gaps in chromatin deoxyribonucleic acid.

    PubMed

    Riley, D E

    1980-06-24

    Production of 10-base multiple DNA ladder fragments during DNase I digestion of chromatin is explained by a model which does not involve site-specific nicking by the DNase I. This model was tested because it explains why 10-base (actually 10.4 base) multiple-related fragments are paradoxically generated by both endonucleolytic (DNase I) and exonucleolytic (exonuclease III) mechanisms. This new model also explains the phenomenon of substantial single-stranded DNA production during DNase I digestion of chromatin. The latter phenomenon has been widely observed but is not explained by previous models. The single-stranded gap model to be presented makes testable predictions. Primarily, these are that DNase I produces single-stranded gaps in chromatin DNA and that the termini of 10-base multiple ladder fragments are separated by single-stranded gaps. Single-stranded gap production by DNase I was confirmed by a number of methods. Sensitivity of ladder band components (from DNase I but not staphylococcal nuclease digests) to S1 nuclease suggested that the ladder fragments themselves may compose a significant portion of these gaps. Separation of ladder fragment termini by single-stranded gaps was verified by demonstrating both resistance to the nick-specific NAD+-dependent ligase and sensitivity to T4 ligase which can ligate across gaps. Many single-stranded gaps, occurring both individually and clusters, were observed by electron microscopy using either cytochrome c labeling (where the gaps) are thinner than duplex) or gene 32 protein labeling (gaps thicker than duplex). Gap sizes were estimated by protecting them with gene 32 protein and digesting away unprotected duplexes. By this method, gap sizes fall into a ladder distribution (from 10 or 20 bases up to 120 bases), which, at least in the region of the shorter sizes, clearly indicates the sizes of single-stranded gaps formed in chromatin by DNase I.

  4. 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

  5. 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.

  6. Effect of mycophenolic acid on TNFα-induced expression of cell adhesion molecules in human venous endothelial cells in vitro

    PubMed Central

    Hauser, Ingeborg A; Johnson, David R; Thévenod, Frank; Goppelt-Strübe, Margarete

    1997-01-01

    Mycophenolic acid (MPA) is an inhibitor of inosine-5′-monophosphate dehydrogenase and therefore interferes with cellular GTP biosynthesis. Recently, MPA has been used as an antiproliferative and immunosuppressive agent. In the present study, the effect of MPA on the expression of the endothelial cell adhesion molecules (CAMs), intercellular (I) CAM-1, vascular (V) CAM-1 and endothelial (E)-selectin, was investigated in tumour necrosis factor-α (TNFα)-activated cultured human venous endothelial cells (EC).Surface expression of CAMs was measured by flow cytometry and mRNA expression by Northern blot analysis. Transcriptional activation of CAMs by the nuclear factor NF-κB was determined by an electromobility shift assay. The function of CAMs was studied by a static adhesion assay with human monocyte-like undifferentiated U937 cells.Pretreatment of TNFα- (5  ng ml−1, 12 h) activated EC with MPA (10 μM, 24 h) increased the binding of U937 cells, which had not been treated with MPA, by ≈amp;2 fold. MPA-pretreatment of EC did not affect TNFα-induced surface expression of ICAM-1. However, VCAM-1 and E-selectin were increased 2–3 fold and remained elevated up to 24 h, by which time TNFα-activated control EC had returned to baseline levels of expression. The effect of MPA on the surface expression of CAMs was half-maximal at ≈amp;1 μM and required ⩾12 h of pretreatment. Guanosine (0.3 mM), a precursor of GTP, did not prevent the effect of MPA on the expression of CAMs in TNFα-activated EC.Kinetics of mRNA expression of CAMs mirrored protein expression: mRNA for ICAM-1 was unaffected, whereas TNFα-induced mRNA expression for E-selectin and VCAM-1 was prolonged and increased by MPA. This effect was not due to increased transcription mediated by the nuclear transcription factor NF-κB. However, half-life for E-selectin mRNA was increased 10 fold by MPA, whereas ICAM-1 mRNA half-life was unchanged.The data demonstrate that apart from its

  7. Lectin affinity chromatography of articular cartilage fibromodulin: Some molecules have keratan sulphate chains exclusively capped by α(2-3)-linked sialic acid.

    PubMed

    Lauder, Robert M; Huckerby, Thomas N; Nieduszynski, Ian A

    2011-10-01

    Fibromodulin from bovine articular cartilage has been subjected to lectin affinity chromatography by Sambucus nigra lectin which binds α(2-6)- linked N-acetylneuraminic acid, and the structure of the keratan sulphate in the binding and non-binding fractions examined by keratanase II digestion and subsequent high pH anion exchange chromatography. It has been confirmed that the keratan sulphate chains attached to fibromodulin isolated from bovine articular cartilage may have the chain terminating N-acetylneuraminic acid residue α(2-3)- or α(2-6)-linked to the adjacent galactose residue. Although the abundance of α(2-6)-linked N-acetylneuraminic acid (ca. 22%) is such that this could cap one of the four chains in almost all fibromodulin molecules, it was found that ca. 34% of the fibromodulin proteoglycan molecules from bovine articular cartilage were capped exclusively with α(2-3)-linked N-acetylneuraminic acid. The remainder of the fibromodulin proteoglycans, which bound to the lectin had a mixture of α(2-3)- and α(2-6)-linked N-acetylneuraminic acid capping structures. The keratan sulphates attached to fibromodulin molecules capped exclusively with α(2-3)- linked N-acetylneuraminic acid were found to have a higher level of galactose sulphation than those from fibromodulin with both α(2-3)- and α(2-6)-linked N-acetylneuraminic acid caps, which bound to the Sambucus nigra lectin. In addition, both pools contained chains of similar length (ca. 8-9 disaccharides). Both also contained α(1-3)-linked fucose, showing that this feature does not co-distribute with α(2-6)-linked N-acetylneuraminic acid, although these two features are present only in mature articular cartilage. These data show that there are discrete populations of fibromodulin within articular cartilage, which may have differing impacts upon tissue processes.

  8. 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

  9. Mitigation of the hematopoietic and gastrointestinal acute radiation syndrome by octadecenyl thiophosphate, a small molecule mimic of lysophosphatidic acid.

    PubMed

    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

    2015-04-01

    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.

  10. 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.

  11. Pharmacological regulation of insulin secretion in MIN6 cells through the fatty acid receptor GPR40: identification of agonist and antagonist small molecules.

    PubMed

    Briscoe, Celia P; Peat, Andrew J; McKeown, Stephen C; Corbett, David F; Goetz, Aaron S; Littleton, Thomas R; McCoy, David C; Kenakin, Terry P; Andrews, John L; Ammala, Carina; Fornwald, James A; Ignar, Diane M; Jenkinson, Stephen

    2006-07-01

    1. Long chain fatty acids have recently been identified as agonists for the G protein-coupled receptors GPR40 and GPR120. Here, we present the first description of GW9508, a small-molecule agonist of the fatty acid receptors GPR40 and GPR120. In addition, we also describe the pharmacology of GW1100, a selective GPR40 antagonist. These molecules were used to further investigate the role of GPR40 in glucose-stimulated insulin secretion in the MIN6 mouse pancreatic beta-cell line. 2. GW9508 and linoleic acid both stimulated intracellular Ca2+ mobilization in human embryonic kidney (HEK)293 cells expressing GPR40 (pEC50 values of 7.32+/-0.03 and 5.65+/-0.06, respectively) or GPR120 (pEC50 values of 5.46+/-0.09 and 5.89+/-0.04, respectively), but not in the parent HEK-293 cell line. 3. GW1100 dose dependently inhibited GPR40-mediated Ca2+ elevations stimulated by GW9508 and linoleic acid (pIC50 values of 5.99+/-0.03 and 5.99+/-0.06, respectively). GW1100 had no effect on the GPR120-mediated stimulation of intracellular Ca2+ release produced by either GW9508 or linoleic acid. 4. GW9508 dose dependently potentiated glucose-stimulated insulin secretion in MIN6 cells, but not in primary rat or mouse islets. Furthermore, GW9508 was able to potentiate the KCl-mediated increase in insulin secretion in MIN6 cells. The effects of GW9508 on insulin secretion were reversed by GW1100, while linoleic acid-stimulated insulin secretion was partially attenuated by GW1100. 5. These results add further evidence to a link between GPR40 and the ability of fatty acids to acutely potentiate insulin secretion and demonstrate that small-molecule GPR40 agonists are glucose-sensitive insulin secretagogues.

  12. A microfluidic platform for transcription- and amplification-free detection of zepto-mole amounts of nucleic acid molecules.

    PubMed

    Mayr, Reinhard; Haider, Michaela; Thünauer, Roland; Haselgrübler, Thomas; Schütz, Gerhard J; Sonnleitner, Alois; Hesse, Jan

    2016-04-15

    Here we report the development of a device for the transcription- and amplification-free detection of DNA and RNA molecules down to the zepto-mole range. A microfluidic chip with a built-in microarray was used for manipulation of nano-liter sample volumes. Specific staining and immobilization of the target molecules was achieved via a double hybridization approach thereby avoiding bias due to enzymatic processes like reverse transcription and PCR amplification. Therefore, target molecules were indirectly labeled by pre-hybridization to complementary Cy5-labeled probes. The remaining single-stranded portion of each target molecule could subsequently hybridize to complementary capture probes of a microarray. Thus a target-mediated immobilization of labeled DNA took place. By means of an ultra-sensitive fluorescence readout, all molecules hybridized to the microarray could be detected. The combination of minimized sample volume and single molecule detection yielded a detection limit of 39 fM (831 molecules in 35.4 nl assay volume) for target DNA and 16 fM (338 molecules) for target RNA after 1h on-chip hybridization.

  13. 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

    2011-03-07

    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.

  14. 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.

  15. 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.

  16. Crystal structure of a 2:1 piroxicam-gentisic acid co-crystal featuring neutral and zwitterionic piroxicam mol-ecules.

    PubMed

    Horstman, Elizabeth M; Bertke, Jeffery A; Woods, Toby J; Kenis, Paul J A

    2016-12-01

    A new 2:1 co-crystal of piroxicam and gentisic acid [systematic name: 4-hy-droxy-1,1-dioxo-N-(pyridin-2-yl)-2H-1λ(6),2-benzo-thia-zine-3-carboxamide-2-(4-oxido-1,1-dioxo-2H-1λ(6),2-benzo-thia-zine-3-amido)-pyridin-1-ium-2,5-di-hydroxy-benzoic acid, 2C15H13N3O4S·C7H6O4] has been synthesized using a microfluidic platform and initially identified using Raman spectroscopy. In the co-crystal, one piroxicam mol-ecule is in its neutral form and an intra-molecular O-H⋯O hydrogen bond is observed. The other piroxicam mol-ecule is zwitterionic (proton transfer from the OH group to the pyridine N atom) and two intra-molecular N-H⋯O hydrogen bonds occur. The gentisic acid mol-ecule shows whole-mol-ecule disorder over two sets of sites in a 0.809 (2):0.191 (2) ratio. In the crystal, extensive hydrogen bonding between the components forms layers propagating in the ab plane.

  17. Crystal Structure of Fatty Acid Amide Hydrolase Bound to the Carbamate Inhibitor URB597: Discovery of a Deacylating Water Molecule and Insight into Enzyme Inactivation

    SciTech Connect

    Mileni, Mauro; Kamtekar, Satwik; Wood, David C.; Benson, Timothy E.; Cravatt, Benjamin F.; Stevens, Raymond C.

    2010-08-12

    The endocannabinoid system regulates a wide range of physiological processes including pain, inflammation, and cognitive/emotional states. URB597 is one of the best characterized covalent inhibitors of the endocannabinoid-degrading enzyme fatty acid amide hydrolase (FAAH). Here, we report the structure of the FAAH-URB597 complex at 2.3 {angstrom} resolution. The structure provides insights into mechanistic details of enzyme inactivation and experimental evidence of a previously uncharacterized active site water molecule that likely is involved in substrate deacylation. This water molecule is part of an extensive hydrogen-bonding network and is coordinated indirectly to residues lining the cytosolic port of the enzyme. In order to corroborate our hypothesis concerning the role of this water molecule in FAAH's catalytic mechanism, we determined the structure of FAAH conjugated to a urea-based inhibitor, PF-3845, to a higher resolution (2.4 {angstrom}) than previously reported. The higher-resolution structure confirms the presence of the water molecule in a virtually identical location in the active site. Examination of the structures of serine hydrolases that are non-homologous to FAAH, such as elastase, trypsin, or chymotrypsin, shows a similarly positioned hydrolytic water molecule and suggests a functional convergence between the amidase signature enzymes and serine proteases.

  18. 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

  19. Review insights into the interactions of amino acids and peptides with inorganic materials using single molecule force spectroscopy.

    PubMed

    Das, Priyadip; Reches, Meital

    2015-09-01

    Understanding the interactions between proteins and inorganic surfaces is important for the development of new biomaterials and implants as they interface with the immune response by proteins. In addition, the adsorption of proteins to inorganic surfaces leads to the formation of a conditioning layer that facilitates bacterial attachments and biofilm formation. As biofilm provides bacterial resistance to antibiotics, biofilm formation is an undesirable process that could be prevented by resisting protein interactions with the substrate. Moreover, the interaction between proteins and inorganic materials is the basis for the formation of composite materials in nature. Understanding the underlying forces that governs these interactions would lead to the design of new and unique composite materials in vitro. This review focuses on the insights gained using single-molecule force spectroscopy by AFM on these interactions. This tool provides molecular information, at the single molecule level, on the interaction between a molecule on the AFM tip and a substrate.

  20. 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

    2015-06-05

    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.

  1. A novel 1:1 canal inclusion network formed by deoxycholic acid dimers (bislactones) with benzene molecules: an x-ray study

    NASA Astrophysics Data System (ADS)

    Stanković, S.; Kálmán, A.; Argay, Gy.; Miljković, D.; Kuhajda, K.; Vicković, I.; Bruwo, M.; Ori, O.

    1990-04-01

    A novel canal inclusion network formed by 3α-hydroxy-5β-cholano-12α-24-bislactone (C 48H 74O 6) with benzene molecule (1:1) in a triclinic crystal lattice has been revealed by X-ray diffraction and 1H NMR spectroscopy. Crystal symmetry P1 with a=15.036(4), b=13.269(4), c=7.196(4) Å, α=78.16(2), β=73.42(2), γ=66.42(2) °, Z=1 (one pair of deoxycholic acid (DCA) dimer and benzene in the unit cell) and Dc=1.091 g cm -3. The structure was refined to R 0.082 for 3083 reflections. The DCA dimers separated by unit translations form infinite canals along the shortest axis c. These hydrophobic canals accommodate the benzene molecules separated by a distance of 4.55(2) Å. In accordance with the vigorous thermal motion of the ring atoms the benzene molecules are bound by weak dispersion forces to the host molecules. However, atom—atom potential calculations indicate that the position and orientation of the benzene ring in the void represent the energy minimum.

  2. Determination of the elastic properties of short ssDNA molecules by mechanically folding and unfolding DNA hairpins.

    PubMed

    Alemany, Anna; Ritort, Felix

    2014-12-01

    The characterization of elastic properties of biopolymers is crucial to understand many molecular reactions determined by conformational bending fluctuations of the polymer. Direct measurement of such elastic properties using single-molecule methods is usually hindered by the intrinsic tendency of such biopolymers to form high-order molecular structures. For example, single-stranded deoxyribonucleic acids (ssDNA) tend to form secondary structures such as local double helices that prevent the direct measurement of the ideal elastic response of the ssDNA. In this work, we show how to extract the ideal elastic response in the entropic regime of short ssDNA molecules by mechanically pulling two-state DNA hairpins of different contour lengths. This is achieved by measuring the force dependence of the molecular extension and stiffness on mechanically folding and unfolding the DNA hairpin. Both quantities are fit to the worm-like chain elastic model giving values for the persistence length and the interphosphate distance. This method can be used to unravel the elastic properties of short ssDNA and RNA sequences and, more generally, any biopolymer that can exhibit a cooperative two-state transition between mechanically folded and unfolded states (such as proteins).

  3. 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.

  4. Membrane-based continuous remover of trifluoroacetic acid in mobile phase for LC-ESI-MS analysis of small molecules and proteins.

    PubMed

    Zhou, Zhigui; Zhang, Jialing; Xing, Jiawei; Bai, Yu; Liao, Yiping; Liu, Huwei

    2012-07-01

    We developed a "continuous" trifluoroacetic acid (TFA) remover based on electrodialysis with bipolar membrane for online coupling of liquid chromatography (LC) and electrospray ionization mass spectrometry (ESI-MS) using TFA containing mobile phase. With the TFA remover as an interface, the TFA anion in the mobile phase was removed based on electrodialysis mechanism, and meanwhile, the anion exchange membrane was self-regenerated by the hydroxide ions produced by the bipolar membrane. So the remover could continuously work without any additional regeneration process. The established LC-TFA remover-MS system has been successfully applied for the qualitative and quantitative analysis of small molecules as well as proteins.

  5. 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.

  6. Fourth 3D structure of the chitosan molecule: conformation of chitosan in its salts with medical organic acids having a phenyl group.

    PubMed

    Kawahara, Makoto; Yui, Toshifumi; Oka, Kunio; Zugenmaier, Peter; Suzuki, Shiho; Kitamura, Shinichi; Okuyama, Kenji; Ogawa, Kozo

    2003-07-01

    Chitosan salts with two medical organic acids having phenyl groups (salicylic and gentisic acids) exhibited fiber diffraction patterns of a new type of crystal which does not compare with known types I and II. The crystals, called type III salts, showed a fiber repeat of 2.550 nm and a meridional reflection at the 5th layer line. These results coupled with a conformational analysis indicate the chain conformation of chitosan with the salts to be a 5/3 helix, this helix differing from those of type I (an extended two-fold helix) and type II (a relaxed two-fold helix or a 4/1 helix). The fiber patterns of all the type III salts were similar. This observation has also been found with type II salts and is an indication that the acid ions are not arranged in regular positions in the crystals. A comparison of solid-state 13C-NMR spectra of the gentisic acid salt and the aspirin salt, which could not be crystallized, suggests that, in the latter salt, the chitosan molecules also formed a 5/3 helix.

  7. 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.

  8. 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

  9. Effects of specific amino acid changes on the antigenicity of hemagglutinin molecules of avian influenza isolates from Mexico

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Amino acid (aa) changes between the hemagglutinin (HA) proteins of a vaccine avian influenza virus and more recent field isolates were detected following prolonged vaccination of Mexican poultry. Using site-directed mutagenesis and reverse genetics (rg), viruses containing identical backbones but d...

  10. 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).

  11. The role of acidic organelles in the development of schistosomula of Schistosoma mansoni and their response to signalling molecules.

    PubMed

    Al-Adhami, B H; Noble, C; Sharaf, O; Thornhill, J; Doenhoff, M J; Kusel, R

    2005-03-01

    The cercariae of Schistosoma mansoni become transformed into schistosomula during host skin penetration. We have found that large acidophilic compartments are detected in schistosomula but not in cercariae or in any other stages of the parasite by use of the fluorescent dye LysoTracker, a dye specific for mammalian lysosomes. Some of these large acidic compartments incorporated monodansylcadaverine, a specific dye for autophagosomes. We have used potent inhibitors (wortmannin and 3-methyladenine) and a potent inducer (starvation) of autophagy to show that the pathway to the formation of the acidic compartments requires specific molecular signals from the environment and from the genome. Certain doses of ultraviolet light inhibited significantly the formation of the acidic compartments, which may indicate disruption of the lysosome/autophagosome pathway. We have also defined two proteins that are commonly associated with lysosomes and autophagosomes in mammalian cells, the microtubule-associated membrane protein (MAP-LC3) and lysosome-associated membrane protein (LAMP-1), in extracts of schistosomula. We suggest that the autophagy pathway could be developed in transformed schistosomula.

  12. 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.

  13. A chemical genetic screen uncovers a small molecule enhancer of the N-acylethanolamine degrading enzyme, fatty acid amide hydrolase, in Arabidopsis

    PubMed Central

    Khan, Bibi Rafeiza; Faure, Lionel; Chapman, Kent D.; Blancaflor, Elison B.

