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Sample records for acid molecules comprising

  1. Method and apparatus for passive optical dosimeter comprising caged dye molecules

    DOEpatents

    Sandison, David R.

    2001-07-03

    A new class of ultraviolet dosimeters is made possible by exposing caged dye molecules, which generate a dye molecule on exposure to ultraviolet radiation, to an exterior environment. Applications include sunburn monitors, characterizing the UV exposure history of UV-sensitive materials, especially including structural plastics, and use in disposable `one-use` optical equipment, especially medical devices.

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

    DOEpatents

    Croteau, Rodney Bruce; Burke, Charles Cullen

    2008-06-24

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

  3. Instability of Amide Bond Comprising the 2-Aminotropone Moiety: Cleavable under Mild Acidic Conditions.

    PubMed

    Balachandra, Chenikkayala; Sharma, Nagendra K

    2015-08-21

    An unusual hydrolysis/solvolysis of the classical acyclic amide bond, derived from N-troponylaminoethylglycine (Traeg) and α-amino acids, is described under mild acidic conditions. The reactivity of this amide bond is possibly owed to the protonation of the troponyl carbonyl functional group. The results suggest that the Traeg amino acid is a potential candidate for protecting and caging of the amine functional group of bioactive molecules via a cleavable amide bond.

  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

    2006-06-06

    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.

  6. 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.

  7. Sugar amino acids in designing new molecules.

    PubMed

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

    2005-03-01

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

  8. 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.

  9. 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.

  10. Acid Strength and Bifunctional Catalytic Behavior of Alloys Comprised of Noble Metals and Oxophilic Metal Promoters

    SciTech Connect

    Hibbitts, David D.; Tan, Qiaohua; Neurock, Matthew

    2014-06-01

    The promotion of metal catalysts with partially oxidized oxophilic MOx species, such as ReOx-promoted Rh, has been demonstrated to produce Brønsted acid sites that can promote hydrogenolysis of oxygenate intermediates such as those found in biomass-derived species. A wide variety of alloy compositions and structures are examined in this work to investigate strongly acidic promoters by using DFT-calculated deprotonation energies (DPE) as a measure of acid strength. Sites with the highest acid strength had DPE less than 1100 kJ mol-1, similar to DPE values of heteropolyacids or acid-containing zeolites, and were found on alloys composed of an oxophilic metal (such as Re or W) with a noble metal (such as Rh or Pt). NH3 adsorbs more strongly to sites with increasing acid strength and the activation barriers for acid-catalyzed ring opening of a furan ring decrease with increasing acid strength, which was also shown to be stronger for OH acid sites bound to multiple oxophilic metal atoms in a three-fold configuration rather than OH sites adsorbed in an atop configuration on one oxophilic metal, indicating that small MOx clusters may yield sites with the highest acid strength.

  11. Topical Formulation Comprising Fatty Acid Extract from Cod Liver Oil: Development, Evaluation and Stability Studies.

    PubMed

    Ilievska, Biljana; Loftsson, Thorsteinn; Hjalmarsdottir, Martha Asdis; Asgrimsdottir, Gudrun Marta

    2016-06-01

    The purpose of this study was to develop a pharmaceutical formulation containing fatty acid extract rich in free omega-3 fatty acids such as eicosapentaenoic acid and docosahexaenoic acid for topical use. Although the health benefits of cod liver oil and other fish oils taken orally as a dietary supplement have been acknowledged and exploited, it is clear that their use can be extended further to cover their antibacterial properties. In vitro evaluation showed that 20% (v/v) fatty acid extract exhibits good activity against strains of the Gram-positive bacteria Staphylococcus aureus, Enterococcus faecalis, Streptoccoccus pyogenes and Streptoccoccus pneumonia. Therefore, free polyunsaturated fatty acids from cod liver oil or other fish oils can be used as safe and natural antibacterial agents. In this study, ointment compositions containing free fatty acids as active antibacterial agents were prepared by using various natural waxes and characterized. The effects of different waxes, such as carnauba wax, ozokerite wax, laurel wax, beeswax, rice bran wax, candelilla wax and microcrystalline wax, in the concentration range of 1% to 5% (w/w) on the ointment texture, consistency and stability were evaluated. The results showed significant variations in texture, sensory and rheological profiles. This was attributed to the wax's nature and chain composition. Microcrystalline wax gave the best results but laurel wax, beeswax and rice bran wax exhibited excellent texturing, similar sensory profiles and well-balanced rheological properties.