    2017-01-01

    N-Acylethanolamines (NAEs) are a group of fatty acid amides that play signaling roles in diverse physiological processes in eukaryotes. Fatty acid amide hydrolase (FAAH) degrades NAE into ethanolamine and free fatty acid to terminate its signaling function. In animals, chemical inhibitors of FAAH have been used for therapeutic treatment of pain and as tools to probe deeper into biochemical properties of FAAH. In a chemical genetic screen for small molecules that dampened the inhibitory effect of N-lauroylethanolamine (NAE 12:0) on Arabidopsis thaliana seedling growth, we identified 6-(2-methoxyphenyl)-1,3-dimethyl-5-phenyl-1H-pyrrolo[3,4-d]pyrimidine-2,4(3 H,6 H)-dione (or MDPD). MDPD alleviated the growth inhibitory effects of NAE 12:0, in part by enhancing the enzymatic activity of Arabidopsis FAAH (AtFAAH). In vitro, biochemical assays showed that MDPD enhanced the apparent Vmax of AtFAAH but did not alter the affinity of AtFAAH for its NAE substrates. Structural analogs of MDPD did not affect AtFAAH activity or dampen the inhibitory effect of NAE 12:0 on seedling growth indicating that MDPD is a specific synthetic chemical activator of AtFAAH. Collectively, our study demonstrates the feasibility of using an unbiased chemical genetic approach to identify new pharmacological tools for manipulating FAAH- and NAE-mediated physiological processes in plants. PMID:28112243

  14. Sequence of a cDNA clone encoding the polysialic acid-rich and cytoplasmic domains of the neural cell adhesion molecule N-CAM.

    PubMed Central

    Hemperly, J J; Murray, B A; Edelman, G M; Cunningham, B A

    1986-01-01

    Purified fractions of the neural cell-adhesion molecule N-CAM from embryonic chicken brain contain two similar polypeptides (Mr, 160,000 and 130,000), each containing an amino-terminal external binding region, a carbohydrate-rich central region, and a carboxyl-terminal region that is associated with the cell. Previous studies indicate that the two polypeptides arise by alternative splicing of mRNAs transcribed from a single gene. We report here the 3556-nucleotide sequence of a cDNA clone (pEC208) that encodes 964 amino acids from the carbohydrate and cell-associated domains of the larger N-CAM polypeptide followed by 664 nucleotides of 3' untranslated sequence. The predicted protein sequence contains attachment sites for polysialic acid-containing oligosaccharides, four tandem homologous regions of polypeptide resembling those seen in the immunoglobulin superfamily, and a single hydrophobic sequence that appears to be the membrane-spanning segment. The cytoplasmic domain carboxyl terminal to this segment includes a block of approximately equal to 250 amino acids present in the larger but not in the smaller N-CAM polypeptide. We designate these the ld (large domain) polypeptide and the sd (small domain) polypeptide. The intracellular domains of the ld and sd polypeptides are likely to be critical for cell-surface modulation of N-CAM by interacting in a differential fashion with other intrinsic proteins or with the cytoskeleton. PMID:3458261

  15. A chemical genetic screen uncovers a small molecule enhancer of the N-acylethanolamine degrading enzyme, fatty acid amide hydrolase, in Arabidopsis

    DOE PAGES

    Khan, Bibi Rafeiza; Faure, Lionel; Chapman, Kent D.; ...

    2017-01-23

    N-Acylethanolamines (NAEs) are a group of fatty acid amides that play signaling roles in diverse physiological processes in eukaryotes. We used fatty acid amide hydrolase (FAAH) degrades NAE into ethanolamine and free fatty acid to terminate its signaling function. In animals, chemical inhibitors of FAAH for therapeutic treatment of pain and as tools to probe deeper into biochemical properties of FAAH. In a chemical genetic screen for small molecules that dampened the inhibitory effect of N-lauroylethanolamine (NAE 12:0) on Arabidopsis thaliana seedling growth, we identified 6-(2-methoxyphenyl)-1,3-dimethyl-5-phenyl-1H-pyrrolo[3,4-d]pyrimidine-2,4(3 H,6 H)-dione (or MDPD). MDPD alleviated the growth inhibitory effects of NAE 12:0, inmore » part by enhancing the enzymatic activity of Arabidopsis FAAH (AtFAAH). In vitro, biochemical assays showed that MDPD enhanced the apparent Vmax of AtFAAH but did not alter the affinity of AtFAAH for its NAE substrates. Furthermore, structural analogs of MDPD did not affect AtFAAH activity or dampen the inhibitory effect of NAE 12:0 on seedling growth indicating that MDPD is a specific synthetic chemical activator of AtFAAH. Our study demonstrates the feasibility of using an unbiased chemical genetic approach to identify new pharmacological tools for manipulating FAAH- and NAE-mediated physiological processes in plants.« less

  16. Killing of Mycobacterium avium by Lactoferricin Peptides: Improved Activity of Arginine- and d-Amino-Acid-Containing Molecules

    PubMed Central

    Silva, Tânia; Magalhães, Bárbara; Maia, Sílvia; Gomes, Paula; Nazmi, Kamran; Bolscher, Jan G. M.; Rodrigues, Pedro N.; Bastos, Margarida

    2014-01-01

    Mycobacterium avium causes respiratory disease in susceptible individuals, as well as disseminated infections in immunocompromised hosts, being an important cause of morbidity and mortality among these populations. Current therapies consist of a combination of antibiotics taken for at least 6 months, with no more than 60% overall clinical success. Furthermore, mycobacterial antibiotic resistance is increasing worldwide, urging the need to develop novel classes of antimicrobial drugs. One potential and interesting alternative strategy is the use of antimicrobial peptides (AMP). These are present in almost all living organisms as part of their immune system, acting as a first barrier against invading pathogens. In this context, we investigated the effect of several lactoferrin-derived AMP against M. avium. Short peptide sequences from both human and bovine lactoferricins, namely, hLFcin1-11 and LFcin17-30, as well as variants obtained by specific amino acid substitutions, were evaluated. All tested peptides significantly inhibited the axenic growth of M. avium, the bovine peptides being more active than the human. Arginine residues were found to be crucial for the display of antimycobacterial activity, whereas the all-d-amino-acid analogue of the bovine sequence displayed the highest mycobactericidal activity. These findings reveal the promising potential of lactoferricins against mycobacteria, thus opening the way for further research on their development and use as a new weapon against mycobacterial infections. PMID:24709266

  17. N,N‧-Dimethylpiperazine mono-betaine complex with two molecules of 3-iodobenzoic acid and water studied by X-ray diffraction, DFT, FTIR and NMR methods

    NASA Astrophysics Data System (ADS)

    Dega-Szafran, Z.; Katrusiak, A.; Szafran, M.

    2008-03-01

    N, N'-Dimethylpiperazine mono-betaine ( N-carboxymethyl- N, N'-dimethylpiperazinium inner salt, MBPZ) forms a crystalline complex with two molecules of 3-iodobenzoic acid (3IBA). The complex crystallizes as a monohydrate, MBPZ(3IBA) 2H 2O. The complex has been characterized by X-ray diffraction and FTIR, Raman, 1H and 13C NMR spectroscopies. The crystals are monoclinic, space group P2 1/ c, with a = 6.7810(17), b = 38.391(4), c = 10.0542(16) Å, β = 90.024(18)°. The piperazinium ring has a chair conformation with the N +CH 2COO - substituent in the axial and both methyl groups in the equatorial positions. The 3IBA molecules interact with the carboxylate group of N +CH 2COO - and N' atom through the O-H···O and O-H···N hydrogen bonds of the lengths 2.550 and 2.695 Å. The water molecules link MBPZ(3IBA) 2 complexes by the O-H···OOCCH 2N + hydrogen bonds of 2.850 and 2.793 Å into infinite chains. The MBPZ(3XBA) 2H 2O (X = I, Br, Cl), MBPZ(3IBA) 2 complexes and MBPZ have been analyzed by the B3LYP/MidiX level of theory. The conformers with the axial CH 2COO - substituent have lower energies than these with the equatorial CH 2COO - one. The bands at 3433, 2790, 2450, 1915 cm -1 assigned to the ν(OH) vibration of the various hydrogen bonds, and two bands attributed to the ν(C dbnd O) (1680 cm -1) and ν as(COO) (1660 cm -1) vibrations in the FTIR spectrum confirm the structure of the title complex. The 1H- 13C HMBC spectrum has been analyzed in order to assign the carbon-13 chemical shifts.

  18. Neural Cell Adhesion Molecule-Associated Polysialic Acid Regulates Synaptic Plasticity and Learning by Restraining the Signaling through GluN2B-Containing NMDA Receptors

    PubMed Central

    Kochlamazashvili, Gaga; Senkov, Oleg; Grebenyuk, Sergei; Robinson, Catrina; Xiao, Mei-Fang; Stummeyer, Katharina; Gerardy-Schahn, Rita; Engel, Andreas K.; Feig, Larry; Semyanov, Alexey; Suppiramaniam, Vishnu; Schachner, Melitta; Dityatev, Alexander

    2017-01-01

    The neural cell adhesion molecule (NCAM) is the predominant carrier of α2,8 polysialic acid (PSA) in the mammalian brain. Abnormalities in PSA and NCAM expression are associated with schizophrenia in humans and cause deficits in hippocampal synaptic plasticity and contextual fear conditioning in mice. Here, we show that PSA inhibits opening of recombinant NMDA receptors composed of GluN1/2B (NR1/NR2B) or GluN1/2A/2B (NR1/NR2A/NR2B) but not of GluN1/2A (NR1/NR2A) subunits. Deficits in NCAM/PSA increase GluN2B-mediated transmission and Ca2+ transients in the CA1 region of the hippocampus. In line with elevation of GluN2B-mediated transmission, defects in long-term potentiation in the CA1 region and contextual fear memory in NCAM/PSA-deficient mice are abrogated by application of a GluN2B-selective antagonist. Furthermore, treatment with the glutamate scavenger glutamic-pyruvic transaminase, ablation of Ras-GRF1 (a mediator of GluN2B signaling to p38 MAPK), or direct inhibition of hyperactive p38 MAPK can restore impaired synaptic plasticity in brain slices lacking PSA/NCAM. Thus, PSA carried by NCAM regulates plasticity and learning by inhibition of the GluN2B-Ras-GRF1-p38 MAPK signaling pathway. These findings implicate carbohydrates carried by adhesion molecules in modulating NMDA receptor signaling in the brain and demonstrate reversibility of cognitive deficits associated with ablation of a schizophrenia-related adhesion molecule. PMID:20237287

  19. 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.

  20. 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.

  1. 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.

  2. Nanomedicine strategy for optimizing delivery to outer hair cells by surface-modified poly(lactic/glycolic acid) nanoparticles with hydrophilic molecules

    PubMed Central

    Wen, Xingxing; Ding, Shan; Cai, Hui; Wang, Junyi; Wen, Lu; Yang, Fan; Chen, Gang

    2016-01-01

    Targeted drug delivery to outer hair cells (OHCs) in the cochlea by nanomedicine strategies forms an effective therapeutic approach for treating hearing loss. Surface chemistry plays a deciding role in nanoparticle (NP) biodistribution, but its influence on such distribution in the cochlea remains largely unknown. Herein, we report the first systematic comparison of poly(lactic/glycolic acid) nanoparticles (PLGA NPs) with or without surface modification of hydrophilic molecules for optimizing the delivery to OHCs both in vitro and in vivo. NPs that were surface modified with poloxamer 407 (P407), chitosan, or methoxy poly(ethylene glycol) and the unmodified NPs were highly biocompatible with L929 and House Ear Institute-organ of Corti 1 cells as well as cochlear tissues. Interestingly, among all the examined NPs, P407-PLGA NPs showed the greatest cellular uptake and prominent fluorescence in cochlear imaging. More importantly, we provide novel evidence that the surface-modified NPs reached the organ of Corti and were transported into the OHCs at a higher level. Together, these observations suggest that surface modification with hydrophilic molecules will allow future clinical applications of PLGA NPs, especially P407-PLGA NPs, in efficient hearing loss therapy. PMID:27877041

  3. Preparation and evaluation of poly(alkyl methacrylate-co-methacrylic acid-co-ethylene dimethacrylate) monolithic columns for separating polar small molecules by capillary liquid chromatography.

    PubMed

    Lin, Shu-Ling; Wu, Yu-Ru; Lin, Tzuen-Yeuan; Fuh, Ming-Ren

    2015-04-29

    In this study, methacrylic acid (MAA) was incorporated with alkyl methacrylates to increase the hydrophilicity of the synthesized ethylene dimethacrylate-based (EDMA-based) monoliths for separating polar small molecules by capillary LC analysis. Different alkyl methacrylate-MAA ratios were investigated to prepare a series of 30% alkyl methacrylate-MAA-EDMA monoliths in fused-silica capillaries (250-μm i.d.). The porosity, permeability, and column efficiency of the synthesized MAA-incorporated monolithic columns were characterized. A mixture of phenol derivatives is employed to evaluate the applicability of using the prepared monolithic columns for separating small molecules. Fast separation of six phenol derivatives was achieved in 5 min with gradient elution using the selected poly(lauryl methacrylate-co-MAA-co-EDMA) monolithic column. In addition, the effect of acetonitrile content in mobile phase on retention factor and plate height as well as the plate height-flow velocity curves were also investigated to further examine the performance of the selected poly(lauryl methacrylate-co-MAA-co-EDMA) monolithic column. Moreover, the applicability of prepared polymer-based monolithic column for potential food safety applications was also demonstrated by analyzing five aflatoxins and three phenicol antibiotics using the selected poly(lauryl methacrylate-co-MAA-co-EDMA) monolithic column.

  4. Dihydrobenzoic acid modified nanoparticle as a MALDI-TOF MS matrix for soft ionization and structure determination of small molecules with diverse structures.

    PubMed

    Tseng, Mei-Chun; Obena, Rofeamor; Lu, Ying-Wei; Lin, Po-Chiao; Lin, Ping-Yu; Yen, Yung-Sheng; Lin, Jiann-Tsuen; Huang, Li-De; Lu, Kuang-Lieh; Lai, Long-Li; Lin, Chun-Cheng; Chen, Yu-Ju

    2010-11-01

    Efficient structural characterization is important for quality control when developing novel materials. In this study, we demonstrated the soft ionization capability of the hybrid of immobilized silica and 2,5-dihydrobenzoic acid (DHB) on iron oxide magnetic nanoparticles in MALDI-TOF MS with a clean background. The ratio between SiO(2) and DHB was examined and was found to affect the surface immobilization of DHB on the nanoparticle, critically controlling the ionization efficiency and interference background. Compared with commercial DHB, the functionalized nanoparticle-assisted MALDI-TOF MS provided superior soft ionization with production of strong molecular ions within 5 ppm mass accuracy on a variety of new types of synthetic materials used for solar cells, light emitting devices, dendrimers, and glycolipids, including analytes with either thermally labile structures or poor protonation tendencies. In addition, the enhancements of the molecular ion signal also provided high-quality product-ion spectra allowing structural characterization and unambiguous small molecule identification. Using this technique, the structural differences among the isomers were distinguished through their characteristic fragment ions and comprehensive fragmentation patterns. With the advantages of long-term stability and simple sample preparation by deposition on a regular sample plate, the use of DHB-functionalized nanoparticles combined with high-resolution MALDI-TOF MS provides a generic platform for rapid and unambiguous structure determination of small molecules.

  5. Polysialic acid modification of the synaptic cell adhesion molecule SynCAM 1 in human embryonic stem cell-derived oligodendrocyte precursor cells.

    PubMed

    Werneburg, Sebastian; Buettner, Falk F R; Mühlenhoff, Martina; Hildebrandt, Herbert

    2015-05-01

    Oligodendrocyte precursor cells (OPCs) are the progenitors of myelinating oligodendrocytes in brain development and repair. Successful myelination depends on the control of adhesiveness during OPC migration and axon contact formation. The decoration of cell surface proteins with the glycan polysialic acid (polySia) is a key regulatory element of OPC interactions during development and under pathological conditions. By far the major protein carrier of polySia is the neural cell adhesion molecule NCAM, but recently, polysialylation of the synaptic cell adhesion molecule SynCAM 1 has been detected in the developing mouse brain. In mice, polySia-SynCAM 1 is associated with cells expressing NG2, a marker of a heterogeneous precursor cell population, which is the primary source for oligodendrocytes in development and myelin repair but can also give rise to astrocytes and possibly neurons. It is not yet clear if polySia-SynCAM 1 is expressed by OPCs and its occurrence in humans is elusive. By generating uniform human embryonic stem cell-derived OPC cultures, we demonstrate that polySia is present on human OPCs but down-regulated during differentiation into myelin basic protein-positive oligodendrocytes. PolySia on NCAM resides on the isoforms NCAM-180 and NCAM-140, and SynCAM 1 is identified as a novel polySia acceptor in human OPCs.

  6. 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.

  7. 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.

  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. 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.

  10. An electrochemical biosensor based on cobalt nanoparticles synthesized in iron storage protein molecules to determine ascorbic acid.

    PubMed

    Rafipour, Ronak; Kashanian, Soheila; Hashemi, Sadegh; Shahabadi, Nahid; Omidfar, Kobra

    2016-09-01

    The electrochemical detection of ascorbic acid (AA) was investigated using a cobalt(III)-ferritin immobilized on a self-assembled monolayer modified gold electrode in phosphate buffer solution (pH 7.5). The modified electrode showed excellent electrochemical activity for oxidation of AA. The response to AA on the modified electrode was examined using cyclic and differential pulse voltammetry techniques. The resulting biosensor showed a linear response to AA in a concentration range from 6.25×10(-6) to 2.31×10(-5) M with sensitivity of 86,437 μAM(-)(1) and detection limit of 4.65 × 10(-6) M based on a signal-to-noise ratio of 3. Electrochemical parameters including the charge transfer coefficient (α) and the apparent heterogeneous electron transfer rate constant (ks ) for AA were found to be 0.52 and 1.054 Sec(-1) , respectively. It has been shown that, using this modified electrode, AA can be determined with high sensitivity, low detection limit, and high selectivity.

  11. Effects of hypoxanthine substitution in peptide nucleic acids targeting KRAS2 oncogenic mRNA molecules: theory and experiment.

    PubMed

    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

    2013-10-03

    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 multimutant specificity could be achieved with a PNA dodecamer incorporating hypoxanthine, which can form Watson-Crick base pairs 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.

  12. Indole-3-acetic acid in plant-pathogen interactions: a key molecule for in planta bacterial virulence and fitness.

    PubMed

    Cerboneschi, Matteo; Decorosi, Francesca; Biancalani, Carola; Ortenzi, Maria Vittoria; Macconi, Sofia; Giovannetti, Luciana; Viti, Carlo; Campanella, Beatrice; Onor, Massimo; Bramanti, Emilia; Tegli, Stefania

    The plant pathogenic bacterium Pseudomonas savastanoi, the causal agent of olive and oleander knot disease, uses the so-called "indole-3-acetamide pathway" to convert tryptophan to indole-3-acetic acid (IAA) via a two-step pathway catalyzed by enzymes encoded by the genes in the iaaM/iaaH operon. Moreover, pathovar nerii of P. savastanoi is able to conjugate IAA to lysine to generate the less biologically active compound IAA-Lys via the enzyme IAA-lysine synthase encoded by the iaaL gene. Interestingly, iaaL is now known to be widespread in many Pseudomonas syringae pathovars, even in the absence of the iaaM and iaaH genes for IAA biosynthesis. Here, two knockout mutants, ΔiaaL and ΔiaaM, of strain Psn23 of P. savastanoi pv. nerii were produced. Pathogenicity tests using the host plant Nerium oleander showed that ΔiaaL and ΔiaaM were hypervirulent and hypovirulent, respectively and these features appeared to be related to their differential production of free IAA. Using the Phenotype Microarray approach, the chemical sensitivity of these mutants was shown to be comparable to that of wild-type Psn23. The main exception was 8 hydroxyquinoline, a toxic compound that is naturally present in plant exudates and is used as a biocide, which severely impaired the growth of ΔiaaL and ΔiaaM, as well as growth of the non-pathogenic mutant ΔhrpA, which lacks a functional Type Three Secretion System (TTSS). According to bioinformatics analysis of the Psn23 genome, a gene encoding a putative Multidrug and Toxic compound Extrusion (MATE) transporter, was found upstream of iaaL. Similarly to iaaL and iaaM, its expression appeared to be TTSS-dependent. Moreover, auxin-responsive elements were identified for the first time in the modular promoters of both the iaaL gene and the iaaM/iaaH operon of P. savastanoi, suggesting their IAA-inducible transcription. Gene expression analysis of several genes related to TTSS, IAA metabolism and drug resistance confirmed the presence of a

  13. 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.

  14. Enhancement of anti-cancer immunity by a lipoteichoic-acid-related molecule isolated from a penicillin-killed group A Streptococcus.

    PubMed

    Okamoto, M; Ohe, G; Oshikawa, T; Furuichi, S; Nishikawa, H; Tano, T; Ahmed, S U; Yoshida, H; Moriya, Y; Saito, M; Sato, M

    2001-10-01

    We isolated the lipoteichoic-acid-related molecule (OK-PSA) from OK-432, a streptococcal preparation, by affinity chromatography on CNBr-activated Sepharose-4B-bound monoclonal antibody TS-2, which neutralizes the interferon (IFN)-gamma-inducing activity of OK-432. We have previously reported that OK-PSA is a potent inducer of Th1-type cytokines in human peripheral blood mononuclear cells in vitro. In this study, we conducted an animal experiment to examine whether OK-PSA exhibits an anti-tumor effect in vivo by acting as a Th1 inducer in syngeneic Meth-A tumor-bearing BALB/c mice, in which the Th2 response is genetically dominant. It was found that OK-PSA induced Th1-type cytokines [IFN-gamma, tumor necrosis factor-alpha, interleukin (IL)-2, IL-12 and IL-18] in BALB/c mice bearing Meth-A tumor and caused a marked anti-tumor effect. Although it was suggested by an in vitro study. using spleen cells derived from the animals, that IL-18 plays the greatest role in the induction of the Th1-dominant state and tumor cell killing induced by OK-PSA, the in vivo experiments demonstrated that both IL-12 and IL-18 are essential in the anti-tumor effect exhibited by OK-PSA. These findings strongly suggest that OK-PSA is a major effector molecule of OK-432 and may be a useful immunotherapeutic agent, as a potent Th1 inducer, for cancer patients with a Th2-dominant state.

  15. Identification of the single amino acid involved in quenching the ent-kauranyl cation by a water molecule in ent-kaurene synthase of Physcomitrella patens.

    PubMed

    Kawaide, Hiroshi; Hayashi, Ken-ichiro; Kawanabe, Ryo; Sakigi, Yuka; Matsuo, Akihiko; Natsume, Masahiro; Nozaki, Hiroshi

    2011-01-01

    ent-Kaurene is a tetracyclic diterpene hydrocarbon and a biosynthetic intermediate of the plant hormone gibberellins. In flowering plants, ent-kaurene is biosynthesized from geranylgeranyl diphosphate (GGDP) by two distinct cyclases, ent-copalyl diphosphate synthase (CPS) and ent-kaurene synthase (KS). Recently, the moss Physcomitrella patens ent-kaurene biosynthetic gene was cloned and functionally characterized. The bifunctional ent-kaurene synthase [P. patens CPS/KS (PpCPS/KS)] produces both ent-kaurene and 16α-hydroxy-ent-kaurane from GGDP via ent-copalyl diphosphate. Here, we cloned and analyzed the function of a cDNA encoding bifunctional ent-kaurene synthase from the liverwort Jungermannia subulata [J. subulata CPS/KS (JsCPS/KS)]. JsCPS/KS catalyzes the cyclization reaction of GGDP to produce ent-kaurene but not 16α-hydroxy-ent-kaurane, even though the PpCPS/KS (881 amino acids) and JsCPS/KS (886 amino acids) sequences share 60% identity. To determine the regions and amino acids involved in 16α-hydroxy-ent-kaurane formation, we analyzed the enzymic functions of JsCPS/KS and PpCPS/KS chimeric proteins. When the C-terminal region of PpCPS/KS was exchanged with the JsCPS/KS C-terminal region, the chimeric cyclases produced only ent-kaurene. The replacement of PpCPS/KS Ala710 with Met or Phe produced a JsCPS/KS-type cyclase that converted GGDP to ent-kaurene as the sole product. In contrast, replacing Ala710 with Gly, Cys or Ser did not affect the PpCPS/KS product profile as much as replacement of Cys of JsCPS/KS by Ala. Thus, the hydrophobicity and size of the side chain residue at the PpCPS/KS amino acid 710 is responsible for quenching the ent-kauranyl cation by the addition of a water molecule.

  16. 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…

  17. Periodic DFT study of acidic trace atmospheric gas molecule adsorption on Ca- and Fe-doped MgO(001) surface basic sites.

    PubMed

    Baltrusaitis, Jonas; Hatch, Courtney; Orlando, Roberto

    2012-08-02

    The electronic properties of undoped and Ca- or Fe-doped MgO(001) surfaces, as well as their propensity toward atmospheric acidic gas (CO2, SO2, and NO2) uptake was investigated with an emphasis on gas adsorption on the basic MgO oxygen surface sites, O(surf), using periodic density functional theory (DFT) calculations. Adsorption energy calculations show that MgO doping will provide stronger interactions of the adsorbate with the O(surf) sites than the undoped MgO for a given adsorbate molecule. Charge transfer from the iron atom in Fe-doped MgO(001) to NO2 was shown to increase the binding interaction between adsorbate by an order of magnitude, when compared to that of undoped and Ca-doped MgO(001) surfaces. Secondary binding interactions of adsorbate oxygen atoms were observed with surface magnesium sites at distances close to those of the Mg-O bond within the crystal. These interactions may serve as a preliminary step for adsorption and facilitate further adsorbate transformations into other binding configurations. Impacts on global atmospheric chemistry are discussed as these adsorption phenomena can affect atmospheric gas budgets via altered partitioning and retention on mineral aerosol surfaces.

  18. 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.

  19. Quality and Quantity of Extracted Deoxyribonucleic Acid (DNA) from Preserved Soft Tissues of Putrefied Unidentifiable Human Corpse

    PubMed Central

    Pooniya, Shashank; Lalwani, Sanjeev; Raina, Anupuma; Millo, Tabin; Dogra, Tirath Das

    2014-01-01

    Context: The appropriate collection and preservation of soft tissues from putrefied unidentifiable human corpse for the purpose of identification using DNA profiling technique is critically important especially in developing countries like India having different levels of health-care set ups with largely varying facilities and varying climatic conditions. Aims: The present study was carried out, mainly focusing on quality and quantity of extracted DNA from the soft tissues of putrefied unidentifiable human corpse stored upto 4 weeks at 4°C and at −80°C for DNA analysis. Materials and Methods: The present study was conducted on 16 different putrefied unidentifiable human corpses after getting approval from institutional ethical committee. Around 2 g of four different tissues (brain, kidney, heart and muscle) were collected and preserved for one month followed by DNA extraction using the organic method, the quality and quantity of high molecular weight-DNA was estimated using the spectrophotometer and gel electrophoresis. Further, the amplification polymerase chain reaction (PCR) was also performed (AmpFLSTR® Indentifiler™ PCR Amplification kit for multiple loci, of Applied Biosystems, Lab India) and was checked using continuous PAGE. Results: The yield of DNA was significantly higher at −80°C for all the four tissues collected and was best for brain followed by heart, kidney and worst for muscles in all cases. Conclusions: It is suggested that the brain tissue preserved at −80°C is the best among soft issues for DNA extraction. Refrigeration or deep freezing facility should be available at all the centers. PMID:24696558

  20. In vitro stimulation of stage-specific deoxyribonucleic acid synthesis in rat seminiferous tubule segments by interleukin-1. alpha

    SciTech Connect

    Parvinen, M.; Soeder, O.M.; Mali, P.; Froeysa, B.R.; Ritzen, E.M. )

    1991-09-01

    Levels of rat testicular interleukin-1-like factor (tIL-1) have been shown to correlate with DNA synthetic activity during the cycle of the rat seminiferous epithelium, suggesting its role as a spermatogonial or meiotic growth factor. To explore this further, a new in vitro model system was developed. Rat seminiferous tubule segments from stages I, V, VIIa, and VIII-IX of the cycle were isolated by transillumination-assisted microdissection, cultured in chemically defined serum-free medium supplemented with human recombinant IL-1 {alpha}, and labeled with (3H)thymidine. During incubation, spontaneous progression of spermatogenesis was noted. Inactive stage VIIa tubule segments differentiated to stage VIII and initiated DNA synthesis, and concomitantly started to secrete IL-1-like factor. DNA synthesis of stages VIII-IX ceased through differentiation of spermatocytes to leptotene-zygotene (stages XII-XIII of the cycle). IL-1 {alpha} stimulated DNA synthesis significantly in spermatogonia of stage I. Meiotic DNA synthesis at stage VIIa was stimulated (48 h/34 C) and maintained at stages VIII-IX (48 h/34 C). IL-1 {alpha} seems to act as a regulator of spermatogenic DNA synthesis in both mitotic and meiotic phases. It has mainly stimulating and maintaining effects, but it may also be inhibitory under certain conditions.

  1. Characterization of total deoxyribonucleic acid of Mycobacterium paratuberculosis (ATCC 19698) and of M. avium complex (ATCC 25291) using restriction enzymes.

    PubMed

    Labidi, A

    1988-01-01

    Total DNA was extracted from M. paratuberculosis (ATCC 19698) and from M. avium complex (ATCC 25291) cultivated on RVB-10 enriched liquid media. Restriction endonuclease analysis was conducted of Total DNA using 34 enzymes and DNA digestion profiles were compared. Fifteen enzymes revealed important differences between the two species. Two pairs of enzymes (EcoRII, BstNI) and (MboI, Sau3AI) provide evidence for the presence of dcmI and dam methylation in DNA of M. avium complex and M. paratuberculosis. The differences in DNA fragments of these two species could be of potential value in differentiating these clinically significant mycobacteria.

  2. Chemical modification of deoxyribonucleic acids: Quantitation of 3-methylthymidine and O4-methylthymidine by tandem mass spectrometry

    NASA Astrophysics Data System (ADS)

    Wood, Joe M.; Hoke, Steven H., II; Graham Cooks, R.; Chae, Whi-Gun; Chang, Ching-Jer

    1991-12-01

    Quantitation of 3-methylthymidine and O4-methylthymidine generated in the reaction of calf thymus DNA with methyl methanesulfonate (MeMS) and 1-methyl-1nitrosourea (MeNU) by mass spectrometry is reported. Quantitative precision of 7% or better is achieved on samples of 10-12 -10-13 mole in the HPLC and a final stage of separation before quantification by tandem mass spectrometry using desorption chemical ionization. Synthetic CD3-labeled nucleosides were used as internal standards for mass spectral quantification. A unique mass spectrometric scanning procedure, which allowed simultaneous MS--MS product ion analysis of both the analyte and the internal standard, was utilized to enchance precision and accuracy in these low level determinations. MeNU (a potent carcinogen) resulted in 18&%; 3-methylation and 0.17% O4-methylation of deoxythymidine whereas MeMS (a weak carcinogen) produced only 6.8% 3-methylation and 0.005% of deoxythymidine. These results demonstrate that the sensitivity and accuracy of this method should be adequate for the detection and quantification of methyl-nucleosides at the sub-picomole level at which mutation is induced in cell cultures.

  3. The Induction of Phenylalanine Ammonia Lyase and Phaseollin by 9-Aminoacridine and Other Deoxyribonucleic Acid Intercalating Compounds 1

    PubMed Central

    Hess, Samuel L.; Hadwiger, Lee A.

    1971-01-01

    Bean pod tissue (Phaseolus vulgaris L. var. Top Crop) is induced to produce phaseollin when challenged with various microorganisms. The pods react in the same manner when challenged with 9-aminoacridine. This compound also caused an increase in concentrations of phenylalanine ammonia lyase, an enzyme of the phaseollin synthesizing pathway. Both the synthesis of phenylalanine ammonia lyase and phaseollin are subject to inhibition by actinomycin D, cycloheximide, or 6-methylpurine. The results suggest that both phaseollin production and increased phenylalanine ammonia lyase, when induced by 9-aminoacridine, require newly synthesized RNA and protein. The concentration of 9-aminoacridine optimal for synthesis of phaseollin and PAL (0.5 mg/ml) does not increase the rate of total protein synthesis. However, there is a differential effect of 9-aminoacridine on synthesis of certain protein fractions. Optimal concentrations of 9-aminoacridine induce phaseollin and phenylalanine ammonia lyase synthesis while reducing the net synthesis of RNA during the period of induction. The planar three-ring structure of 9-aminoacridine appears to be a desirable feature for phaseollin and phenylalanine ammonia lyase induction. Similar compounds, all DNA intercalators, having dimethylamino, diethylamino, amino, or 9-alkylamino substitutions of a three-ring acridine skeleton, are also inducers of phenylalanine ammonia lyase and phaseollin synthesis. It is suggested that 9-aminoacridine and other DNA intercalators function as inducers of phaseollin and phenylalanine ammonia lyase synthesis by reacting with the DNA template. PMID:16657762

  4. Developing an electrochemical deoxyribonucleic acid (DNA) biosensor on the basis of human interleukine-2 gene using an electroactive label.

    PubMed

    Pournaghi-Azar, M H; Hejazi, M S; Alipour, E

    2006-06-16

    Development of an electrochemical DNA biosensor based on a human interleukine-2 (IL-2) gene probe, using a pencil graphite electrode (PGE) as transducer and methylene blue (MB) as electroactive label is described. The sensor relies on the immobilization of a 20-mer single stranded oligonucleotide probe (hIL-2) related to the IL-2 gene on the electrode. The hybridization between the probe and its complementary sequence (chIL-2) as the target was studied by square wave voltammetry (SWV) of MB accumulated on the PGE. In this approach the extent of hybridization is evaluated on the basis of the difference between SWV signals of MB accumulated on the probe-PGE and MB accumulated on the probe-target-PGE. Some hybridization experiments with non-complementary oligonucleotides were carried out to assess whether the suggested DNA sensor responds selectively to the target. Some experimental variables affecting the performance of the biosensor including: polishing of PGE, its electrochemical activation conditions (i.e., activation potential and activation time) and probe immobilization conditions on the electrodes (i.e., immobilization potential and time) were investigated and the optimum values of 1.80 V and 300 s for PGE activation, and -0.5 V and 400s for the probe immobilization on the electrode were suggested.

  5. 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.

  6. Screening of Israeli Holstein-Friesian cattle for restriction fragment length polymorphisms using homologous and heterologous deoxyribonucleic acid probes.

    PubMed

    Hallerman, E M; Nave, A; Soller, M; Beckmann, J S

    1988-12-01

    Genomic DNA of Israeli Holstein-Friesian dairy cattle were screened with a battery of 17 cloned or subcloned DNA probes in an attempt to document restriction fragment length polymorphisms at a number of genetic loci. Restriction fragment length polymorphisms were observed at the chymosin, oxytocin-neurophysin I, lutropin beta, keratin III, keratin VI, keratin VII, prolactin, and dihydrofolate reductase loci. Use of certain genomic DNA fragments as probes produced hybridization patterns indicative of satellite DNA at the respective loci. Means for distinguishing hybridizations to coding sequences for unique genes from those to satellite DNA were developed. Results of this study are discussed in terms of strategy for the systematic development of large numbers of bovine genomic polymorphisms.

  7. Psoralen-deoxyribonucleic acid photoreaction. Characterization of the monoaddition products from 8-methoxypsoralen and 4,5',8-trimethylpsoralen

    SciTech Connect

    Kanne, D.; Straub, K.; Rapoport, H.; Hearst, J.E.

    1982-01-01

    The isolation and structural characterization are described of the major monoaddition products formed in the photoreaction of two naturally occurring psoralens, 8-methoxypsoralen and 4,5',8-trimethylpsoralen, with high molecular weight, double-stranded DNA. Hydrolysis of the psoralen-modified DNA and subsequent chromatography resulted in the isolation of four modified nucleosides from each psoralen. Structural characterization was accomplished by mass spectrometry and /sup 1/H NMR analysis. The major products, accounting for 44 to 52% of the covalently bound psoralen, are two diastereomeric thymidine adducts formed by cycloaddition between the 5,6 double bond of the pyrimidine and the 4',5' (furan) double bond of the psoralen. All of the isolated adducts have cis-syn stereochemistry. The stereochemistry and product distribution of the adducts are determined in part by the constraints imposed by the DNA helix on the geometry of the noncovalent intercalation complex formed by psoralen and DNA prior to irradiation.

  8. Bio Organic-Semiconductor Field-Effect Transistor (BioFET) Based on Deoxyribonucleic Acid (DNA) Gate Dielectric

    DTIC Science & Technology

    2010-03-31

    floating gate devices and metal-insulator-oxide-semiconductor (MIOS) devices. First attempts to use polarizable gate insulators in combination with...organic semiconductors. The field effect transistors showed floating gate effects, but the potential for organic memories was not realized. Recently...

  9. 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.

  10. Free-radical-induced formation of an 8,5'-cyclo-2'-deoxyguanosine moiety in deoxyribonucleic acid.

    PubMed Central

    Dizdaroglu, M

    1986-01-01

    Isolation and identification of a novel .OH-induced product, namely an 8,5'-cyclo-2'-deoxyguanosine moiety, in DNA and 2'-deoxyguanosine are described. .OH radicals were generated in dilute aqueous solutions by gamma-irradiation. Analyses of 2'-deoxyguanosine and enzymic hydrolysates of DNA by gas chromatography-mass spectrometry (g.c.-m.s.) after trimethylsilylation showed the presence of 8,5-cyclo-2'-deoxyguanosine on the basis of its fragment ions. This product was isolated by h.p.l.c. Its u.v. and n.m.r. spectra taken were in agreement with the structure suggested by its mass spectrum. Exact masses of the typical ions from the mass spectrum of the trimethylsilyl derivative of this product were measured by high-resolution m.s. The values found were in excellent agreement with the theoretical mass derived from the suggested fragmentation patterns. Both (5'R)- and (5'S)-epimers of 8,5'-cyclo-2'-deoxyguanosine were observed. These two diastereomers were separated from each other by g.c. as well as by h.p.l.c. The assignment of the epimers was accomplished on the basis of the n.m.r. data. The formation of 8,5'-cyclo-2'-deoxyguanosine was suppressed by the presence of O2 in the solutions. The use of g.c.-m.s. with the selected-ion monitoring technique facilitated the detection of 8,5'-cyclo-2'-deoxyguanosine in DNA at radiation doses as low as 1 Gy. Its mechanism of formation probably involves hydrogen atom abstraction by .OH radicals from the C-5' of the 2'-deoxyguanosine moiety followed by intramolecular cyclization with the formation of a covalent bond between the C-5' and C-8 and subsequent oxidation of the resulting N-7-centred radical. PMID:3800936

  11. 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.

  12. Deoxyribonucleic acid (DNA) methyltransferase contributes to p16 promoter CpG island methylation in lung adenocarcinoma with smoking.

    PubMed

    Sun, Rongju; Liu, Jiahong; Wang, Bo; Ma, Lingyun; Quan, Xiaojiao; Chu, Zhixiang; Li, Tanshi

    2015-01-01

    In this study, the relationship between CpG island methylation and smoking and DNA methyltransferase in the occurrence and development of lung adenocarcinoma was explored by detecting p16 promoter methylation status. Protein and mRNA levels of p16 were detected by immunohistochemistry and in situ hybridization assays. p16 gene promoter and exon 1 CpG island locus Hap II sites methylation status was analyzed with the methylation-specific PCR. Only 4 of 40 p16-positive cases were detected to methylate on CpG islands with 10% methylating rate whereas 18 of p16-negative cases were methylated up to 36.73% of methylating rate. The methylating rates of both p16-positive and p16-negative groups were significantly different. 17 of 50 cases with smoking from total 89 lung adenocarcinoma cases were detected to methylate on CpG islands while only 5 of the remaining 39 non-smokers to methylate. The difference of the methylating rates in both smokers and non-smokers was significant to suggest the closely association of CpG island methylation of p16 with smoking. Furthermore, p16 promoter CpG islands were detected to methylate in 15 of 35 cases with higher DNA methyltransferase activity whereas only 7 detected to methylate in the remaining 54 cases with lower DNA methyltransferase activity. p16 promoter CpG island methylation likely made p16 expressing silence thus contributed to the tumorigenesis of lung adenocarcinoma. Smoking is likely to promote p16 CpG island methylation or by its effect of the activity and metabolism of DNA methyltransferase 1 (DNMT) on CpG island methylation status.

  13. Adrenocortical nuclear progesterone-binding protein: Identification by photoaffinity labeling and evidence for deoxyribonucleic acid binding and stimulation by adrenocorticotropin

    SciTech Connect

    Demura, T.; Driscoll, W.J.; Lee, Y.C.; Strott, C.A. )

    1991-01-01

    Nuclei of the guinea pig adrenal cortex contain a protein that specifically binds progesterone and that, biochemically, is clearly distinct from the classical progesterone receptor. The adrenocortical nuclear progesterone-binding protein has now been purified more than 2000-fold by steroid-affinity chromatography with a 75% yield. The purified protein preparation demonstrated three major bands on sodium dodecyl sulfate-polyacrylamide gel of 79K, 74K, and 50K. To determine which of the three might represent the progesterone-binding protein, steroid photoaffinity labeling was performed which resulted in the specific and exclusive labeling of a 50K band. Thus, the adrenocortical nuclear progesterone-binding protein appears to be distinct from the classical progesterone receptor not only biochemically, but also on the basis of molecular size. To test whether the adrenocortical nuclear progesterone-binding protein can be hormonally stimulated, guinea pigs were treated with ACTH. The chronic administration of ACTH caused a 4- to 6-fold increase in the specific progesterone binding capacity without a change in the binding affinity. There appeared to be no significant difference in nuclear progesterone binding between the zona fasciculata and zona reticularis. This finding suggests a mediating role for the progesterone-binding protein in ACTH action. In addition, the nuclear progesterone-binding protein bound to nonspecific DNA sequences, further suggesting a possible transcriptional regulatory role.