  12. Topical Formulation Comprising Fatty Acid Extract from Cod Liver Oil: Development, Evaluation and Stability Studies

    PubMed Central

    Ilievska, Biljana; Loftsson, Thorsteinn; Hjalmarsdottir, Martha Asdis; Asgrimsdottir, Gudrun Marta

    2016-01-01

    The purpose of this study was to develop a pharmaceutical formulation containing fatty acid extract rich in free omega-3 fatty acids such as eicosapentaenoic acid and docosahexaenoic acid for topical use. Although the health benefits of cod liver oil and other fish oils taken orally as a dietary supplement have been acknowledged and exploited, it is clear that their use can be extended further to cover their antibacterial properties. In vitro evaluation showed that 20% (v/v) fatty acid extract exhibits good activity against strains of the Gram-positive bacteria Staphylococcus aureus, Enterococcus faecalis, Streptoccoccus pyogenes and Streptoccoccus pneumonia. Therefore, free polyunsaturated fatty acids from cod liver oil or other fish oils can be used as safe and natural antibacterial agents. In this study, ointment compositions containing free fatty acids as active antibacterial agents were prepared by using various natural waxes and characterized. The effects of different waxes, such as carnauba wax, ozokerite wax, laurel wax, beeswax, rice bran wax, candelilla wax and microcrystalline wax, in the concentration range of 1% to 5% (w/w) on the ointment texture, consistency and stability were evaluated. The results showed significant variations in texture, sensory and rheological profiles. This was attributed to the wax’s nature and chain composition. Microcrystalline wax gave the best results but laurel wax, beeswax and rice bran wax exhibited excellent texturing, similar sensory profiles and well-balanced rheological properties. PMID:27258290

  13. Nucleic acids encoding phloem small RNA-binding proteins and transgenic plants comprising them

    DOEpatents

    Lucas, William J.; Yoo, Byung-Chun; Lough, Tony J.; Varkonyi-Gasic, Erika

    2007-03-13

    The present invention provides a polynucleotide sequence encoding a component of the protein machinery involved in small RNA trafficking, Cucurbita maxima phloem small RNA-binding protein (CmPSRB 1), and the corresponding polypeptide sequence. The invention also provides genetic constructs and transgenic plants comprising the polynucleotide sequence encoding a phloem small RNA-binding protein to alter (e.g., prevent, reduce or elevate) non-cell autonomous signaling events in the plants involving small RNA metabolism. These signaling events are involved in a broad spectrum of plant physiological and biochemical processes, including, for example, systemic resistance to pathogens, responses to environmental stresses, e.g., heat, drought, salinity, and systemic gene silencing (e.g., viral infections).

  14. Electrochemical method for producing a biodiesel mixture comprising fatty acid alkyl esters and glycerol

    DOEpatents

    Lin, YuPo J; St. Martin, Edward J

    2013-08-13

    The present invention relates to an integrated method and system for the simultaneous production of biodiesel from free fatty acids (via esterification) and from triglycerides (via transesterification) within the same reaction chamber. More specifically, one preferred embodiment of the invention relates to a method and system for the production of biodiesel using an electrodeionization stack, wherein an ion exchange resin matrix acts as a heterogeneous catalyst for simultaneous esterification and transesterification reactions between a feedstock and a lower alcohol to produce biodiesel, wherein the feedstock contains significant levels of free fatty acid. In addition, because of the use of a heterogeneous catalyst, the glycerol and biodiesel have much lower salt concentrations than raw biodiesel produced by conventional transesterification processes. The present invention makes it much easier to purify glycerol and biodiesel.

  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. Model of the initiation of signal transduction by ligands in a cell culture: Simulation of molecules near a plane membrane comprising receptors

    NASA Astrophysics Data System (ADS)

    Plante, Ianik; Cucinotta, Francis A.