  14. 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

  15. Isolation and Properties of Deoxyribonucleic Acid from Protoplasts of Cell Suspension Cultures of Ammi visnaga and Carrot (Daucus carota) 1

    PubMed Central

    Ohyama, K.; Gamborg, O. L.; Miller, R. A.

    1972-01-01

    A procedure is described for the isolation of native DNA from protoplasts of ammi (Ammi visnaga) and carrot (Daucus carota) cells. Protoplasts were produced from 40 grams of fresh cells by enzyme hydrolysis and lysed with sodium dodecyl sulfate. The DNA was purified by treatment with pronase and ribonuclease. Final isolation was achieved by sucrose density gradient centrifugation. The melting temperature of ammi and carrot DNA in 0.15 m NaCl and 15 mm trisodium citrate buffer, pH 7.0, was 84.0 C and 84.5 C, respectively. The molecular weight for ammi DNA was 1.43 × 108, and for carrot DNA it was 1.56 × 108. Ammi DNA exhibited a single band at 1.690 grams per cubic centimeter in CsCl, whereas carrot DNA showed two bands, one at 1.693 grams per cubic centimeter and another at 1.706 grams per cubic centimeter. Ammi DNA consisted of a doublestranded form, since denaturation of the DNA caused a complete upward shift of 0.020 grams per cubic centimeter. PMID:16658166

  16. Deoxyribonucleic acid damage-associated biomarkers of ionising radiation: current status and future relevance for radiology and radiotherapy

    PubMed Central

    Rothkamm, K

    2013-01-01

    Diagnostic and therapeutic radiation technology has developed dramatically in recent years, and its use has increased significantly, bringing clinical benefit. The use of diagnostic radiology has become widespread in modern society, particularly in paediatrics where the clinical benefit needs to be balanced with the risk of leukaemia and brain cancer increasing after exposure to low doses of radiation. With improving long-term survival rates of radiotherapy patients and the ever-increasing use of diagnostic and interventional radiology procedures, concern has risen over the long-term risks and side effects from such treatments. Biomarker development in radiology and radiotherapy has progressed significantly in recent years to investigate the effects of such use and optimise treatment. Recent biomarker development has focused on improving the limitations of established techniques by the use of automation, increasing sensitivity and developing novel biomarkers capable of quicker results. The effect of low-dose exposure (0–100 mGy) used in radiology, which is increasingly linked to cancer incidences, is being investigated, as some recent research challenges the linear-no-threshold model. Radiotherapy biomarkers are focused on identifying radiosensitive patients, determining the treatment-associated risk and allowing for a tailored and more successful treatment of cancer patients. For biomarkers in any of these areas to be successfully developed, stringent criteria must be applied in techniques and analysis of data to reduce variation among reports and allow data sets to be accurately compared. Newly developed biomarkers can then be used in combination with the established techniques to better understand and quantify the individual biological response to exposures associated with radiology tests and to personalise treatment plans for patients. PMID:23659923

  17. Molecular aspect on the interaction of zinc-ofloxacin complex with deoxyribonucleic acid, proposed model for binding and cytotoxicity evaluation

    PubMed Central

    Ahmadi, F.; Ebrahimi-Dishabi, N.; Mansouri, K.; Salimi, F.

    2014-01-01

    Recently, several studies have shown that the metal-fluoroquinolone complexes have more antibacterial and cytotoxic effects in comparison with free fluoroquinolones. These results may introduce new drugs for chemotherapy with fewer side effects. In this work a bidentated zinc (II) complex with ofloxacin (OZC) was synthesized and cytotoxicity activities and DNA binding of the resulted complex was studied. The in-vitro anti proliferative and cytotoxic effects of the free ofloxacin (OFL) and OZC against MCF-7, CaCo2 and SKNMC cell lines were tested by using Trypan blue and lactate dehyrogenase (LDH) assay methods. Results revealed that the OZC exhibits better anti proliferative and cytotoxic activities as compared with the OFL. This may be due to the more interaction of OZC with DNA. Therefore, the interaction of OZC with DNA was investigated by using voltammetry, UV-Vis, fluorescence, FT-IR and circular dichroism spectroscopy methods, and the equilibrium binding constant (Kb), binding site size, and thermodynamic parameters were measured. The results revealed that the OZC interacts with DNA via two modes: electrostatic and outside hydrogen binding. The proposed DNA binding modes may support the greater in-vitro cytotoxicity of OZC compared to OFL alone. PMID:25657809

  18. 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)

  19. 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.

  20. 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)

  1. 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.

  2. Maternal serum uric acid concentration is associated with the expression of tumour necrosis factor-α and intercellular adhesion molecule-1 in patients with preeclampsia.

    PubMed

    Zhao, J; Zheng, D-Y; Yang, J-M; Wang, M; Zhang, X-T; Sun, L; Yun, X-G

    2016-07-01

    We aimed to investigate whether there is a correlation between elevated serum uric acid (SUA) concentration and endothelial inflammatory response in women with preeclampsia (PE). On the basis of clinical and laboratory findings, patients were assigned to three groups: normal blood pressure (Control (Con)), gestational hypertension (GH) and PE (n=50 in each group). SUA concentration was measured by spectrophotometry, and serum tumour necrosis factor-α (TNF-α) and intercellular adhesion molecule-1 (ICAM-1) levels were measured by enzyme-linked immunosorbent assay. Western blotting and immunohistochemical staining were also used to detect the changes in TNF-α and ICAM-1 expression in subcutaneous fat tissue. PE patients showed significantly higher systolic and diastolic blood pressures compared with Con and GH pregnant women (P=0.02 and P=0.02, respectively). The changes of body mass index (ΔBMI) before and after pregnancy and 24-h urine protein were significantly different among the three groups (P<0.001). Maternal SUA, TNF-α and soluble ICAM-1 (sICAM-1) levels were significantly increased in the patients with PE (P<0.05) compared with the other two groups. Scatterplot analysis revealed that elevated SUA concentration positively correlated with TNF-α and sICAM-1 in pregnant women. Moreover, vessels in subcutaneous fat tissues of preeclamptic patients showed intense TNF-α and ICAM-1 staining compared with Con and GH patients. The results support that, to a certain extent, elevated SUA concentration is significantly associated with inflammation of maternal systemic vasculature as indicated by increased TNF-α and ICAM-1 expression in women with PE.

  3. 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

  4. Quick chip assay using locked nucleic acid modified epithelial cell adhesion molecule and nucleolin aptamers for the capture of circulating tumor cells

    PubMed Central

    Maremanda, Nihal G.; Roy, Kislay; Kanwar, Rupinder K.; Shyamsundar, Vidyarani; Ramshankar, Vijayalakshmi; Krishnamurthy, Arvind; Krishnakumar, Subramanian; Kanwar, Jagat R.

    2015-01-01

    The role of circulating tumor cells (CTCs) in disease diagnosis, prognosis, monitoring of the therapeutic efficacy, and clinical decision making is immense and has attracted tremendous focus in the last decade. We designed and fabricated simple, flat channel microfluidic devices polydimethylsiloxane (PDMS based) functionalized with locked nucleic acid (LNA) modified aptamers (targeting epithelial cell adhesion molecule (EpCAM) and nucleolin expression) for quick and efficient capture of CTCs and cancer cells. With optimized flow rates (10 μl/min), it was revealed that the aptamer modified devices offered reusability for up to six times while retaining optimal capture efficiency (>90%) and specificity. High capture sensitivity (92%) and specificity (100%) was observed in whole blood samples spiked with Caco-2 cells (10–100 cells/ml). Analysis of blood samples obtained from 25 head and neck cancer patients on the EpCAM LNA aptamer functionalized chip revealed that an average count of 5 ± 3 CTCs/ml of blood were captured from 22/25 samples (88%). EpCAM intracellular domain (EpICD) immunohistochemistry on 9 oral squamous cell carcinomas showed the EpICD positivity in the tumor cells, confirming the EpCAM expression in CTCs from head and neck cancers. These microfluidic devices also maintained viability for in vitro culture and characterization. Use of LNA modified aptamers provided added benefits in terms of cost effectiveness due to increased reusability and sustainability of the devices. Our results present a robust, quick, and efficient CTC capture platform with the use of simple PDMS based devices that are easy to fabricate at low cost and have an immense potential in cancer diagnosis, prognosis, and therapeutic planning. PMID:26487896

  5. 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

  6. 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

  7. 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

  8. Azelaic acid.

    PubMed

    Nazzaro-Porro, M

    1987-12-01

    This review is an update on the literature accumulated over the past 10 years following the original observation that azelaic acid, a naturally occurring and nontoxic C9 dicarboxylic acid, possesses significant biologic properties and a potential as a therapeutic agent. These studies have shown that azelaic acid is a reversible inhibitor of tyrosinase and other oxidoreductases in vitro and that it inhibits mitochondrial respiration. It can also inhibit anaerobic glycolysis. Both in vitro and in vivo it has an antimicrobial effect on both aerobic and anaerobic (Propionibacterium acnes) microorganisms. In tissue culture it exerts a dose- and time-dependent cytotoxic effect on malignant melanocytes, associated with mitochondrial damage and inhibition of deoxyribonucleic acid (DNA) synthesis. Tumoral cell lines not containing tyrosinase are equally affected. Normal cells in culture exposed to the same concentrations of the diacid that are toxic for tumoral cells are in general not damaged. Radioactive azelaic acid has been shown to penetrate tumoral cells at a higher level than normal cells of the corresponding line. Topically applied (a 20% cream), it has been shown to be of therapeutic value in skin disorders of different etiologies. Its beneficial effect on various forms of acne (comedogenic, papulopustular, nodulocystic) has been clearly demonstrated. Particularly important is its action on abnormal melanocytes, which has led to the possibility of obtaining good results on melasma and highly durable therapeutic responses on lentigo maligna. It is also capable of causing regression of cutaneous malignant melanoma, but its role in melanoma therapy remains to be investigated.(ABSTRACT TRUNCATED AT 250 WORDS)

  9. 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.

  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. Mind Molecules

    PubMed Central

    Snyder, Solomon H.

    2011-01-01

    Scientific styles vary tremendously. For me, research is largely about the unfettered pursuit of novel ideas and experiments that can test multiple ideas in a day, not a year, an approach that I learned from my mentor Julius “Julie” Axelrod. This focus on creative conceptualizations has been my métier since working in the summers during medical school at the National Institutes of Health, during my two years in the Axelrod laboratory, and throughout my forty-five years at Johns Hopkins University School of Medicine. Equally important has been the “high” that emerges from brainstorming with my students. Nothing can compare with the eureka moments when, together, we sense new insights and, better yet, when high-risk, high-payoff experiments succeed. Although I have studied many different questions over the years, a common theme emerges: simple biochemical approaches to understanding molecular messengers, usually small molecules. Equally important has been identifying, purifying, and cloning the messengers' relevant biosynthetic, degradative, or target proteins, at all times seeking potential therapeutic relevance in the form of drugs. In the interests of brevity, this Reflections article is highly selective, and, with a few exceptions, literature citations are only of findings of our laboratory that illustrate notable themes. PMID:21543333

  12. 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.

  13. The use of multiple probe molecules for the study of the acid-base properties of aluminium hydroxyfluoride having the hexagonal tungsten bronze structure: FTIR and [36Cl] radiotracer studies.

    PubMed

    Dambournet, Damien; Leclerc, Hervé; Vimont, Alexandre; Lavalley, Jean-Claude; Nickkho-Amiry, Mahmood; Daturi, Marco; Winfield, John M

    2009-03-07

    The combination of several probe molecules has enabled the construction of a detailed picture of the surface of aluminium hydroxyl fluoride, AlF(2.6)(OH)(0.4), which has the hexagonal tungsten bronze (HTB) structure. Using pyridine as a probe leads to features at 1628 cm(-1), ascribed to very strong Lewis acid sites, and at 1620-1623 cm(-1), which is the result of several different types of Lewis sites. This heterogeneity is indicated also from CO adsorption at 100 K; the presence of five different types of Lewis site is deduced and is suggested to arise from the hydroxylated environment. Brønsted acid sites of medium strength are indicated by adsorption of lutidine and CO. Adsorption of lutidine occurs at OH groups, which are exposed at the surface and CO reveals that these OH groups have a single environment that can be correlated with their specific location inside the bulk, assuming that the surface OH group may reflect the bulk OH periodicity. A correlation between the data obtained from CO and pyridine molecules has been established using co-adsorption experiments, which also highlight the inductive effect produced by pyridine. Adsorption of the strong Brønsted acid, anhydrous hydrogen chloride, detected by monitoring the beta(-) emission of [(36)Cl]-HCl at the surface, indicates that surface hydroxyl groups can behave also as a Brønsted base and that H(2)O-HCl interactions, either within the hexagonal channels or at the surface are possible. Finally, the formation of strongly bound H(36)Cl as a result of the room temperature dehydrochlorination of [(36)Cl]-labelled tert-butyl chloride provides additional evidence that HTB-AlF(2.6)(OH)(0.4) can behave as a Lewis acid.

  14. 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.

  15. 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.

  16. Hydrothermal crystal growth and Vernier structures of the metal benzenedicarboxylates MIL-47 and MIL-53 containing guest molecules of benzenecarboxylic acid

    SciTech Connect

    Wang, Xiqu; Jacobson, Allan J.

    2016-04-15

    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 H{sub 2}bdc molecules that have been reported to be disordered, except for [In(OH)bdc](H{sub 2}bdc){sub 3/4}, 1, which has a inorganic-organic hybrid Vernier structure with the H{sub 2}bdc 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)](H{sub 2}bdc){sub 5/7}, 2, MIL-53Al, [Al(OH)(bdc)](H{sub 2}bdc){sub 11/16}, 3, and MIL-53Ga, [Ga(OH)(bdc)](H{sub 2}bdc){sub 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 P2{sub 1}, a=23.903(2), b=17.191(2), c=25.722(2) Å, β=105.914(8)°; 3, P2{sub 1}/n, a=105.224(4), b=12.2441(5), c=17.0143(6) Å, β=89.99(1)°; 4, P2{sub 1}, a=114.562(5), b=12.1503(5), c=17.4275(7) Å, β=89.99(1)°. The number of guest H{sub 2}bdc 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. - Graphical abstract: The sinusoidal modulation along the channel axis direction involving all atoms in the structure of [Al(OH)(bdc)](H{sub 2}bdc){sub 11/16}. - Highlights: • Crystal growth of MIL-47, MIL-53Al, and MIL-53Ga. • The Vernier structures have corner-sharing MO6 octrahedral chains and chains of H2BDC molecules. • The stoichiometry is determined by the ratio of the host framework to the guest H2BDC column lengths. • A correlation is established between the stoichiometry and the radius of the metal ion

  17. The nucleotide sequence of cysteine transfer ribonucleic acid from baker's yeast. Identification of the products from partial degradation of the molecule and derivation of the complete sequence.

    PubMed Central

    Holness, N J; Atfield, G

    1976-01-01

    1. A series of large oligonucleotide fragments derived from tRNA Cys, were separated chromatographically and the sequence of each was deduced by examination of the products of digestion with pancreatic and T1 ribonucleases. 2. The location of the specific cleavage points in the nucleotide chain was similar to that produced by brief treatment with pancreatic ribonuclease. 3. The fragments could be arranged into two alternative sequences. The correct sequence was deduced by the sequential removal and identification of the first nine nucleotides from the 3'-end of the terminal half of the molecules. PMID:819006

  18. Structural requirements for charged lipid molecules to directly increase or suppress K+ channel activity in smooth muscle cells. Effects of fatty acids, lysophosphatidate, acyl coenzyme A and sphingosine

    PubMed Central

    1994-01-01

    We determined the structural features necessary for fatty acids to exert their action on K+ channels of gastric smooth muscle cells. Examination of the effects of a variety of synthetic and naturally occurring lipid compounds on K+ channel activity in cell-attached and excised membrane patches revealed that negatively charged analogs of medium to long chain fatty acids (but not short chain analogs) as well as certain other negatively charged lipids activate the channels. In contrast, positively charged, medium to long chain analogs suppress activity, and neutral analogs are without effect. The key requirements for effective compounds seem to be a sufficiently hydrophobic domain and the presence of a charged group. Furthermore, those negatively charged compounds unable to "flip" across the bilayer are effective only when applied at the cytosolic surface of the membrane, suggesting that the site of fatty acid action is also located there. Finally, because some of the effective compounds, for example, the fatty acids themselves, lysophosphatidate, acyl Coenzyme A, and sphingosine, are naturally occurring substances and can be liberated by agonist- activated or metabolic enzymes, they may act as second messengers targeting ion channels. PMID:8195783

  19. Human Serum Albumin and HER2-Binding Affibody Fusion Proteins for Targeted Delivery of Fatty Acid-Modified Molecules and Therapy.

    PubMed

    Dong, Daoyuan; Xia, Guanjun; Li, Zhijun; Li, Zhiyu

    2016-10-03

    Human epidermal growth factor receptor 2 (HER2) is a well-studied therapeutic target as well as a biomarker of breast cancer. HER2-targeting affibody (ZHER2:342) is a novel small scaffold protein with an extreme high affinity against HER2 screened by phage display. However, the small molecular weight of ZHER2:342 has limited its pharmaceutical application. Human serum albumin (HSA) and ZHER2:342 fusion protein may not only extend the serum half-life of ZHER2:342 but also preserve the biological function of HSA to bind and transport fatty acids, which can be used to deliver fatty acid-modified therapeutics to HER2-positive cancer cells. Two HSA and ZHER2:342 fusion proteins, one with a single ZHER2:342 domain fused to the C terminus of HSA (rHSA-ZHER2) and another with two tandem copies of ZHER2:342 fused to the C terminus of HSA (rHSA-(ZHER2)2), have been constructed, expressed, and purified. Both fusion proteins possessed the HER2 and fatty acid (FA) binding abilities demonstrated by in vitro assays. Interestingly, rHSA-(ZHER2)2, not rHSA-ZHER2, was able to inhibit the proliferation of SK-BR-3 cells at a relatively low concentration, and the increase of HER2 and ERK1/2 phosphorylation followed by rHSA-(ZHER2)2 treatment has been observed. HSA fusion proteins are easy and economical to express, purify, and formulate. As expected, HSA fusion proteins and fusion protein-bound fatty acid-modified FITC could be efficiently taken up by cells. These results proved the feasibility of using HSA fusion proteins as therapeutic agents as well as carriers for targeted drug delivery.

  20. Effect of parenteral nutrition supplemented with short-chain fatty acids on adaptation to massive small bowel resection.

    PubMed

    Koruda, M J; Rolandelli, R H; Settle, R G; Zimmaro, D M; Rombeau, J L

    1988-09-01

    After massive small bowel resection, total parenteral nutrition (TPN) is prescribed to maintain nutritional status. However, TPN reduces the mass of the remaining intestinal mucosa, whereas adaptation to small bowel resection is associated with increased mucosal mass. Short-chain fatty acids (SCFAs) have been shown to stimulate mucosal cell mitotic activity. This study determined whether the addition of SCFAs to TPN following small bowel resection would prevent intestinal mucosal atrophy produced by TPN. Adult rats underwent an 80% small bowel resection and then received either standard TPN or TPN supplemented with SCFAs (sodium acetate, propionate, and butyrate). After 1 wk, jejunal and ileal mucosal weights, deoxyribonucleic acid, ribonucleic acid, and protein contents were measured and compared with the parameters obtained at the time of resection. Animals receiving TPN showed significant loss of jejunal mucosal weight, deoxyribonucleic acid, ribonucleic acid, and protein and ileal mucosal weight and deoxyribonucleic acid after small bowel resection, whereas animals receiving SCFA-supplemented TPN showed no significant change in the jejunal mucosal parameters and a significant increase in ileal mucosal protein. These data demonstrate that SCFA-supplemented TPN reduces the mucosal atrophy associated with TPN after massive bowel resection and thys may facilitate adaptation to small bowel resection.

  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. 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.

  3. Work-Function and Surface Energy Tunable Cyanoacrylic Acid Small-Molecule Derivative Interlayer on Planar ZnO Nanorods for Improved Organic Photovoltaic Performance.