    2011-11-01

    Cell communication is a key mechanism in tissue responses to radiation. Several molecules are implicated in radiation-induced signaling between cells, but their contributions to radiation risk are poorly understood. Meanwhile, Green's functions for diffusion-influenced reactions have appeared in the literature, which are applied to describe the diffusion of molecules near a plane membrane comprising bound receptors with the possibility of reversible binding of a ligand and activation of signal transduction proteins by the ligand-receptor complex. We have developed Brownian dynamics algorithms to simulate particle histories in this system which can accurately reproduce the theoretical distribution of distances of a ligand from the membrane, the number of reversibly bound particles, and the number of receptor complexes activating signaling proteins as a function of time, regardless of the number of time steps used for the simulation. These simulations will be of great importance to model interactions at low doses where stochastic effects induced by a small number of molecules or interactions come into play.

  17. 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.

  18. 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.

  19. 2-hydroxyoleic acid: a new hypotensive molecule.

    PubMed

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

    2004-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-04-01

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

  1. 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.

  2. Analysis of single nucleic acid molecules with protein nanopores

    PubMed Central

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

    2011-01-01

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

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

    SciTech Connect

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

    2009-09-10

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

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

    PubMed

    Kato, Haruhisa; Nakamura, Ayako; Horie, Masanori

    2015-01-01

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

  5. Acid Fluid-Rock Interactions with Shales Comprising Unconventional Hydrocarbon Reservoirs and with Shale Capping Carbon Storage Reservoirs: Experimental Insights

    NASA Astrophysics Data System (ADS)

    Kaszuba, J. P.; Bratcher, J.; Marcon, V.; Herz-Thyhsen, R.

    2015-12-01

    Injection of HCl is often a first stage in the hydraulic fracturing process. These acidic fluids react with marls or shales in unconventional reservoirs, reactions generally comparable to reaction between shale caprocks and acidic, carbonated formation waters in a carbon storage reservoir. Hydrothermal experiments examine acid fluid-rock interaction with 1) an unconventional shale reservoir and 2) a model shale capping a carbon storage reservoir. In the former, unconventional reservoir rock and hydraulic fracturing fluid possessing a range of ionic strengths (I = 0.01, 0.15) and initial pH values (2.5 and 7.3) reacted at 115°C and 35 MPa for 28 days. In the latter, a model carbon storage reservoir (Fe-rich dolomite), shale caprock (illite), and shale-reservoir mixture each reacted with formation water (I = 0.1 and pH 6.3) at 160°C and 25 MPa for ~15 days. These three experiments were subsequently injected with sufficient CO2 to maintain CO2 saturation in the water and allowed to react for ~40 additional days. Acidic frac fluid was rapidly buffered (from pH 2.5 to 6.2 after 38 hrs) by reaction with reservoir rock whereas the pH of near-neutral frac fluid decreased (from 7.3 to 6.9) after 47 hrs. Carbonate dissolution released Ca and Sr into solution and feldspar dissolution released SiO2 and Li; the extent of reaction was greater in the experiment containing acidic frac fluid. All three carbon storage experiments displayed a similar pH decrease of 1.5 units after the addition of CO2. The pH remained low for the duration of the experiments because the immiscible supercritical CO2 phase provided an infinite reservoir of carbonic acid that could not be consumed by reaction with the rock. In all three experiments, Ca, Fe, Mg, Mn and SO4 increase with injection, but slowly decline through termination of the experiments. This trend suggests initial dissolution followed by re-precipitation of carbonates, which can be seen in modeling and SEM results. New clay minerals

  6. A review of the developments of multi-purpose primers and adhesives comprising novel dithiooctanoate monomers and phosphonic acid monomers.