    PubMed

    Ambade, Swapnil B; Ambade, Rohan B; Bagde, Sushil S; Lee, Soo-Hyoung

    2016-12-28

    The issue of work-function and surface energy is fundamental to "decode" the critical inorganic/organic interface in hybrid organic photovoltaics, which influences important photovoltaic events like exciton dissociation, charge transfer, photocurrent (Jsc), open-circuit voltage (Voc), etc. We demonstrate that by incorporating an interlayer of cyanoacrylic acid small molecular layer (SML) on solution-processed, spin-coated, planar ZnO nanorods (P-ZnO NRs), higher photovoltaic (PV) performances were achieved in both inverted organic photovoltaic (iOPV) and hybrid organic photovoltaic (HOPV) devices, where ZnO acts as an "electron-transporting layer" and as an "electron acceptor", respectively. For the tuned range of surface energy from 52.5 to 33 mN/m, the power conversion efficiency (PCE) in bulk heterojunction (BHJ) iOPVs based on poly(3-hexylthiophene) (P3HT) and phenyl-C60-butyric acid methyl ester (PC60BM) increases from 3.16% to 3.68%, and that based on poly[4,8-bis(5-(2-ethylhexyl)thiophen-2-yl)benzo[1,2-b;4,5b']dithiophene-2,6-diyl-alt-(4-(2-ethylhexyl)-3-fluorothieno[3,4-b]thiophene)-2-carboxylate-2-6-diyl)] (PTB7:Th):[6,6]-phenyl C71 butyric acid methyl ester (PC71BM) photoactive BHJ increases from 6.55% to 8.0%, respectively. The improved PV performance in iOPV devices is majorly attributed to enhanced photocurrents achieved as a result of reduced surface energy and greater electron affinity from the covalent attachment of the strong electron-withdrawing cyano moiety, while that in HOPV devices, where PCE increases from 0.21% to 0.79% for SML-modified devices, is ascribed to a large increase in Voc benefitted due to reduced work function effected from the presence of strong dipole moment in SML that points away from P-ZnO NRs.

  4. Interactions of collagen molecules in the presence of N-hydroxysuccinimide activated adipic acid (NHS-AA) as a crosslinking agent.

    PubMed

    Zhang, Min; Wu, Kun; Li, Guoying

    2011-11-01

    The effect of crosslinking agent on pepsin-soluble bovine collagen solution was examined using N-hydroxysuccinimide activated adipic acid (NHS-AA) as a crosslinker. Electrophoretic patterns indicated that crosslinks formed when NHS-AA was added. A higher polarity level deduced from the changes in the fluorescence emission spectrum of pyrene in the crosslinked collagen solution indicated that the formation of well-ordered aggregates was suppressed. The random aggregation of collagens was also observed by atomic force microscopy (AFM). Furthermore, the association of collagens into fibrils was influenced by crosslinking. Self-assembly was suppressed at 37°C; however, as temperature was increased to 39°C, a small amount of NHS-AA leaded to an improvement in the ability of self-aggregation. Although more random structure was brought about by crosslinking, self-aggregation might still be promoted as temperature was increased, accompanying by the thermal stability improvement of fibrils.

  5. 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.

  6. 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 ...

  7. [Cu3(Hmesox)3]3-: a precursor for the rational design of chiral molecule-based magnets (H4mesox = 2-dihydroxymalonic acid).

    PubMed

    Sanchiz, Joaquín; Pasán, Jorge; Fabelo, Oscar; Lloret, Francesc; Julve, Miguel; Ruiz-Pérez, Catalina

    2010-09-06

    Two new compounds K(3)[Cu(3)(Hmesox)(3)(H(2)O)] x 4 H(2)O (1) and {(PPh(4))(2)[CoCu(3)(Hmesox)(3)Cl]} (2) [H(4)mesox = mesoxalic acid (2-dihydroxymalonic acid) and PPh(4)(+) = tetraphenylphosphonium cation] have been prepared and magneto-structurally characterized. Compound 1 contains the [Cu(3)(Hmesox)(3)](3-) entity which can be considered as a new precursor for molecular magnetism. In 1 the triangular arrangement of three copper(II) ions bridged by alkoxo groups are further connected to a symmetry-related tricopper(II) unit through a double oxo(carboxylate) bridge. The resulting hexacopper(II) entities are joined further through anti-syn carboxylate groups into an anionic three-dimensional network of formula [Cu(3)(Hmesox)(3)(H(2)O)](n)(3n-) whose charge is neutralized by univalent potassium cations. The strong decrease of the chi(M)T product [per three copper(II) ions] in the high temperature range with the occurrence of a plateau for a spin doublet at T < 65 K is as expected for the coexistence of two antiferromagnetic interactions within the quasi isosceles tricopper(II) core of 1 [J = -194(1) cm(-1) and j = -3(4) cm(-1), the Hamiltonian being defined as H = -J(S(1) x S(2) + S(2) x S(3)) - j(S(1) x S(2))]. Compound 2 exhibits a chiral three-dimensional structure which is made up of an anionic [Co(II)Cu(II)(3)(mu(3)-Cl)(Hmesox)(3)](n)(2n-) framework with a (10,3)-a topology whose cavities are filled by PPh(4)(+) cations. The [Cu(II)(3)(mu(3)-Cl)(Hmesox)(3)](3-) tricopper(II) unit in 2 acts as a tris-bidentate ligand through the Hmesox groups toward three cobalt(II) ions, these latter ones being tris-chelated. Alternating current (ac) and direct current (dc) magnetic susceptibility measurements of 2 show a ferrimagnetic behavior with a magnetic ordering at T(c) = 18.5 K and a coercive field H(c) = 5000 G. As shown by the magneto-structural study of 2, the use as a ligand of 1 versus metal ions other than cobalt(II) or preformed complexes whose coordination

  8. 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

  9. Improved small molecule drug release from in situ forming poly(lactic-co-glycolic acid) scaffolds incorporating poly(β-amino ester) and hydroxyapatite microparticles.

    PubMed

    Fisher, Paul D; Palomino, Pablo; Milbrandt, Todd A; Hilt, J Zach; Puleo, David A

    2014-01-01

    In situ forming implants are an attractive choice for controlled drug release into a fixed location. Currently, rapidly solidifying solvent exchange systems suffer from a high initial burst, and sustained release behavior is tied to polymer precipitation and degradation rate. The present studies investigated addition of hydroxyapatite (HA) and drug-loaded poly(β-amino ester) (PBAE) microparticles to in situ forming poly(lactic-co-glycolic acid) (PLGA)-based systems to prolong release and reduce burst. PBAEs were synthesized, imbibed with simvastatin (osteogenic) or clodronate (anti-resorptive), and then ground into microparticles. Microparticles were mixed with or without HA into a PLGA solution, and the mixture was injected into buffer, leading to precipitation and creating solid scaffolds with embedded HA and PBAE microparticles. Simvastatin release was prolonged through 30 days, and burst release was reduced from 81 to 39% when loaded into PBAE microparticles. Clodronate burst was reduced from 49 to 32% after addition of HA filler, but release kinetics were unaffected after loading into PBAE microparticles. Scaffold dry mass remained unchanged through day 15, with a pronounced increase in degradation rate after day 30, while wet scaffolds experienced a mass increase through day 25 due to swelling. Porosity and pore size changed throughout degradation, likely due to a combination of swelling and degradation. The system offers improved release kinetics, multiple release profiles, and rapid solidification compared to traditional in situ forming implants.

  10. Improved small molecule drug release from in situ forming poly(lactic-co-glycolic acid) scaffolds incorporating poly(β-amino ester) and hydroxyapatite microparticles

    PubMed Central

    Fisher, Paul D.; Palomino, Pablo; Milbrandt, Todd A.; Hilt, J. Zach; Puleo, David A.

    2014-01-01

    In situ forming implants are an attractive choice for controlled drug release into a fixed location. Currently, rapidly solidifying solvent exchange systems suffer from a high initial burst, and sustained release behavior is tied to polymer precipitation and degradation rate. The present studies investigated addition of hydroxyapatite (HA) and drug-loaded poly(β-amino ester) (PBAE) microparticles to in situ forming poly(lactic-co-glycolic acid) (PLGA)–based systems to prolong release and reduce burst. PBAEs were synthesized, imbibed with simvastatin (osteogenic) or clodronate (anti-resorptive), and then ground into microparticles. Microparticles were mixed with or without HA into a PLGA solution, and the mixture was injected into buffer, leading to precipitation and creating solid scaffolds with embedded HA and PBAE microparticles. Simvastatin release was prolonged through 30 days, and burst release was reduced from 81% to 39% when loaded into PBAE microparticles. Clodronate burst was reduced from 49% to 32% after addition of HA filler, but release kinetics were unaffected after loading into PBAE microparticles. Scaffold dry mass remained unchanged through day 15, with a pronounced increase in degradation rate after day 30, while wet scaffolds experienced a mass increase through day 25 due to swelling. Porosity and pore size changed throughout degradation, likely due to a combination of swelling and degradation. The system offers improved release kinetics, multiple release profiles, and rapid solidification compared to traditional in situ forming implants. PMID:24903524

  11. The role of hyaluronic acid inclusion on the energetics of encapsulation and release of a protein molecule from chitosan-based nanoparticles.

    PubMed

    Al-Qadi, Sonia; Alatorre-Meda, Manuel; Martin-Pastor, Manuel; Taboada, Pablo; Remuñán-López, Carmen

    2016-05-01

    The synergistic effects of the polysaccharides chitosan (CS) and hyaluronic acid (HA) formulated into hybrid nanoparticles are promising for drug delivery. In the present work, we performed a detailed analysis of the molecular interactions involved in the TPP-assisted ionotropic gelation of CS hybrid nanoparticles with the objective of investigating the impact of HA inclusion on the particle formulation and on the in vitro release of insulin (INS) as a protein cargo. To do that, an in-depth thermodynamic study was carried out by isothermal titration calorimetry (ITC), nuclear magnetic resonance (NMR) and differential scanning calorimetry (DSC) techniques. Such analysis allowed us to elucidate the type and extent of interactions established by INS within the hybrid nanoparticles and to get further knowledge on the nature of its release mechanism in vitro. Overall, INS release from the CS nanoparticles was thermodynamically driven, and when including HA a weaker INS binding to the nanoparticles, hence, a faster release rate in vitro were observed. As a negative polyelectrolyte, HA might have sterically blocked the activated sites of CS, such as the amino groups, through chain entanglement, thereby, attenuating the competitive binding interactions of INS. As a consequence, INS might have experienced a spatial exclusion onto the surface of the hybrid nanoparticles to a greater extent which, in turn, would explain its initial abrupt release.

  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

    NASA Astrophysics Data System (ADS)

    Zhang, Tingting; Wang, Qilin; Ye, Liu; Batstone, Damien; Yuan, Zhiguo

    2015-11-01

    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.

  14. Combined free nitrous acid and hydrogen peroxide pre-treatment of waste activated sludge enhances methane production via organic molecule breakdown.

    PubMed

    Zhang, Tingting; Wang, Qilin; Ye, Liu; Batstone, Damien; Yuan, Zhiguo

    2015-11-13

    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.

  15. Chicoric acid is an antioxidant molecule that stimulates AMP kinase pathway in L6 myotubes and extends lifespan in Caenorhabditis elegans.

    PubMed

    Schlernitzauer, Audrey; Oiry, Catherine; Hamad, Raphael; Galas, Simon; Cortade, Fabienne; Chabi, Béatrice; Casas, François; Pessemesse, Laurence; Fouret, Gilles; Feillet-Coudray, Christine; Cros, Gérard; Cabello, Gérard; Magous, Richard; Wrutniak-Cabello, Chantal

    2013-01-01

    Chicoric acid (CA) is a caffeoyl derivative previously described as having potential anti-diabetic properties. As similarities in cellular mechanism similarities between diabetes and aging have been shown, we explored on L6 myotubes the effect of CA on the modulation of intracellular pathways involved in diabetes and aging. We also determined its influence on lifespan of Caenorhabditis elegans worm (C. elegans). In L6 myotubes, CA was a potent reactive oxygen species (ROS) scavenger, reducing ROS accumulation under basal as well as oxidative stress conditions. CA also stimulated the AMP-activated kinase (AMPK) pathway and displayed various features associated with AMPK activation: CA (a) enhanced oxidative enzymatic defences through increase in glutathion peroxidase (GPx) and superoxide dismutase (SOD) activities, (b) favoured mitochondria protection against oxidative damage through up-regulation of MnSOD protein expression, (c) increased mitochondrial biogenesis as suggested by increases in complex II and citrate synthase activities, along with up-regulation of PGC-1α mRNA expression and (d) inhibited the insulin/Akt/mTOR pathway. As AMPK stimulators (e.g. the anti-diabetic agent meformin or polyphenols such as epigallocatechingallate or quercetin) were shown to extend lifespan in C. elegans, we also determined the effect of CA on the same model. A concentration-dependant lifespan extension was observed with CA (5-100 μM). These data indicate that CA is a potent antioxidant compound activating the AMPK pathway in L6 myotubes. Similarly to other AMPK stimulators, CA is able to extend C. elegans lifespan, an effect measurable even at the micromolar range. Future studies will explore CA molecular targets and give new insights about its possible effects on metabolic and aging-related diseases.

  16. Chicoric Acid Is an Antioxidant Molecule That Stimulates AMP Kinase Pathway in L6 Myotubes and Extends Lifespan in Caenorhabditis elegans

    PubMed Central

    Schlernitzauer, Audrey; Oiry, Catherine; Hamad, Raphael; Galas, Simon; Cortade, Fabienne; Chabi, Béatrice; Casas, François; Pessemesse, Laurence; Fouret, Gilles; Feillet-Coudray, Christine; Cros, Gérard; Cabello, Gérard; Magous, Richard; Wrutniak-Cabello, Chantal

    2013-01-01

    Chicoric acid (CA) is a caffeoyl derivative previously described as having potential anti-diabetic properties. As similarities in cellular mechanism similarities between diabetes and aging have been shown, we explored on L6 myotubes the effect of CA on the modulation of intracellular pathways involved in diabetes and aging. We also determined its influence on lifespan of Caenorhabditis elegans worm (C. elegans). In L6 myotubes, CA was a potent reactive oxygen species (ROS) scavenger, reducing ROS accumulation under basal as well as oxidative stress conditions. CA also stimulated the AMP-activated kinase (AMPK) pathway and displayed various features associated with AMPK activation: CA (a) enhanced oxidative enzymatic defences through increase in glutathion peroxidase (GPx) and superoxide dismutase (SOD) activities, (b) favoured mitochondria protection against oxidative damage through up-regulation of MnSOD protein expression, (c) increased mitochondrial biogenesis as suggested by increases in complex II and citrate synthase activities, along with up-regulation of PGC-1α mRNA expression and (d) inhibited the insulin/Akt/mTOR pathway. As AMPK stimulators (e.g. the anti-diabetic agent meformin or polyphenols such as epigallocatechingallate or quercetin) were shown to extend lifespan in C. elegans, we also determined the effect of CA on the same model. A concentration-dependant lifespan extension was observed with CA (5–100 μM). These data indicate that CA is a potent antioxidant compound activating the AMPK pathway in L6 myotubes. Similarly to other AMPK stimulators, CA is able to extend C. elegans lifespan, an effect measurable even at the micromolar range. Future studies will explore CA molecular targets and give new insights about its possible effects on metabolic and aging-related diseases. PMID:24244361

  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.

  18. 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

  19. Ferulic acid exerts its antidiabetic effect by modulating insulin-signalling molecules in the liver of high-fat diet and fructose-induced type-2 diabetic adult male rat.

    PubMed

    Narasimhan, Akilavalli; Chinnaiyan, Mayilvanan; Karundevi, Balasubramanian

    2015-08-01

    Ferulic acid (FA) is a phenolic phytochemical known for its antidiabetic property The present study is designed to evaluate the mechanism behind its antidiabetic property in high-fat and fructose-induced type 2 diabetic adult male rats. Animals were divided into 5 groups: (i) control, (ii) diabetic control, (iii) diabetic animals treated with FA (50 mg/(kg body weight · day)(-1), orally) for 30 days, (iv) diabetic animals treated with metformin (50 mg/(kg body weight · day)(-1), orally) for 30 days, and (v) control rats treated with FA. FA treatment to diabetic animals restored blood glucose, serum insulin, glucose tolerance, and insulin tolerance to normal range. Hepatic glycogen concentration, activity of glycogen synthase, and glucokinase were significantly decreased, whereas activity of glycogen phosphorylase and enzymes of gluconeogenesis (phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase)) were increased in diabetic animals and FA restored these to normal levels similar to that of metformin. FA improved the insulin signalling molecules and reduced the negative regulators of insulin signalling. The messenger RNA of gluconeogenic enzyme genes (PEPCK and G6Pase) and the interaction between forkhead transcription factor-O1 and promoters of gluconeogenic enzyme genes (PEPCK and G6Pase) was reduced significantly by ferulic acid. It is concluded from the present study that FA treatment to type 2 diabetic rats improves insulin sensitivity and hepatic glycogenesis but inhibits gluconeogenesis and negative regulators of insulin signalling to maintain normal glucose homeostasis.

  20. 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 ...

  1. A multi-matrix HILIC-MS/MS method for the quantitation of endogenous small molecule neurological biomarker N-acetyl aspartic acid (NAA).

    PubMed

    Sangaraju, Dewakar; Shahidi-Latham, Sheerin K; Burgess, Braydon L; Dean, Brian; Ding, Xiao

    2017-03-14

    A multi-matrix hydrophilic interaction liquid chromatography tandem mass spectrometric method (HILIC-MS/MS) was developed for the quantitation of N-Acetyl Aspartic acid (NAA) using stable isotope labeled internal standard, D3-NAA in various biological matrices such as human plasma, human CSF, mouse plasma, brain and spinal cord. A high throughput 96-well plate format supported liquid extraction (SLE) procedure was developed and used for sample preparation. Mass spectrometric analysis of NAA was performed using selected reaction monitoring transitions in positive electrospray ionization mode. As NAA is endogenously present, a surrogate matrix approach was used for quantitation of NAA and the method was qualified over linear calibration curve range of 0.01-10μg/mL. Intra and inter assay precision indicated by percent relative standard deviation (%RSD) was less than 7.1% for low, medium, medium high and high QCs. The accuracy of the method ranged from 92.6-107.0% of nominal concentration for within-run and between-run for the same QCs. Extraction recovery of NAA and D3-NAA was greater than 76%. Stability of NAA was established in the above biological matrices under bench top (RT, 5h), freeze thaw (-20±10°C, 3 cycles) and moues/human plasma sample collection (Wet ice, RT) conditions. HILIC-MS/MS method was then used to quantify and compare the NAA levels in human plasma and CSF of ALS patients versus control human subjects. NAA CSF levels in control human subjects (73.3±31.0ng/mL,N=10) were found to be slightly higher than ALS patients (46.1±22.6ng/mL, N=10) (P=0.04). No differences were observed in NAA plasma levels in human control subjects (49.7±13.8ng/mL,N=9) as compared to ALS patients (49.6±8.1ng/mL, N=10) (P=0.983). NAA endogenous concentrations in mouse plasma, brain and spinal cord were found to be 243.8±56.8ng/mL (N=6), 1029.8±115.2μg/g tissue weight (N=5) and 487.6±178.4μg/g tissue weight (N=5) respectively.

  2. 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

  3. 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.

  4. 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.

  5. Methods and applications in single molecule electronics

    NASA Astrophysics Data System (ADS)

    Hihath, Joshua

    In recent years it has become possible to measure charge transport in a single molecule contacted to two metal electrodes. However, a thorough understanding of how a molecule behaves while contacted to two electrodes and how it interacts with its environment is still lacking. This thesis demonstrates various experimental methods for understanding and controlling charge transport in a single molecule junction and the application of these methods to various molecular systems to help elucidate the conduction mechanisms invoked. First, the conductance of DNA is examined in a controlled environment while varying the length, sequence, base-pair matching, bias, temperature, and electrochemical gate of the molecule. These studies show that the conductance of DNA is extremely sensitive to changes in length, sequence, and base-matching, but not as sensitive to temperature and electrochemical gate. Despite the variety of experimental methods applied, the subtleties of the conduction mechanism remain uncertain, and as such necessitate the development of additional tools for understanding the behavior of a single molecule junction. Next, the Conductance Screening Tool for Molecules (CSTM) is described. This is a new tool capable of creating 1000's of single molecules junctions in a matter of minutes. This tool has been used to study the conductance of alkanedithiols, molecules in an array, and single amino acid residues. This system allows for greater speed and flexibility in determining the conductance of a single molecule junction, and provides a capability for performing large-scale systematic studies of molecular systems to determine the conduction mechanism. Finally, an additional experimental method capable of extracting information about the interaction between a molecule and its environment is developed. Here, electron-phonon interactions in a single molecule contacted to two electrodes are studied. This method allows one to obtain a specific, chemical signature of a

  6. 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.