    PubMed

    Ikemura, Kunio; Endo, Takeshi; Kadoma, Yoshinori

    2012-02-01

    This paper reviews the developments of dithiooctanoate monomers and acidic adhesive monomers, and their roles in multi-purpose primers and adhesives in promoting adhesion to multiple substrate materials. Novel dithiooctanoate monomers exhibited excellent bonding to precious metals and alloys when compared against conventional sulfur-containing monomers. Newly developed phosphonic acid monomers, endowed with a water-soluble nature, enabled sufficient demineralization of dental hard tissues and thus improved bonding to both ground enamel and dentin. The optimal combination for bonding to dental hard tissues and precious and non-precious metals and alloys was 5.0 wt% 10-methacryloyloxydecyl 6,8-dithiooctanoate (10-MDDT) and 1.0 wt% 6-methacryloyloxyhexyl phosphonoacetate (6-MHPA). For bonding to dental porcelain, alumina, zirconia, and gold (Au) alloy, a ternary combination of silane coupling agent, acidic adhesive monomers, and dithiooctanoate monomers seemed promising. The latest development was a single-bottle, multi-purpose, self-etching adhesive which contained only acidic adhesive monomers and dithiooctanoate monomers but which produced strong adhesion to ground enamel and dentin, sandblasted zirconia, and Au alloy.

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

    PubMed

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

    2002-02-01

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

  8. The world of beta- and gamma-peptides comprised of homologated proteinogenic amino acids and other components.

    PubMed

    Seebach, Dieter; Beck, Albert K; Bierbaum, Daniel J

    2004-08-01

    The origins of our nearly ten-year research program of chemical and biological investigations into peptides based on homologated proteinogenic amino acids are described. The road from the biopolymer poly[ethyl (R)-3-hydroxybutanoate] to the beta-peptides was primarily a step from organic synthesis methodology (the preparation of enantiomerically pure compounds (EPCs)) to supramolecular chemistry (higher-order structures maintained through non-covalent interactions). The performing of biochemical and biological tests on the beta- and gamma-peptides, which differ from natural peptides/proteins by a single or two additional CH(2) groups per amino acid, then led into bioorganic chemistry and medicinal chemistry. The individual chapters of this review article begin with descriptions of work on beta-amino acids, beta-peptides, and polymers (Nylon-3) that dates back to the 1960s, even to the times of Emil Fischer, but did not yield insights into structures or biological properties. The numerous, often highly physiologically active, or even toxic, natural products containing beta- and gamma-amino acid moieties are then presented. Chapters on the preparation of homologated amino acids with proteinogenic side chains, their coupling to provide the corresponding peptides, both in solution (including thioligation) and on the solid phase, their isolation by preparative HPLC, and their characterization by mass spectrometry (HR-MS and MS sequencing) follow. After that, their structures, predominantly determined by NMR spectroscopy in methanolic solution, are described: helices, pleated sheets, and turns, together with stack-, crankshaft-, paddlewheel-, and staircase-like patterns. The presence of the additional C--C bonds in the backbones of the new peptides did not give rise to a chaotic increase in their secondary structures as many protein specialists might have expected: while there are indeed more structure types than are observed in the alpha-peptide realm - three different

  9. Effective atomic numbers and electron densities of bacteriorhodopsin and its comprising amino acids in the energy range 1 keV-100 GeV

    NASA Astrophysics Data System (ADS)

    Ahmadi, Morteza; Lunscher, Nolan; Yeow, John T. W.

    2013-04-01

    Recently, there has been an interest in fabrication of X-ray sensors based on bacteriorhodopsin, a proton pump protein in cell membrane of Halobacterium salinarium. Therefore, a better understanding of interaction of X-ray photons with bacteriorhodopsin is required. We use WinXCom program to calculate the mass attenuation coefficient of bacteriorhodopsin and its comprising amino acids for photon energies from 1 keV to 100 GeV. These amino acids include alanine, arginine, asparagine, aspartic acid, glutamine, glutamic acid, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine, Asx1, Asx2, Glx1 and Glx2. We then use that data to calculate effective atomic number and electron densities for the same range of energy. We also emphasize on two ranges of energies (10-200 keV and 1-20 MeV) in which X-ray imaging and radiotherapy machines work.

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

    NASA Astrophysics Data System (ADS)

    Eustis, Soren Newman

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

  11. In Vivo Evaluation of Nerve Guidance Conduits Comprised of a Salicylic Acid-based Poly(anhydride-ester) Blend

    NASA Astrophysics Data System (ADS)

    Lee, Yong Soo

    Unlike the central nervous system, peripheral nervous system can regenerate from injury. However, without surgical intervention, the results are often poor. Autologous nerve grafting is the golden standard for repairing peripheral nerve injury; but limited donor availability and donor site morbidity led researchers to seek alternative methods. Among the many alternative treatment options, synthetic nerve guidance conduits (NGCs) have been most actively developed. The goal of NGCs is to serve as a physical scaffold that aids the axonal regeneration process while preventing scar tissue formation that interferes with regeneration. Biocompatible and biodegradable NGCs would provide additional benefits: minimize foreign body reaction and avoid secondary surgeries to remove NGCs. We developed a unique NGC that incorporated the characteristics described above and can release an anti-inflammatory drug, salicylic acid. In this work, in vivo assays were performed to evaluate NGCs fabricated from a poly(anhydride-ester) blend. To further assist in the regeneration process, bovine native collagen type I hydrogel were inserted into the NGCs lumen which was then implanted in femoral nerve of mice for up to 16 weeks. These studies demonstrated in vivo biodegradability, biocompatibility, and axonal regeneration following an injury to the peripheral nerve. These studies provide greater insights into the importance of designing NGCs and how they aid in regeneration and functional recovery of subjects.

  12. Effect of chemical composition on corneal cellular response to photopolymerized materials comprising 2-hydroxyethyl methacrylate and acrylic acid.

    PubMed

    Lai, Jui-Yang

    2013-10-01

    Characterization of corneal cellular response to hydrogel materials is an important issue in ophthalmic applications. In this study, we aimed to investigate the relationship between the feed composition of 2-hydroxyethyl methacrylate (HEMA)/acrylic acid (AAc) and material compatibility towards corneal stromal and endothelial cells. The monomer solutions of HEMA and AAc were mixed at varying volume ratios of 92:0, 87:5, 82:10, 77:15, and 72:20, and were subjected to UV irradiation. Results of electrokinetic measurements showed that an increase in absolute zeta potential of photopolymerized membranes is observed with increasing the volume ratios of AAc/HEMA. Following 4 days of incubation with various hydrogels, the primary rabbit corneal stromal and endothelial cell cultures were examined for viability, proliferation, and pro-inflammatory gene expression. The samples prepared from the solution mixture containing 0-10 vol.% AAc displayed good cytocompatibility. However, with increasing volume ratio of AAc and HEMA from 15:77 to 20:72, the decreased viability, inhibited proliferation, and stimulated inflammation were noted in both cell types, probably due to the stronger charge-charge interactions. On the other hand, the ionic pump function of corneal endothelial cells exposed to photopolymerized membranes was examined by analyzing the Na(+),K(+)-ATPase alpha 1 subunit (ATP1A1) expression level. The presence of material samples having higher anionic charge density (i.e., zeta potential of -38 to -56 mV) may lead to abnormal transmembrane transport. It is concluded that the chemical composition of HEMA/AAc has an important influence on the corneal stromal and endothelial cell responses to polymeric biomaterials. PMID:23910267

  13. Effect of chemical composition on corneal tissue response to photopolymerized materials comprising 2-hydroxyethyl methacrylate and acrylic acid.

    PubMed

    Lai, Jui-Yang

    2014-01-01

    The purpose of this work was to investigate the relationship between the feed composition of 2-hydroxyethyl methacrylate (HEMA)/acrylic acid (AAc) and hydrogel material compatibility towards ocular anterior segment tissues, particularly the corneal endothelium. The monomer solutions of HEMA and AAc were mixed at varying volume ratios of 92:0, 87:5, 82:10, 77:15, and 72:20, and were subjected to UV irradiation. Then, the 7-mm-diameter membrane implants made from photopolymerized materials were placed into the ocular anterior chamber for 4days and assessed by biomicroscopic examinations, corneal thickness measurements, and quantitative real-time reverse transcription polymerase chain reaction analyses. The poly(HEMA-co-AAc) implants prepared from the solution mixture containing 0-10vol.% AAc displayed good biocompatibility. However, with increasing volume ratio of AAc and HEMA from 15:77 to 20:72, the enhanced inflammatory response, decreased endothelial cell density, and increased ocular score and corneal thickness were observed, probably due to the influence of surface charge of copolymer membranes. On the other hand, the ionic pump function of corneal endothelium exposed to photopolymerized membranes was examined by analyzing the Na(+),K(+)-ATPase alpha 1 subunit (ATP1A1) expression level. The presence of the implants having higher amount of AAc incorporated in the copolymers (i.e., 15.1 to 24.7μmol) and zeta potential (i.e., -38.6 to -56.5mV) may lead to abnormal transmembrane transport. It is concluded that the chemical composition of HEMA/AAc has an important influence on the corneal tissue responses to polymeric biomaterials. PMID:24268266