  7. Effect of maternal aging on transgene heritability in transgenic founder mice derived from zygotes microinjected with retroviral long terminal repeat-containing recombinant deoxyribonucleic acid.

    PubMed

    Wang, T H; Yang, W K; Hoyt, P R; Ch'ang, L Y; Savin, T J

    1993-05-01

    To determine the stability of artificially introduced recombinant DNA in the mouse germline throughout the reproductive life, founder mice derived from fertilized eggs injected with retroviral long-terminal-repeat-containing recombinant DNAs were mated with congenic FVB/N mice. Tail DNA of all progeny were screened and restriction fragment patterns of the transgenes were examined. Litter size and percentage of transgene transmission at various reproductive age periods were analyzed. Microinjection of 1737 eggs with four different recombinant DNAs resulted in 12 female and 11 male transgenic mice; 2 males were sterile and the remaining 21 mice served as founders to produce 1087 F1 progeny. With increasing parental age, litter size decreased generally. The percentage of progeny inheriting the transgenes declined markedly with increasing aging of 4 female founders; this aging effect was not observed in male founders (p < 0.005). No apparent change in transgenes was detected in progeny from late reproductive stages.

  8. Restriction endonuclease analysis of total deoxyribonucleic acid of Mycobacterium tuberculosis H37RV (ATCC 27294) and of M. bovis (ATCC 19210).

    PubMed

    Labidi, A

    1988-01-01

    Total DNA from two slowly-growing pathogenic mycobacterial species propagated in vitro was isolated, digested with each of 34 restriction endonucleases and analyzed by agarose gel electrophoresis. The most distinct profiles for M. tuberculosis (ATCC 27294) and for M. bovis (ATCC 19210) were obtained respectively using (BamHI, DraI, ClaI, EcoRI, EcoRV, HindIII, HpaI, SalI, SmaI, XbaI, and XmaI). The patterns produced for these strains were reproducible and distinguishable from each other. However, with several enzymes the patterns for M. tuberculosis and M. bovis were similar. Evidence was obtained for the presence of dam and dcmI methylations in the DNA of each mycobacterial species.

  9. Decreased activity of superoxide dismutase in the seminal plasma of infertile men correlates with increased sperm deoxyribonucleic acid fragmentation during the first hours after sperm donation.

    PubMed

    Wdowiak, Artur; Bakalczuk, Szymon; Bakalczuk, Grzegorz

    2015-07-01

    Sperm DNA fragmentation varies between individuals and is more pronounced with increased patient age and time after sperm donation. The intensification of DNA fragmentation depends on the balance of the oxidoreductive system, which is regulated mainly by two enzymes - superoxide dismutase (SOD) and catalase. The objective of this study was to determine the relationship between sperm DNA fragmentation dynamics, fertility and seminal SOD and catalase activity. The study was conducted in 2013 and 2014 at the Non-Public Health Care Unit 'Ovum Reproduction and Andrology' in Lublin, Lublin, Poland, and covered 218 men aged 25-35 (85 fertile and 133 patients treated for infertility). Percentage of fragmented DNA was measured in a modified chromatin dispersion test at four time points after sperm donation (t = 0, 3, 6, 12 h). SOD and catalase activities were determined spectrophotometrically. We confirmed that the activity of SOD in the seminal plasma of men with reproductive disorders was lower compared with fertile men. Conversely, no significant correlations were found between fertility and catalase activity. Sperm DNA of infertile males was initially more fragmented than fertile male sperm DNA. SOD and catalase activity did not correlate with the degree of DNA fragmentation in fertile men. In men with reproductive disorders, the rate of DNA fragmentation was slow within first 3 h after sperm donation and then increased between 6 and 12 h. In this group of infertile men, those with higher SOD activity had a lower DNA fragmentation index (DFI) after 12 h, and a reduced rate of intensity of fragmentation from 6 to 12 h. Alternatively, higher catalase activity among men treated for infertility was accompanied by higher initial DFI and higher rate of DNA fragmentation from 6 to 12 h. These results highlight the importance of determining a proper time window between sperm donation and procedures of assisted reproductive technology.

  10. 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.

  11. Deoxyribonucleic acid methyl transferases 3a and 3b associate with the nuclear orphan receptor COUP-TFI during gene activation.

    PubMed

    Gallais, Rozenn; Demay, Florence; Barath, Peter; Finot, Laurence; Jurkowska, Renata; Le Guével, Rémy; Gay, Frédérique; Jeltsch, Albert; Métivier, Raphaël; Salbert, Gilles

    2007-09-01

    Transcriptional activation of silent genes can require the erasure of epigenetic marks such as DNA methylation at CpGs (cytosine-guanine dinucleotide). Active demethylation events have been observed, and associated processes are repeatedly suspected to involve DNA glycosylases such as mCpG binding domain protein 4, thymine DNA glycosylase (TDG), Demeter, and repressor of silencing 1. A complete characterization of the molecular mechanisms occurring in metazoan is nonetheless awaited. Here, we report that activation of the endogenous vitronectin gene in P19 cells by the nuclear receptor chicken ovalbumin upstream promoter-transcription factor I (COUP-TFI) is observed in parallel with the recruitment of TDG and p68 RNA helicase, two components of a putative demethylation complex. Interestingly, when activated, the vitronectin gene was loaded with DNA methyltransferases 3a and 3b (Dnmt3a/b), and a strand-biased decrease in CpG methylation was detected. Dnmt3a was further found to associate with COUP-TFI and TDG in vivo, and cotransfection experiments demonstrated that Dnmt3a/b can enhance COUP-TFI-mediated activation of a methylated reporter gene. These results suggest that Dnmt3a/b could cooperate with the orphan receptor COUP-TFI to regulate transcription of the vitronectin gene.

  12. 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.

  13. Exponential Increase in Relative Biological Effectiveness Along Distal Edge of a Proton Bragg Peak as Measured by Deoxyribonucleic Acid Double-Strand Breaks

    PubMed Central

    Cuaron, John J.; Chang, Chang; Lovelock, Michael; Higginson, Daniel S.; Mah, Dennis; Cahlon, Oren; Powell, Simon

    2016-01-01

    Purpose To quantify the relative biological effectiveness (RBE) of the distal edge of the proton Bragg peak, using an in vitro assay of DNA double-strand breaks (DSBs). Methods and Materials U2OS cells were irradiated within the plateau of a spread-out Bragg peak and at each millimeter position along the distal edge using a custom slide holder, allowing for simultaneous measurement of physical dose. A reference radiation signal was generated using photons. The DNA DSBs at 3 hours (to assess for early damage) and at 24 hours (to assess for residual damage and repair) after irradiation were measured using the γH2AX assay and quantified via flow cytometry. Results were confirmed with clonogenic survival assays. A detailed map of the RBE as a function of depth along the Bragg peak was generated using γH2AX measurements as a biological endpoint. Results At 3 hours after irradiation, DNA DSBs were higher with protons at every point along the distal edge compared with samples irradiated with photons to similar doses. This effect was even more pronounced after 24 hours, indicating that the impact of DNA repair is less after proton irradiation relative to photons. The RBE demonstrated an exponential increase as a function of depth and was measured to be as high as 4.0 after 3 hours and as high as 6.0 after 24 hours. When the RBE-corrected dose was plotted as a function of depth, the peak effective dose was extended 2-3 mm beyond what would be expected with physical measurement. Conclusions We generated a highly comprehensive map of the RBE of the distal edge of the Bragg peak, using a direct assay of DNA DSBs in vitro. Our data show that the RBE of the distal edge increases with depth and is significantly higher than previously reported estimates. PMID:27084629

  14. Evaluation of the oxidative deoxyribonucleic acid damage biomarker 8-hydroxy-2'-deoxyguanosine in the urine of leukemic children by micellar electrokinetic capillary chromatography.

    PubMed

    Zhang, Pingping; Lian, Kaoqi; Wu, Xiaoli; Yao, Min; Lu, Xin; Kang, Weijun; Jiang, Lingling

    2014-04-04

    Determining the level of urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG), an oxidative DNA damage biomarker, is vital to the study of clinical pathogenesis and drug toxicity. The principal limitation of capillary electrophoresis (CE) with UV detection is its low sensitivity. To overcome this shortcoming, we developed a micellar electrokinetic capillary chromatography (MEKC) with solid-phase extraction (SPE) for urinary 8-OHdG analysis. The sensitivity of MEKC-UV was improved using a reasonable UV system, injection mode, and SPE. The parameters affecting MEKC and SPE were also optimized. The calibration curve was linear within the range from 1 to 500 μg L(-1). The limits of detection and quantification were 0.27 μg L(-1) and 0.82 μg L(-1), respectively. Interday and intraday precision were both <5.6%. The recovery of 8-OHdG in urine ranged from 94.5% to 103.2%. This method was used to measure urinary 8-OHdG from eight normal children, eight newly diagnosed leukemic children, and eight leukemic children undergoing chemotherapy. The results show that the proposed method can be used to assess oxidative stress in patients and the side effects of chemotherapeutic drugs by measuring urinary 8-OHdG.

  15. 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.

  16. Formation and subsequent removal of O6-methylguanine from deoxyribonucleic acid in rat liver and kidney after small doses of dimethylnitrosamine

    PubMed Central

    Pegg, Anthony E.; Hui, Georgiani

    1978-01-01

    1. The amounts of 7-methylguanine and O6-methylguanine present in the DNA of liver and kidney of rats 4h and 24h after administration of low doses of dimethylnitrosamine were measured. 2. O6-Methylguanine was rapidly removed from liver DNA so that less than 15% of the expected amount (on the basis of 7-methylguanine found) was present within 4h after doses of 0.25mg/kg body wt. or less. Within 24h of administration of dimethylnitrosamine at doses of 1mg/kg or below, more than 85% of the expected amount of O6-methylguanine was removed. Removal was most efficient (defined in terms of the percentage of the O6-methylguanine formed that was subsequently lost within 24h) after doses of 0.25–0.5mg/kg body wt. At doses greater or less than this the removal was less efficient, even though the absolute amount of O6-methylguanine lost during 24h increased with the dose of dimethylnitrosamine over the entire range of doses from 0.001 to 20mg/kg body wt. 3. Alkylation of kidney DNA after intraperitoneal injections of 1–50μg of dimethylnitrosamine/kg body wt. occurred at about one-tenth the extent of alkylation of liver DNA. Removal of O6-methylguanine from the DNA also took place in the kidney, but was slower than in the liver. 4. After oral administration of these doses of dimethylnitrosamine, the alkylation of kidney DNA was much less than after intraperitoneal administration and represented only 1–2% of that found in the liver. 5. Alkylation of liver and kidney DNA was readily detectable when measured 24h after the final injection in rats that received daily injections of 1μg of [3H]dimethylnitrosamine/kg for 2 or 3 weeks. After 3 weeks, O6-methylguanine contents in the liver DNA were about 1% of the 7-methylguanine contents. The amount of 7-methylguanine in the liver DNA was 10 times that in the kidney DNA, but liver O6-methylguanine contents were only twice those in the kidney. 6. Extracts able to catalyse the removal of O6-methylguanine from alkylated DNA in vitro were isolated from liver and kidney. These extracts did not lead to the loss of 7-methylguanine from DNA. 7. The possible relevance of the formation and removal of O6-methylguanine in DNA to the risk of tumour induction by exposure to low concentrations of dimethylnitrosamine is discussed. PMID:708371

  17. 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.

  18. New 1,4-Dihydropyridines Down-regulate Nitric Oxide in Animals with Streptozotocin-induced Diabetes Mellitus and Protect Deoxyribonucleic Acid against Peroxynitrite Action.

    PubMed

    Leonova, Elina; Sokolovska, Jelizaveta; Boucher, Jean-Luc; Isajevs, Sergejs; Rostoka, Evita; Baumane, Larisa; Sjakste, Tatjana; Sjakste, Nikolajs

    2016-07-01

    Diabetes mellitus (DM) and its complications cause numerous health and social problems throughout the world. Pathogenic actions of nitric oxide (NO) are responsible to a large extent for development of complications of DM. Search for compounds regulating NO production in patients with DM is thus important for the development of pharmacological drugs. Dihydropyridines (1,4-DHPs) are prospective compounds from this point of view. The goals of this study were to study the in vivo effects of new DHPs on NO and reactive nitrogen and oxygen species production in a streptozotocin (STZ)-induced model of DM in rats and to study their ability to protect DNA against nocive action of peroxynitrite. STZ-induced diabetes caused an increase in NO production in the liver, kidneys, blood and muscles, but a decrease in NO in adipose tissue of STZ-treated animals. Cerebrocrast treatment was followed by normalization of NO production in the liver, kidneys and blood. Two other DHPs, etaftorone and fenoftorone, were effective in decreasing NO production in kidneys, blood and muscles of diabetic animals. Furthermore, inhibitors of nitric oxide synthase (NOS) and an inhibitor of xanthine oxidoreductase (XOR) decreased NO production in kidneys of diabetic animals. Treatment with etaftorone decreased expression of inducible NOS and XOR in kidneys, whereas it increased the expression of endothelial NOS. In vitro, the studied DHPs did not significantly inhibit the activities of NOS and XOR but affected the reactivity of peroxynitrite with DNA. These new DHPs thus appear of strong interest for treatment of DM complications.

  19. Prebiotically Important Molecules in Orion KL

    NASA Astrophysics Data System (ADS)

    Kuan, Yi-Jehng; Chuang, Yo-Ling

    Many interstellar, complex organic molecules are known to be prebiotically important and have essential functions in terrestrial biochemistry. Observations of complex organic molecular species in molecular clouds can thus enable us to test the origin of the primitive organic material found in the Solar System. Interstellar pyrimidine and glycine, the building block of nucleic acid and the simplest amino acid, respectively, are key molecules for astrobiology and were both detected in meteorites and comets. Although the formation of prebiotic molecules in extraterrestrial environments and their contribution to prebiotic chemistry and the origin of life remains unsettled, the connection between interstellar organic chemistry, meteoritic pyrimidines and amino acids, and the emergence of life on the early Earth would be strengthened with the discovery of interstellar pyrimidine and glycine. We have therefore observed the Orion KL hot molecular core to search for interstellar pyrimidine and for the confirmation of interstellar glycine using the ALMA array. We will present some of the encouraging, positive results.

  20. Formation of Ultracold Molecules

    SciTech Connect

    Cote, Robin

    2016-01-28

    Advances in our ability to slow down and cool atoms and molecules to ultracold temperatures have paved the way to a revolution in basic research on molecules. Ultracold molecules are sensitive of very weak interactions, even when separated by large distances, which allow studies of the effect of those interactions on the behavior of molecules. In this program, we have explored ways to form ultracold molecules starting from pairs of atoms that have already reached the ultracold regime. We devised methods that enhance the efficiency of ultracold molecule production, for example by tuning external magnetic fields and using appropriate laser excitations. We also investigates the properties of those ultracold molecules, especially their de-excitation into stable molecules. We studied the possibility of creating new classes of ultra-long range molecules, named macrodimers, thousand times more extended than regular molecules. Again, such objects are possible because ultra low temperatures prevent their breakup by collision. Finally, we carried out calculations on how chemical reactions are affected and modified at ultracold temperatures. Normally, reactions become less effective as the temperature decreases, but at ultracold temperatures, they can become very effective. We studied this counter-intuitive behavior for benchmark chemical reactions involving molecular hydrogen.

  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. 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)

  3. Porous organic molecules

    NASA Astrophysics Data System (ADS)

    Holst, James R.; Trewin, Abbie; Cooper, Andrew I.

    2010-11-01

    Most synthetic materials that show molecular-scale porosity consist of one-, two- or three-dimensional networks. Porous metal-organic frameworks in particular have attracted a lot of recent attention. By contrast, discrete molecules tend to pack efficiently in the solid state, leaving as little empty space as possible, which leads to non-porous materials. This Perspective discusses recent developments with discrete organic molecules that are porous in the solid state. Such molecules, which may be either crystalline or amorphous, can be categorized as either intrinsically porous (containing permanent covalent cavities) or extrinsically porous (inefficiently packed). We focus on the possible advantages of organic molecules over inorganic or hybrid systems in terms of molecular solubility, choice of components and functionalities, and structural mobility and responsiveness in non-covalent extended solids. We also highlight the potential for 'undiscovered' porous systems among the large number of cage-like organic molecules that are already known.

  4. Fatty Acid Composition of Unicellular Strains of Blue-Green Algae1

    PubMed Central

    Kenyon, C. N.

    1972-01-01

    The fatty acids of 34 strains of unicellular blue-green algae provisionally assigned to the genera Synechococcus, Aphanocapsa, Gloeocapsa, Microcystis, and Chlorogloea by Stanier et al. have been chemically characterized. The strains analyzed can be divided into a series of compositional groups based upon the highest degree of unsaturation of the major cellular fatty acids. Twenty strains fall into the group characterized by one trienoic fatty acid isomer (α-linolenic acid), and seven strains fall into a group characterized by another trienoic acid isomer (γ-linolenic acid). These groups in many cases correlate well with groupings based upon other phenotypic characters of the strains, e.g., deoxyribonucleic acid base composition. The assignment of a strain to a compositional group is not altered when the strain is grown under a variety of different culture conditions. All strains contain glycolipids with the properties of mono- and digalactosyldiglycerides. PMID:4621688

  5. 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.

  6. Dynamics of Activated Molecules

    SciTech Connect

    Mullin, Amy S.

    2016-11-16

    Experimental studies have been performed to investigate the collisional energy transfer processes of gas-phase molecules that contain large amounts of internal energy. Such molecules are prototypes for molecules under high temperature conditions relevant in combustion and information about their energy transfer mechanisms is needed for a detailed understanding and modeling of the chemistry. We use high resolution transient IR absorption spectroscopy to measure the full, nascent product distributions for collisions of small bath molecules that relax highly vibrationally excited pyrazine molecules with E=38000 cm-1 of vibrational energy. To perform these studies, we developed new instrumentation based on modern IR light sources to expand our experimental capabilities to investigate new molecules as collision partners. This final report describes our research in four areas: the characterization of a new transient absorption spectrometer and the results of state-resolved collision studies of pyrazine(E) with HCl, methane and ammonia. Through this research we have gained fundamental new insights into the microscopic details of relatively large complex molecules at high energy as they undergo quenching collisions and redistribute their energy.

  7. Behavior of atypical amphiphilic molecules

    NASA Astrophysics Data System (ADS)

    Ko, John

    1997-08-01

    The physical behavior of several atypical amphiphilic molecules was studied in various environments including micelles, model bilayer membranes, and emulsions. The molecules under investigation were nor-chenodeoxycholic acid (nor-CDCA), ursodeoxycholic acid (UDCA), sphingosine (Sp), sphingosine hydrochloride (SpċHCl), and tetrahydrolipstatin (THL). The bile acids, nor-CDCA and UDCA, were studied using 13C-Nuclear Magnetic Resonance ([13C) -NMR) in micelles of taurocholate and in bilayers of phosphatidylcholine. The pK a values of the bile acids in each environment were determined by [13C) -NMR and are as follows: 6.08 ±.03 for nor-CDCA and 6.27 ±.01 for UDCA in micelles, and 7.04 ± 12 for nor-CDCA and 6.89 ±.05 for UDCA in vesicles. Using line shape analysis, the transbilayer movement rate at 36oC for nor-CDCA and UDCA was calculated to be 580 sec--1 and 409 sec-1, respectively. [13C) -NMR titration of Sp gave pK a values of 9.09 ±.02 in micelles and 9.69 ±.21 in bilayers. Differential scanning calorimetry (DSC) and X-ray diffraction were used to establish the Spċwater and SpċHClċwater phase diagrams. Anhydrous and hydrated samples ranging from 5- 90% water were analyzed. The DSC thermograms traced out the transition temperatures of each molecule while the X- ray diffraction patterns revealed their chain and crystalline lattice packing structures. In general, sphingosine exists as a hydrated crystal with β packing phase below 43oC and melts into an Lα phase. Sphingosine hydrochloride, however, exists as a gel phase (L_beta or /beta/sp') below 42oC that swells to 61% hydration. At low water concentrations (0-64%), a lamellar liquid crystal phase (L_alpha) is formed above the chain melting transition of 42oC. At medium concentration (65%), a Hexagonal I phase is present, and at high water concentrations (66-90%), a micellar phase is present. THL, a specific inhibitor of lipases, was analyzed with [ 13C) -NMR to study its behavior in various environments

  8. 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)

  9. Nalidixic Acid and Macromolecular Metabolism in Tetrahymena pyriformis: Effects on Protein Synthesis

    PubMed Central

    de Castro, J. F.; Carvalho, J. F. O.; Moussatché, N.; de Castro, F. T.