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

    PubMed Central

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

    1971-01-01

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

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

    PubMed

    Copple, Bryan L; Li, Tiangang

    2016-02-01

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

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

    PubMed Central

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

    2015-01-01

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

  17. 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.

  18. 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

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

    PubMed

    Scheler, Ott; Glynn, Barry; Kurg, Ants

    2014-05-01

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

  20. 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 ...

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  2. 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.

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

    PubMed

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

    2011-09-01

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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1995-10-01

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

  6. 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.

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

    PubMed

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

    2016-03-01

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

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

    SciTech Connect

    Román-Leshkov, Yuriy; Davis, Mark E.

    2011-09-28

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

  9. Abundances of Triacylglycerol Positional Isomers and Enantiomers Comprised of a Dipalmitoylglycerol Backbone and Short- or Medium-chain Fatty Acids in Bovine Milk Fat.

    PubMed

    Nagai, Toshiharu; Watanabe, Natsuko; Yoshinaga, Kazuaki; Mizobe, Hoyo; Kojima, Koichi; Kuroda, Ikuma; Odanaka, Yuki; Saito, Tadao; Beppu, Fumiaki; Gotoh, Naohiro

    2015-01-01

    Bovine milk fat (BMF) is composed of triacylglycerols (TAG) rich in palmitic acid (P), oleic acid (O), and short-chain or medium-chain fatty acids (SCFAs or MCFAs). The composition and binding positions of the fatty acids on the glycerol backbone determine their physical and nutritional properties. SCFAs and MCFAs are known to characteristically bind to the sn-3 position of the TAGs in BMF; however, there are very few non-destructive analyses of TAG enantiomers binding the fatty acids at this position. We previously reported a method to resolve the enantiomers of TAGs, binding both long-chain saturated fatty acid and unsaturated fatty acid at the sn-1 and 3 positions, in palm oil, fish oil, and marine mammal oil using chiral HPLC. Here, we further developed a method to resolve several TAG enantiomers containing a dipalmitoyl (PP) glycerol backbone and one SCFA (or MCFA) in BMF. We revealed that the predominant TAG structure in BMF was homochiral, such as 1,2-dipalmitoyl-3-butyroyl-sn-glycerol. This is the first quantitative determination of many TAG enantiomers, which bind to a SCFA or MCFA, in BMF was evaluated simultaneously. Furthermore, the results indicated that the amount ratios of the positional isomers and enantiomers of TAGs consisting of a dipalmitoyl (PP) glycerol backbone and SCFA (or MCFA), resembled the whole TAG structures containing the other diacylglycerol backbones consisting of P, O, myristic acid, and/or stearic acid in BMF. PMID:26329769

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

    PubMed

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

    2002-01-01

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

  11. 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.

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

    PubMed

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

    2016-08-01

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

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

    PubMed

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

    2016-12-01

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

  14. 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.

  15. A novel once daily microparticulate dosage form comprising lansoprazole to prevent nocturnal acid breakthrough in the case of gastro-esophageal reflux disease: preparation, pharmacokinetic and pharmacodynamic evaluation.

    PubMed

    Alai, Milind; Lin, Wen Jen

    2013-01-01

    The objective of this study was to formulate and evaluate the lansoprazole (LPZ)-loaded microparticles to prevent nocturnal acid breakthrough in the case of gastro-esophageal reflux disease (GERD). The microparticulate delivery system was prepared by solvent evaporation method using Eudragit RS100 as a matrix polymer followed by enteric coated with Eudragit S100 and hydroxypropyl methylcellulose phthalate HP55 using spray drying method. The enteric coated microparticles were stable in gastric pH condition. In vivo pharmacokinetic and pharmacodynamic studies in male Wistar rats demonstrated that enteric coated microparticles sustained release of LPZ and promoted ulcer healing activity. In other words, the microparticulate dosage form provided effective drug concentration for a longer period as compared to conventional extended release dosage form, and showed sufficient anti-acid secretion activity to treat acid related disorders including the enrichment of nocturnal acid breakthrough event based on a once daily administration.

  16. 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.

  17. Elastomer coated filler and composites thereof comprising at least 60% by weight of a hydrated filler and an elastomer containing an acid substituent

    NASA Technical Reports Server (NTRS)

    Mueller, W. A.; Ingham, J. D.; Reilly, W. W. (Inventor)

    1983-01-01

    The impact resistance of flame retardant composites, especially thermoplastic molding: compounds containing over 60% hydrated mineral filler such as Al(OH)3 or Mg(OH)2 as improved by coating the filler with 1 to 20% of an elastomer. The composite will fail by crazing or shearing rather than by brittle fracture. A well bonded elastomeric interphase resulted by utilizing acidic substituted resins such as ethyl-hexyl acrylate-acrylic acid copolymers which bond to and are cross-linked by the basic filler particles. Further improvement in impact resistance was provided by incorporating 1 to 10% of a resin fiber reinforcement such as polyvinyl alcohol fibers that decompose to yield at least 30% water when heated to decomposition temperature.

  18. 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

  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 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.

  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 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.

  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. 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.

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

    PubMed

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

    2013-06-25

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

  6. Acid catalyzed hydrocarbon conversion processes utilizing a catalyst comprising a group ivb, vb or vib metal oxide on an inorganic refractory oxide support

    SciTech Connect

    Grenoble, D.C.; Kim, C.J.; Murrell, L.L.

    1980-11-11

    It has been discovered and forms the basis of the disclosure that various acid catalyzed hydrocarbon conversion processes such as catalytic cracking of gas oil; xylene isomerization; toluene disproportionation; dealkylation of aromatics; ethylene, butylene , isobutylene, propylene polymerization; olefin isomerization; alcohol dehydration; olefin hydration; alkylation; heavy ends cat cracking, etc. are dramatically improved insofar as percent conversion, and selectivity are concerned by the use of a catalyst selected from the group consisting of the oxides of tungsten, niobium and mixtures thereof, and tungsten or niobium oxides in combination with one or more additional metal oxides selected from the group consisting of tantalum oxide, hafnium oxide, chromium oxide, titanium oxide and zirconium oxide, supported on an inorganic refractory oxide support. These catalysts may be prepared by the methods known in the art, I.E., incipient wetness, impregnation, coprecipitation, etc. Of the metal oxide precursor onto or with the supports followed by conversion into the oxide form. Before use, the metal oxide/support combination is preferably subjected to steaming at elevated temperatures either before introduction into the reactor or in situ in the process reactor. Conventional catalytic cracking catalysts are unstable at the elevated temperatures where the metal oxide/support combinations of the present invention are uniquely stable.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  8. 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.

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

    PubMed

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

    1989-11-01

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

  10. 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.

  11. 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.

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

    SciTech Connect

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

    2014-01-14

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

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

    PubMed

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

    2006-02-23

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

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

    PubMed

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

    2016-08-15

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

  15. 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).

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

    PubMed

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

    2011-07-12

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-08-01

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

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

    PubMed Central

    Colpitts, Che C.

    2014-01-01

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

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

    PubMed

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

    2014-11-01

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

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

    PubMed

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

    2006-03-01

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

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

    PubMed

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

    2015-06-01

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

  3. 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

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

    PubMed

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

    2012-12-21

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

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

    PubMed

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

    2012-11-01

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

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

    PubMed

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

    2016-07-01

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

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

    PubMed

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

    2016-07-01

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

  9. 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.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Josephs, Eric Alan

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

  12. Neutron detectors comprising boron powder

    SciTech Connect

    Wang, Zhehui; Morris, Christopher; Bacon, Jeffrey Darnell; Makela, Mark F; Spaulding, Randy Jay

    2013-05-21

    High-efficiency neutron detector substrate assemblies comprising a first conductive substrate, wherein a first side of the substrate is in direct contact with a first layer of a powder material comprising .sup.10boron, .sup.10boron carbide or combinations thereof, and wherein a conductive material is in proximity to the first layer of powder material; and processes of making said neutron detector substrate assemblies.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Throop, Henry B.