    1975-01-01

    A study on the effect of nalidixic acid on macromolecular metabolism, particularly of protein, in Tetrahymena pyriformis was performed. It was shown that the compound is a potent inhibitor of deoxyribonucleic acid, ribonucleic acid, and protein synthesis for this organism. A conspicuous breakdown of polysomes, accompanied by the accumulation of 80S ribosomes, occurred in cells incubated for 10 min with the drug; polysome formation was prevented. The accumulating 80S particles were shown to be run-off ribosomal units. The incorporation of amino acids by a cell-free system is not affected by nalidixic acid. In nonproliferating cells the incorporation was also not prevented, unless the cells were previously incubated with the drug. These results are discussed in terms of the possible mechanism of action of nalidixic acid in T. pyriformis. PMID:807153

  10. 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.

  11. Positronium ions and molecules

    NASA Technical Reports Server (NTRS)

    Ho, Y. K.

    1990-01-01

    Recent theoretical studies on positronium ions and molecules are discussed. A positronium ion is a three particle system consisting of two electrons in singlet spin state, and a positron. Recent studies include calculations of its binding energy, positron annihilation rate, and investigations of its doubly excited resonant states. A positronium molecule is a four body system consisting of two positrons and two electrons in an overall singlet spin state. The recent calculations of its binding energy against the dissociation into two positronium atoms, and studies of auto-detaching states in positronium molecules are discussed. These auto-dissociating states, which are believed to be part of the Rydberg series as a result of a positron attaching to a negatively charged positronium ion, Ps-, would appear as resonances in Ps-Ps scattering.

  12. Single-Molecule Bioelectronics

    PubMed Central

    Rosenstein, Jacob K.; Lemay, Serge G.; Shepard, Kenneth L.

    2014-01-01

    Experimental techniques which interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. Here we review several technologies which can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms. PMID:25529538

  13. 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.

  14. Polarization of deuterium molecules

    SciTech Connect

    J. F. J. van den Brand; H. J. Bulten; M. Ferro-Luzzi; Z.-L. Zhou; Ricardo Alarcon; T. Botto; M. Bouwhuis; Rolf Ent; Peter Heimberg; Douglas W. Higinbotham; Kees de Jager; J. Lang; D. J. de Lange; I. Passchier; H. R. Poolman; J. J. M. Steijger; O. Unal; H. de Vries

    1997-08-01

    For molecular systems, spin relaxation is expected to be suppressed compared to the case of atoms, since the paired electrons in a hydrogen or deuterium molecule are chemically stable, and only weakly interact with the spin of the nucleus. Such systems would be largely insensitive to polarization losses due to spin-exchange collisions, to the interaction of the electron spins with external fields (e.g. the RF-field of a bunched charged-particle beam), and/or to the presence of container walls. Here, we discuss the results of a recent experiment where we obtained evidence that nuclear polarization is maintained, when polarized atoms recombine to molecules on a copper surface (in a magnetic field of 23 mT and at a density of about 10{sup 12} molecules {center_dot} cm{sup -3}).

  15. 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.

  16. Single molecule diffraction.

    PubMed

    Spence, J C H; Doak, R B

    2004-05-14

    For solving the atomic structure of organic molecules such as small proteins which are difficult to crystallize, the use of a jet of doped liquid helium droplets traversing a continuous high energy electron beam is proposed as a means of obtaining electron diffraction patterns (serial crystallography). Organic molecules (such as small proteins) within the droplet (and within a vitreous ice jacket) may be aligned by use of a polarized laser beam. Iterative methods for solving the phase problem are indicated. Comparisons with a related plan for pulsed x-ray diffraction from single proteins in a molecular beam are provided.

  17. Enzyme molecules as nanomotors.

    PubMed

    Sengupta, Samudra; Dey, Krishna K; Muddana, Hari S; Tabouillot, Tristan; Ibele, Michael E; Butler, Peter J; Sen, Ayusman

    2013-01-30

    Using fluorescence correlation spectroscopy, we show that the diffusive movements of catalase enzyme molecules increase in the presence of the substrate, hydrogen peroxide, in a concentration-dependent manner. Employing a microfluidic device to generate a substrate concentration gradient, we show that both catalase and urease enzyme molecules spread toward areas of higher substrate concentration, a form of chemotaxis at the molecular scale. Using glucose oxidase and glucose to generate a hydrogen peroxide gradient, we induce the migration of catalase toward glucose oxidase, thereby showing that chemically interconnected enzymes can be drawn together.

  18. 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.

  19. 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.

  20. Atoms-in-molecules study of the genetically encoded amino acids. III. Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding.

    PubMed

    Matta, Chérif F; Bader, Richard F W

    2003-08-15

    This article presents a study of the molecular charge distributions of the genetically encoded amino acids (AA), one that builds on the previous determination of their equilibrium geometries and the demonstrated transferability of their common geometrical parameters. The properties of the charge distributions are characterized and given quantitative expression in terms of the bond and atomic properties determined within the quantum theory of atoms-in-molecules (QTAIM) that defines atoms and bonds in terms of the observable charge density. The properties so defined are demonstrated to be remarkably transferable, a reflection of the underlying transferability of the charge distributions of the main chain and other groups common to the AA. The use of the atomic properties in obtaining an understanding of the biological functions of the AA, whether free or bound in a polypeptide, is demonstrated by the excellent statistical correlations they yield with experimental physicochemical properties. A property of the AA side chains of particular importance is the charge separation index (CSI), a quantity previously defined as the sum of the magnitudes of the atomic charges and which measures the degree of separation of positive and negative charges in the side chain of interest. The CSI values provide a correlation with the measured free energies of transfer of capped side chain analogues, from the vapor phase to aqueous solution, yielding a linear regression equation with r2 = 0.94. The atomic volume is defined by the van der Waals isodensity surface and it, together with the CSI, which accounts for the electrostriction of the solvent, yield a linear regression (r2 = 0.98) with the measured partial molar volumes of the AAs. The changes in free energies of transfer from octanol to water upon interchanging 153 pairs of AAs and from cyclohexane to water upon interchanging 190 pairs of AAs, were modeled using only three calculated parameters (representing electrostatic and

  1. Sweeping molecules with light

    NASA Astrophysics Data System (ADS)

    Hutzler, Nicholas R.

    2017-03-01

    Many areas of physics—precision measurements, quantum information, and physical chemistry, to name a few—are starting to benefit from the enormous advantages offered by cold and ultracold polar molecules. Molecules have more states, more interactions, and more chemical properties compared to atoms, which make them exciting to study but difficult to tame. In particular, the powerful techniques of atomic laser cooling cannot be naïvely applied to molecules due to their complicated structure. Developments over the past few years have made directly laser cooled and trapped molecules a reality, and now much effort is focused on making these samples larger, denser, and colder—an important step to realizing many of their exciting applications. A careful experimental and numerical study by Truppe et al (2017 New J. Phys. 19 022001) demonstrates a significant improvement and advance in understanding of one of the most limiting steps in laser cooling and trapping of molecules—slowing them from a molecular beam to a near-standstill, with small enough kinetic energy that they can be loaded into a trap.

  2. Disentangling DNA molecules.

    PubMed

    Vologodskii, Alexander

    2016-09-01

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

  3. 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…

  4. 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…

  5. 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.

  6. Single molecules: Thermodynamic limits

    NASA Astrophysics Data System (ADS)

    Liphardt, Jan

    2012-09-01

    Technologies aimed at single-molecule resolution of non-equilibrium systems increasingly require sophisticated new ways of thinking about thermodynamics. An elegant extension to standard fluctuation theory grants access to the kinetic intermediate states of these systems -- as DNA-pulling experiments now demonstrate.

  7. Disentangling DNA molecules

    NASA Astrophysics Data System (ADS)

    Vologodskii, Alexander

    2016-09-01

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

  8. Three new 'nonterrestrial' molecules

    NASA Astrophysics Data System (ADS)

    Thaddeus, P.; Guelin, M.; Linke, R. A.

    1981-05-01

    Eight new interstellar lines have been detected from three molecules not previously observed spectroscopically in space or in the laboratory. One is a linear or nearly linear molecule with microwave constants B0 equals 21,337.15 plus or minus 0.06 MHz, D0 equals 21.4 plus or minus 1.5 kHz. This is the thioformyl ion HCS(plus), first identified because B0 and D0 are close to those calculated, and now confirmed by laboratory detection of one of the present lines (Gudeman et al.). The second molecule, also linear or nearly so, has microwave constants B0 equals 10,691,406 plus or minus 0.043 MHz, D0 equals 1.84 plus or minus 0.91 kHz close to those expected for the isoelectronic systems HOCO(plus) and HOCN; a choice between the two cannot be made on the basis of the available astronomical data. The existence of a third molecule is deduced from an unidentified line at 85,338 MHz that has been found in many sources, is fairly intense in several, and may be self-absorbed in Sgr B2.

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. Molecules in Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Berdyugina, Svetlana

    2015-08-01

    Molecules probe cool matter in the Universe and various astrophysical objects. Their ability to sense magnetic fields provides new insights into magnetic properties of these objects. During the past fifteen years we have carried out a theoretical study of molecular magnetic effects such as the Zeeman, Paschen-Back and Hanle effects and their applications for inferring magnetic structures and spatial inhomogeneities on the Sun, cool stars, brown dwarfs, and exoplanets from molecular spectro-polarimetry (e.g., Berdyugina 2011). Here, we present an overview of this study and compare our theoretical predictions with recent laboratory measurements of magnetic properties of some molecules. We present also a new web-based tool to compute molecular magnetic effects and polarized spectra which is supported by the ERC Advanced Grant HotMol.

  15. Strange skyrmion molecules

    NASA Astrophysics Data System (ADS)

    Kopeliovich, Vladimir B.; Stern, Boris E.

    1997-05-01

    Composed skyrmions with B=2, strangeness content close to 0.5 and the binding energy of several tens of Mev are described. These skyrmions are obtained starting from the system of two B=1 hedgehogs located in different SU(2) subgroups of SU(3) and have the mass and baryon number distribution of molecular (dipole) type. The quantization of zero modes of skyrmion molecules and physics consequences of their existence are discussed.

  16. Strange skyrmion molecules

    SciTech Connect

    Kopeliovich, Vladimir B.; Stern, Boris E.

    1997-05-20

    Composed skyrmions with B=2, strangeness content close to 0.5 and the binding energy of several tens of Mev are described. These skyrmions are obtained starting from the system of two B=1 hedgehogs located in different SU(2) subgroups of SU(3) and have the mass and baryon number distribution of molecular (dipole) type. The quantization of zero modes of skyrmion molecules and physics consequences of their existence are discussed.

  17. Model molecules mimicking asphaltenes.

    PubMed

    Sjöblom, Johan; Simon, Sébastien; Xu, Zhenghe

    2015-04-01

    Asphalthenes are typically defined as the fraction of petroleum insoluble in n-alkanes (typically heptane, but also hexane or pentane) but soluble in toluene. This fraction causes problems of emulsion formation and deposition/precipitation during crude oil production, processing and transport. From the definition it follows that asphaltenes are not a homogeneous fraction but is composed of molecules polydisperse in molecular weight, structure and functionalities. Their complexity makes the understanding of their properties difficult. Proper model molecules with well-defined structures which can resemble the properties of real asphaltenes can help to improve this understanding. Over the last ten years different research groups have proposed different asphaltene model molecules and studied them to determine how well they can mimic the properties of asphaltenes and determine the mechanisms behind the properties of asphaltenes. This article reviews the properties of the different classes of model compounds proposed and present their properties by comparison with fractionated asphaltenes. After presenting the interest of developing model asphaltenes, the composition and properties of asphaltenes are presented, followed by the presentation of approaches and accomplishments of different schools working on asphaltene model compounds. The presentation of bulk and interfacial properties of perylene-based model asphaltene compounds developed by Sjöblom et al. is the subject of the next part. Finally the emulsion-stabilization properties of fractionated asphaltenes and model asphaltene compounds is presented and discussed.

  18. Single Molecule Mechanochemistry

    NASA Astrophysics Data System (ADS)

    Li, Shaowei; Zhang, Yanxing; Ho, Wilson; Wu, Ruqian; Ruqian Wu, Yanxing Zhang Team; Wilson Ho, Shaowei Li Team

    Mechanical forces can be used to trigger chemical reactions through bending and stretching of chemical bonds. Using the reciprocating movement of the tip of a scanning tunneling microscope (STM), mechanical energy can be provided to a single molecule sandwiched between the tip and substrate. When the mechanical pulse center was moved to the outer ring feature of a CO molecule, the reaction rate was significantly increased compared with bare Cu surface and over Au atoms. First, DFT calculations show that the presence of CO makes the Cu cavity more attractive toward H2 Second, H2 prefers the horizontal adsorption geometry in the Cu-Cu and Au-Cu cavities and no hybridization occurs between the antibonding states of H2 and states of Cu atoms. While H2 loses electrons from its bonding state in all three cavities, the filling of its anti-bonding state only occurs in the CO-Cu cavity. Both make the CO-Cu cavity much more effectively to chop the H2 molecule. Work was supported by the National Science Foundation Center for Chemical Innovation on Chemistry at the Space-Time Limit (CaSTL) under Grant No. CHE-1414466.

  19. 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.

  20. Design and characterization of symmetric nucleic acids via molecular dynamics simulations.

    PubMed

    Pant, Pradeep; Afshan Shaikh, Saher; Jayaram, B

    2017-04-01

    Asymmetry (5'→3') associated with each strand of the deoxyribonucleic acid (DNA) is inherent in the sugar-phosphate backbone connectivity and is essential for replication and transcription. We note that this asymmetry is due to one single chemical bond (C3' to C2' ) in each nucleotide unit, and the absence of this bond results in directionally symmetric nucleic acids. We also discovered that creation of an extra chemical bond (C5' to C2' ) can lead to a symmetric backbone. Keeping their potential synthetic and therapeutic interest in mind, we designed a few novel symmetric nucleic acids. We investigated their conformational stability and flexibility via detailed all atom explicit solvent 100-ns long molecular dynamics simulations and compared the resulting structures with that of regular B-DNA. Quite interestingly, some of the symmetric nucleic acids retain the overall double helical structure indicating their potential for integration in physiological DNA without causing major structural perturbations.

  1. Negative ions of polyatomic molecules.

    PubMed Central

    Christophorou, L G

    1980-01-01

    In this paper general concepts relating to, and recent advances in, the study of negative ions of polyatomic molecules area discussed with emphasis on halocarbons. The topics dealt with in the paper are as follows: basic electron attachment processes, modes of electron capture by molecules, short-lived transient negative ions, dissociative electron attachment to ground-state molecules and to "hot" molecules (effects of temperature on electron attachment), parent negative ions, effect of density, nature, and state of the medium on electron attachment, electron attachment to electronically excited molecules, the binding of attached electrons to molecules ("electron affinity"), and the basic and the applied significance of negative-ion studies. PMID:7428744

  2. Negative ions of polyatomic molecules.

    PubMed

    Christophorou, L G

    1980-06-01

    In this paper general concepts relating to, and recent advances in, the study of negative ions of polyatomic molecules area discussed with emphasis on halocarbons. The topics dealt with in the paper are as follows: basic electron attachment processes, modes of electron capture by molecules, short-lived transient negative ions, dissociative electron attachment to ground-state molecules and to "hot" molecules (effects of temperature on electron attachment), parent negative ions, effect of density, nature, and state of the medium on electron attachment, electron attachment to electronically excited molecules, the binding of attached electrons to molecules ("electron affinity"), and the basic and the applied significance of negative-ion studies.

  3. 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)

  4. Carbon nanodots as a matrix for the analysis of low-molecular-weight molecules in both positive- and negative-ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and quantification of glucose and uric acid in real samples.

    PubMed

    Chen, Suming; Zheng, Huzhi; Wang, Jianing; Hou, Jian; He, Qing; Liu, Huihui; Xiong, Caiqiao; Kong, Xianglei; Nie, Zongxiu

    2013-07-16

    Carbon nanodots were applied for the first time as a new matrix for the analysis of low-molecular-weight compounds by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in both positive- and negative-ion modes. A wide range of small molecules including amino acids, peptides, fatty acids, as well as β-agonists and neutral oligosaccharides were analyzed by MALDI MS with carbon nanodots as the matrix, and the lowest 0.2 fmol limits-of-detection were obtained for octadecanoic acid. Clear sodium and potassium adducts and deprotonated signals were produced in positive- and negative-ion modes. Furthermore, the glucose and uric acid in real samples were quantitatively determined by the internal standard method with the linear range of 0.5-9 mM and 0.1-1.8 mM (R(2) > 0.999), respectively. This work gives new insight into the application of carbon nanodots and provides a general approach for rapid analysis of low-molecular-weight compounds.

  5. 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

  6. 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.

  7. Do we know whether potential G-quadruplexes actually form in long functional RNA molecules?

    PubMed Central

    Weldon, Carika; Eperon, Ian C.; Dominguez, Cyril

    2016-01-01

    The roles of deoxyribonucleic acid (DNA) G-quadruplex structures in gene expression and telomere maintenance have been well characterized. Recent results suggest that such structures could also play pivotal roles in ribonucleic acid (RNA) biology, such as splicing or translation regulation. However, it has been difficult to show that RNA G-quadruplexes (G4s) exist in specific long RNA sequences, such as precursor messenger RNA, in a functional or cellular context. Most current methods for identifying G4s involve the use of short, purified RNA sequences in vitro, in the absence of competition with secondary structures or protein binding. Therefore, novel methods need to be developed to allow the characterization of G4s in long functional RNAs and in a cellular context. This need has in part been met by our recent development of a method based on a comparison of RNA and 7-deaza-RNA that provides a test for identifying RNA G4s in such conditions. PMID:27913687

  8. 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)

  9. 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.

  10. Covalent Chemistry beyond Molecules.

    PubMed

    Jiang, Juncong; Zhao, Yingbo; Yaghi, Omar M

    2016-03-16

    Linking molecular building units by covalent bonds to make crystalline extended structures has given rise to metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), thus bringing the precision and versatility of covalent chemistry beyond discrete molecules to extended structures. The key advance in this regard has been the development of strategies to overcome the "crystallization problem", which is usually encountered when attempting to link molecular building units into covalent solids. Currently, numerous MOFs and COFs are made as crystalline materials in which the large size of the constituent units provides for open frameworks. The molecular units thus reticulated become part of a new environment where they have (a) lower degrees of freedom because they are fixed into position within the framework; (b) well-defined spatial arrangements where their properties are influenced by the intricacies of the pores; and (c) ordered patterns onto which functional groups can be covalently attached to produce chemical complexity. The notion of covalent chemistry beyond molecules is further strengthened by the fact that covalent reactions can be carried out on such frameworks, with full retention of their crystallinity and porosity. MOFs are exemplars of how this chemistry has led to porosity with designed metrics and functionality, chemically-rich sequences of information within their frameworks, and well-defined mesoscopic constructs in which nanoMOFs enclose inorganic nanocrystals and give them new levels of spatial definition, stability, and functionality.

  11. Dihydrino molecule identification

    SciTech Connect

    Mills, R.L.; Good, W.R. ); Shaubach, R.M. )

    1994-01-01

    Three sets of heat production and [open quotes]ash[close quotes] identification data are presented. An exothermic reaction is reported wherein the electrons of hydrogen and deuterium atoms are stimulated to relax to quantized potential energy levels below that of the [open quotes]ground state[close quotes] via electrochemical reactants K[sup +] and K[sup +]; Pd[sup 2+] and Li[sup +]; or Pd and O[sub 2] of redox energy resonant with the energy hole that stimulates this transition. Calorimetry of pulsed current and continuous electrolysis of aqueous potassium carbonate (K[sup +]/K[sup +] electrocatalytic couple) at a nickel cathode were performed. The excess output power of 41 W exceeded by a factor >8 the total input power given by the product of the electrolysis voltage and current. The product of the exothermic reaction is atoms having electrons of energy below the ground state, which are predicted to form molecules. The predicted molecules were identified by their lack of reactivity with oxygen, by separation from molecular deuterium by cryofiltration, and by mass spectroscopic analysis. 15 refs., 12 figs., 9 tabs.

  12. 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.

  13. 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.

  14. Synthesis, crystal structure and self-organization of molecules containing 2,5-bis( o-amino-phenyl)-1,3,4-oxadiazoles unit and N-tos- L-amino acid residues

    NASA Astrophysics Data System (ADS)

    Zhao, Hongwu; Wei, Yongge; Hua, Wenting

    2000-10-01

    The title compound has been synthesized by the acylation reaction of 2,5-bis( o-amino-phenyl)-1,3,4-oxadiazoles with excess chiral N-tosyl- L-leucyl chloride in dry pyridine. Its crystal structure has been determined, the crystal data are: C 40H 46N 6O 7S 2, Monoclinic, p2(1), a=11.168(2) Å, b=15.967(3) Å, c=11.641(2) Å, α=90°, β=95.28(3)°, γ=90°, V=2067.0(6) Å3, Z=2. The molecule via its intermolecular CH⋯O and NH⋯O hydrogen bonds and planar conjugate aromatic heterocycles aggregation forms a unique regular aggregation.

  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. 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

  17. Biochips - Can molecules compute?

    NASA Astrophysics Data System (ADS)

    Tucker, J. B.

    1984-02-01

    In recent years the possibility has been considered to build 'biochip' computers, in which the silicon transistors of present machines would be replaced by large organic molecules or genetically engineered proteins. Two major advantages of such biochips over current devices would be related to vastly increased densities of computing elements, and entirely new styles of data processing, suited to such high-level tasks as pattern recognition and context-dependent analysis. The limitations of the semiconductor chip with respect to the density of elementary units due to size considerations and heat development could be overcome by making use of molecular switches. Attention is given to soliton switching, soliton logic, bulk molecular devices, analog biochips, 'intelligent' switches based on the employment of enzymes, robot vision, questions of biochip fabrication, protein engineering, and a strategy for the development of biochips.

  18. Molecules in the Spotlight

    SciTech Connect

    Cryan, James

    2010-01-26

    SLAC has just unveiled the world's first X-ray laser, the LCLS. This machine produces pulses of X-rays that are ten billion times brighter than those from conventional sources. One of the goals of this machine is to make movies of chemical reactions, including reactions necessary for life and reactions that might power new energy technologies. This public lecture will show the first results from the LCLS. As a first target, we have chosen nitrogen gas, the main component of the air we breathe. Using the unprecedented power of the LCLS X-rays as a blasting torch, we have created new forms of this molecule and with unique electronic arrangements. Please share with us the first insights from this new technology.

  19. Fiber-mesh photonic molecule

    NASA Astrophysics Data System (ADS)

    Mishra, Subodha; Satpathy, Sashi

    2008-03-01

    Analogous to the photonic crystal, we introduce the concept of a fiber-mesh photonic molecule made up of optical fibers and study its transmission characteristics. We consider a specific example of a photonic molecule, inspired by the well-known C60 molecule, with the arms of the molecule formed out of single-moded optical fibers. The transmittance consists of sharp peaks determined by the pole structure of the scattering matrix in the complex energy plane. A molecule can be designed to control the positions and the widths of the transmission peaks, opening up the possibility of building new photonic devices such as high quality band-pass filters.

  20. Antiangiogenic and anticancer molecules in cartilage.

    PubMed

    Patra, Debabrata; Sandell, Linda J

    2012-01-19

    Cartilage is one of the very few naturally occurring avascular tissues where lack of angiogenesis is the guiding principle for its structure and function. This has attracted investigators who have sought to understand the biochemical basis for its avascular nature, hypothesising that it could be used in designing therapies for treating cancer and related malignancies in humans through antiangiogenic applications. Cartilage encompasses primarily a specialised extracellular matrix synthesised by chondrocytes that is both complex and unique as a result of the myriad molecules of which it is composed. Of these components, a few such as thrombospondin-1, chondromodulin-1, the type XVIII-derived endostatin, SPARC (secreted protein acidic and rich in cysteine) and the type II collagen-derived N-terminal propeptide (PIIBNP) have demonstrated antiangiogenic or antitumour properties in vitro and in vivo preclinical trials that involve several complicated mechanisms that are not completely understood. Thrombospondin-1, endostatin and the shark-cartilage-derived Neovastat preparation have also been investigated in human clinical trials to treat several different kinds of cancers, where, despite the tremendous success seen in preclinical trials, these molecules are yet to show success as anticancer agents. This review summarises the current state-of-the-art antiangiogenic characterisation of these molecules, highlights their most promising aspects and evaluates the future of these molecules in antiangiogenic applications.

  1. Functional group dependent dissociative electron attachment to simple organic molecules

    NASA Astrophysics Data System (ADS)

    Prabhudesai, Vaibhav S.; Nandi, Dhananjay; Kelkar, Aditya H.; Krishnakumar, E.

    2008-04-01

    Dissociative electron attachment (DEA) cross sections for simple organic molecules, namely, acetic acid, propanoic acid, methanol, ethanol, and n-propyl amine are measured in a crossed beam experiment. We find that the H- ion formation is the dominant channel of DEA for these molecules and takes place at relatively higher energies (>4eV) through the core excited resonances. Comparison of the cross sections of the H- channel from these molecules with those from NH3, H2O, and CH4 shows the presence of functional group dependence in the DEA process. We analyze this new phenomenon in the context of the results reported on other organic molecules. This discovery of functional group dependence has important implications such as control in electron induced chemistry and understanding radiation induced damage in biological systems.

  2. Coordinative alignment of molecules in chiral metal-organic frameworks.

    PubMed

    Lee, Seungkyu; Kapustin, Eugene A; Yaghi, Omar M

    2016-08-19

    A chiral metal-organic framework, MOF-520, was used to coordinatively bind and align molecules of varying size, complexity, and functionality. The reduced motional degrees of freedom obtained with this coordinative alignment method allowed the structures of molecules to be determined by single-crystal x-ray diffraction techniques. The chirality of the MOF backbone also served as a reference in the structure solution for an unambiguous assignment of the absolute configuration of bound molecules. Sixteen molecules representing four common functional groups (primary alcohol, phenol, vicinal diol, and carboxylic acid), ranging in complexity from methanol to plant hormones (gibberellins, containing eight stereocenters), were crystallized and had their precise structure determined. We distinguished single and double bonds in gibberellins, and we enantioselectively crystallized racemic jasmonic acid, whose absolute configuration had only been inferred from derivatives.

  3. Cellular Site in Bacillus subtilis of a Nuclease Which Preferentially Degrades Single-Stranded Nucleic Acids

    PubMed Central

    Birnboim, H. C.

    1966-01-01

    Birnboim, H. C. (Albert Einstein College of Medicine, New York, N.Y.). Cellular site in Bacillus subtilis of a nuclease which preferentially degrades single-stranded nucleic acids. J. Bacteriol. 91:1004–1011. 1966.—A nuclease, identified by a marked preference for single-stranded nucleic acids, has been demonstrated in extracts of Bacillus subtilis. The enzyme was associated with the cell wall-membrane fraction of mechanically disrupted cells and was released from cells which had been converted to protoplasts by lysozyme. The nuclease activity prepared by the latter procedure was found to be activated and solubilized by treatment with trypsin. The enzyme had about 2% activity on native deoxyribonucleic acid (DNA) as compared with denatured DNA. By use of CsCl analytical density gradient ultracentrifugation, this preparation was shown to degrade denatured DNA selectively in mixtures of native and denatured DNA. PMID:4956329

  4. First molecules, biological chirality, origin(s) of life.

    PubMed

    Caglioti, Luciano; Micskei, Károly; Pályi, Gyula

    2011-01-01

    Origin(s) of biological chirality appear(s) to be intimately connected to origin(s) of life. Prebiotic evolution toward these important turning points can be traced back to single chiral molecules. These can be small (monomeric) units as amino acids or monosaccharides or oligomers as oligo-RNA type molecules. Earlier speculations about these two kinds of entries to biological chirality are critically reviewed.

  5. Computer display and manipulation of biological molecules

    NASA Technical Reports Server (NTRS)

    Coeckelenbergh, Y.; Macelroy, R. D.; Hart, J.; Rein, R.

    1978-01-01

    This paper describes a computer model that was designed to investigate the conformation of molecules, macromolecules and subsequent complexes. Utilizing an advanced 3-D dynamic computer display system, the model is sufficiently versatile to accommodate a large variety of molecular input and to generate data for multiple purposes such as visual representation of conformational changes, and calculation of conformation and interaction energy. Molecules can be built on the basis of several levels of information. These include the specification of atomic coordinates and connectivities and the grouping of building blocks and duplicated substructures using symmetry rules found in crystals and polymers such as proteins and nucleic acids. Called AIMS (Ames Interactive Molecular modeling System), the model is now being used to study pre-biotic molecular evolution toward life.

  6. 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.

  7. Electron-excited molecule interactions

    SciTech Connect

    Christophorou, L.G. Tennessee Univ., Knoxville, TN . Dept. of Physics)

    1991-01-01

    In this paper the limited but significant knowledge to date on electron scattering from vibrationally/rotationally excited molecules and electron scattering from and electron impact ionization of electronically excited molecules is briefly summarized and discussed. The profound effects of the internal energy content of a molecule on its electron attachment properties are highlighted focusing in particular on electron attachment to vibrationally/rotationally and to electronically excited molecules. The limited knowledge to date on electron-excited molecule interactions clearly shows that the cross sections for certain electron-molecule collision processes can be very different from those involving ground state molecules. For example, optically enhanced electron attachment studies have shown that electron attachment to electronically excited molecules can occur with cross sections 10{sup 6} to 10{sup 7} times larger compared to ground state molecules. The study of electron-excited molecule interactions offers many experimental and theoretical challenges and opportunities and is both of fundamental and technological significance. 54 refs., 15 figs.

  8. Computer systems for annotation of single molecule fragments

    DOEpatents

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  9. Micro injector sample delivery system for charged molecules

    DOEpatents

    Davidson, James C.; Balch, Joseph W.

    1999-11-09

    A micro injector sample delivery system for charged molecules. The injector is used for collecting and delivering controlled amounts of charged molecule samples for subsequent analysis. The injector delivery system can be scaled to large numbers (>96) for sample delivery to massively parallel high throughput analysis systems. The essence of the injector system is an electric field controllable loading tip including a section of porous material. By applying the appropriate polarity bias potential to the injector tip, charged molecules will migrate into porous material, and by reversing the polarity bias potential the molecules are ejected or forced away from the tip. The invention has application for uptake of charged biological molecules (e.g. proteins, nucleic acids, polymers, etc.) for delivery to analytical systems, and can be used in automated sample delivery systems.

  10. Electrochromic Graphene Molecules

    DOE PAGES

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were foundmore » to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.« less

  11. Single molecule tracking

    DOEpatents

    Shera, E.B.

    1987-10-07

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photons are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions. 3 figs.

  12. Single molecule tracking

    DOEpatents

    Shera, E. Brooks

    1988-01-01

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photones are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions.

  13. Atmospheric trace molecule spectroscopy

    NASA Technical Reports Server (NTRS)

    Farmer, C. B.

    1982-01-01

    The Spacelab investigation entitled Atmospheric Trace Molecule Spectroscopy (ATMOS) is designed to obtain fundamental information related to the chemistry and physics of the Earth's upper atmosphere using the techniques of infrared absorption spectroscopy. There are two principal objectives to be met. The first is the determination, on a global scale, of the compositional structure of the upper atmosphere and its spatial variability. The establishment of this variability represents the first step toward determining the characteristic residence times for the upper atmospheric constituents; the magnitudes of their sources and sinks; and, ultimately, an understanding of their effects on the stability of the stratosphere. The second objective is to provide the high-resolution, calibrated spectral information which is essential for the detailed design of advanced instrumentation for subsequent global monitoring of specific species found to be critical to atmospheric stability. This information will be disseminated in the form of a three dimensional atlas of solar absorption spectra obtained over a range of latitudes, longitudes, and altitudes.

  14. Evaluation of genotoxicity testing of FDA approved large molecule therapeutics.

    PubMed

    Sawant, Satin G; Fielden, Mark R; Black, Kurt A

    2014-10-01

    Large molecule therapeutics (MW>1000daltons) are not expected to enter the cell and thus have reduced potential to interact directly with DNA or related physiological processes. Genotoxicity studies are therefore not relevant and typically not required for large molecule therapeutic candidates. Regulatory guidance supports this approach; however there are examples of marketed large molecule therapeutics where sponsors have conducted genotoxicity studies. A retrospective analysis was performed on genotoxicity studies of United States FDA approved large molecule therapeutics since 1998 identified through the Drugs@FDA website. This information was used to provide a data-driven rationale for genotoxicity evaluations of large molecule therapeutics. Fifty-three of the 99 therapeutics identified were tested for genotoxic potential. None of the therapeutics tested showed a positive outcome in any study except the peptide glucagon (GlucaGen®) showing equivocal in vitro results, as stated in the product labeling. Scientific rationale and data from this review indicate that testing of a majority of large molecule modalities do not add value to risk assessment and support current regulatory guidance. Similarly, the data do not support testing of peptides containing only natural amino acids. Peptides containing non-natural amino acids and small molecules in conjugated products may need to be tested.

  15. Supramolecular Photochemistry in Solution and on Surfaces: Encapsulation and Dynamics of Guest Molecules and Communication between Encapsulated and Free Molecules.

    PubMed

    Ramamurthy, V; Jockusch, Steffen; Porel, Mintu

    2015-05-26

    Supramolecular assemblies that help to preorganize reactant molecules have played an important role in the development of concepts related to the control of excited-state processes. This has led to a persistent search for newer supramolecular systems (hosts), and this review briefly presents our work with octa acid (OA) to a host to control excited-state processes of organic molecules. Octa acid, a water-soluble host, forms 1:1, 2:1, and 2:2 (host-guest) complexes with various organic molecules. A majority of the guest molecules are enclosed within a capsule made up of two molecules of OA whereas OA by itself remains as a monomer or aggregates. Luminescence and (1)H NMR spectroscopy help to characterize the structure and dynamics of these host-guest complexes. The guest molecule as well as the host-guest complex as a whole undergoes various types of motion, suggesting that the guests possess freedom inside the confined space of the octa acid capsule. In addition, the confined guests are not isolated but are able to communicate (energy, electron, and spin) with molecules present closer to the capsule. The host-guest complexes are stable even on solid surfaces such as silica, clay, α-Zr phosphate, TiO2, and gold nanoparticles. This opens up new opportunities to explore the interaction between confined guests and active surfaces of TiO2 and gold nanoparticles. In addition, this allows the possibility of performing energy and electron transfer between organic molecules that do not adsorb on inert surfaces of silica, clay, or α-Zr phosphate. The results summarized here, in addition to providing a fundamental understanding of the behavior of molecules in a confined space provided by the host OA, are likely to have a long-range effect on the capture and release of solar energy.

  16. Chiral Sensitivity in Electron-Molecule Interactions

    NASA Astrophysics Data System (ADS)

    Dreiling, Joan

    2015-09-01

    All molecular forms of life possess a chiral asymmetry, with amino acids and sugars found respectively in L- and D-enantiomers only. The primordial origin of this enantiomeric excess is unknown. One possible explanation is given by the Vester- Ulbricht hypothesis, which suggests that left-handed electrons present in beta-radiation, produced by parity-violating weak decays, interacted with biological precursors and preferentially destroyed one of the two enantiomers. Experimental tests of this idea have thus far yielded inconclusive results. We show direct evidence for chirally-dependent bond breaking through a dissociative electron attachment (DEA) reaction when spin-polarized electrons are incident on gas-phase chiral molecules. This provides unambiguous evidence for a well-defined, chirally-sensitive destructive molecular process and, as such, circumstantial evidence for the Vester-Ulbricht hypothesis. I will also present the results of our systematic study of the DEA asymmetry for different chiral halocamphor molecules. Three halocamphor molecules were investigated: 3-bromocamphor (C10H15BrO), 3-iodocamphor(C10H15IO), and 10-iodocamphor. The DEA asymmetries collected for bromocamphor and iodocamphor are qualitatively different, suggesting that the atomic number of the heaviest atom in the molecule plays a crucial role in the asymmetric interactions. The DEA asymmetry data for 3- and 10-iodocamphor have the same qualitative behavior, but the 10-iodocamphor asymmetry is about twice as large at the lowest energies investigated, so the location of the heavy atom in the camphor molecule also affects the asymmetries. This work was performed at the University of Nebraska-Lincoln. This project is funded by NSF Grant PHY-1206067.

  17. Diverse locations of amino acids in HLA-DR beta chains involved in polymorphic antibody binding epitopes on DR(alpha, beta 1*0101), DR(alpha, beta 1*1101), and DR(alpha,beta 3*0202) molecules.

    PubMed

    Fu, X T; Klohe, E; Alber, C; Yu, W Y; Ferrara, G B; Pistillo, M P; Ballas, M; Karr, R W

    1992-03-01

    In a previous study, we used transfectants expressing hybrid HLA-DR(beta 1*0403)/DR(beta 1*0701) chains to map sequences involved in polymorphic antibody binding epitopes on DR(alpha, beta 1*0403) or DR(alpha, beta 1*0701) molecules. Amino acids 1-40 of the beta 1 domain were found to make the major contributions to most of the antibody binding epitopes studied. To begin to localize sequences that contribute to polymorphic antibody epitopes on DR(alpha,beta 1*0101), DR(alpha,beta 1*1101) and DR(alpha,beta 3*0202) molecules, we used indirect immunofluorescence and flow cytometry to assess the binding of mAb to transfectants expressing hybrid DR(beta 1*0101)/DR(beta 1*1101) or DR(beta 1*1101)/DR(beta 3*0202) chains that divide the DR beta chain into three segments: amino acids 1-40, 41-97, and the beta 2 domain. The results indicate that amino acids 41-97 of the beta 1 domain on DR(beta 1*0101), DR(beta 1*1101), or DR(beta 3*0202) are critical in most of the epitopes, including those recognized by human antibodies MP4 and MP12, and mouse mAb GS88.2, I-LR1, 21r5, and 7.3.19.1, whereas amino acids 1-40 of DR(beta 1*1101) are critical in the epitope recognized by the MCS-7 mAb, and both segments 1-40 and 41-97 of DR(beta 1*1101) are important in the epitopes recognized by the I-LR2 and UL-52 mAbs. Based on these data and comparison of DR beta allelic protein sequences, the residues that may play critical roles in these antibody binding epitopes are predicted.

  18. Proteins.

    ERIC Educational Resources Information Center

    Doolittle, Russell F.

    1985-01-01

    Examines proteins which give rise to structure and, by virtue of selective binding to other molecules, make genes. Binding sites, amino acids, protein evolution, and molecular paleontology are discussed. Work with encoding segments of deoxyribonucleic acid (exons) and noncoding stretches (introns) provides new information for hypotheses. (DH)

  19. Geochemical Origin of Biological Molecules

    NASA Astrophysics Data System (ADS)

    Bassez, Marie-Paule

    2013-04-01

    A model for the geochemical origin of biological molecules is presented. Rocks such as peridotites and basalts, which contain ferromagnesian minerals, evolve in the presence of water. Their hydrolysis is an exothermic reaction which generates heat and a release of H2 and of minerals with modified structures. The hydrogen reacts with the CO2 embedded inside the rock or with the CO2 of the environment to form CO in an hydrothermal process. With the N2 of the environment, and with an activation source arising from cosmic radiation, ferromagnesian rocks might evolve towards the abiotic formation of biological molecules, such as peptide like macromolecules which produce amino acids after acid hydrolysis. The reactions concerned are described. The production of hydrothermal CO is discussed in geological sites containing ferromagnesian silicate minerals and the low intensity of the Earth's magnetic field during Paleoarchaean Era is also discussed. It is concluded that excitation sources arising from cosmic radiation were much more abundant during Paleoarchaean Era and that macromolecular structures of biological relevance might consequently form during Archaean Eon, as a product of the chemical evolution of the rocks and of their mineral contents. This synthesis of abiotically formed biological molecules is consecutively discussed for meteorites and other planets such as Mars. This model for the geochemical origin of biological molecules has first been proposed in 2008 in the context of reactions involving catalysers such as kaolinite [Bassez 2008a] and then presented in conferences and articles [Bassez 2008b, 2009, 2012; Bassez et al. 2009a to 2012b]. BASSEZ M.P. 2008a Synthèse prébiotique dans les conditions hydrothermales, CNRIUT'08, Lyon 29-30/05/2008, Conf. and open access article:http://liris.cnrs.fr/~cnriut08/actes/ 29 mai 11h-12h40. BASSEZ M.P. 2008b Prebiotic synthesis under hydrothermal conditions, ISSOL'08, P2-6, Firenze-Italy, 24-29/08/2008. Poster at the

  20. Vibrational autoionization in polyatomic molecules.

    PubMed

    Pratt, S T

    2005-01-01

    The vibrationally autoionizing Rydberg states of small polyatomic molecules provide a fascinating laboratory in which to study fundamental nonadiabatic processes. In this review, recent results on the vibrational mode dependence of vibrational autoionization are discussed. In general, autoionization rates depend strongly on the character of the normal mode driving the process and on the electronic character of the Rydberg electron. Although quantitative calculations based on multichannel quantum defect theory are available for some polyatomic molecules, including H3, only qualitative information exists for most molecules. This review shows how qualitative information, such as Walsh diagrams along different normal coordinates of the molecule, can provide insight into the vibrational autoionization rates.