    2011-04-01

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

  15. 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

  16. 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

  17. 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

  18. Metal-polymer composites comprising nanostructures and applications thereof

    DOEpatents

    Wang, Hsing-Lin; Jeon, Sea Ho; Mack, Nathan H.

    2011-08-02

    Metal-polymer composites, and methods of making and use thereof, said composites comprising a thermally-cured dense polyaniline substrate; an acid dopant; and, metal nanostructure deposits wherein the deposits have a morphology dependent upon the acid dopant.

  19. Metal-polymer composites comprising nanostructures and applications thereof

    DOEpatents

    Wang, Hsing-Lin; Jeon, Sea Ho; Mack, Nathan H.

    2012-04-03

    Metal-polymer composites, and methods of making and use thereof, said composites comprising a thermally-cured dense polyaniline substrate; an acid dopant; and, metal nanostructure deposits wherein the deposits have a morphology dependent upon the acid dopant.

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  2. 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.

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

    PubMed

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

    2015-12-16

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

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

    PubMed

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

    2015-12-16

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

  5. Articles comprising ferritic stainless steels

    DOEpatents

    Rakowski, James M.

    2016-06-28

    An article of manufacture comprises a ferritic stainless steel that includes a near-surface region depleted of silicon relative to a remainder of the ferritic stainless steel. The article has a reduced tendency to form an electrically resistive silica layer including silicon derived from the steel when the article is subjected to high temperature oxidizing conditions. The ferritic stainless steel is selected from the group comprising AISI Type 430 stainless steel, AISI Type 439 stainless steel, AISI Type 441 stainless steel, AISI Type 444 stainless steel, and E-BRITE.RTM. alloy, also known as UNS 44627 stainless steel. In certain embodiments, the article of manufacture is a fuel cell interconnect for a solid oxide fuel cell.

  6. 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.

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

    PubMed

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

    2015-08-01

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

  8. Bi-anchoring organic sensitizers of type D-(π-A)2 comprising thiophene-2-acetonitrile as π-spacer and malonic acid as electron acceptor for dye sensitized solar cell applications

    NASA Astrophysics Data System (ADS)

    Reddy, Gachumale Saritha; Ramkumar, Sekar; Asiri, Abdullah M.; Anandan, Sambandam

    2015-06-01

    Two new bi-anchoring organic sensitizers of type D-(π-A)2 comprising the identical π-spacer (thiophene-2-acetonitrile) and electron acceptor (malonic acid) but different aryl amine as electron donors (diphenylamine and carbazole) were synthesized, characterized and fabricated metal free dye-sensitized solar cell devices. The intra molecular charge transfer property and electrochemical property of these dyes were investigated by molecular absorption, emission, cyclic voltammetric experiments and in addition, quantum chemical calculation studies were performed to provide sufficient driving force for the electron injection into the conduction band of TiO2 which leads to efficient charge collection. Among the fabricated devices, carbazole based device exhibits high current conversion efficiency (η = 4.7%) with a short circuit current density (JSC) 15.3 mA/cm2, an open circuit photo voltage (VOC) of 0.59 V and a fill factor of 0.44 under AM 1.5 illumination (85 mW/cm2) compared to diphenylamine based device.

  9. Tricarbonyltechnetium(I) and tricarbonylrhenium(I) complexes of amino acids: crystal and molecular structure of a novel cyclic dimeric Re(CO)3-amino acid complex comprised of the OON donor atom set of the tridentate ligand.

    PubMed

    Nayak, Dipak Kumar; Halder, Kamal Krishna; Baishya, Rinku; Sen, Tuhinadri; Mitra, Partha; Debnath, Mita Chatterjee

    2013-10-01

    Radiolabeled complexes of monoamino polycarboxylic, polyamino monocarboxylic and thiol containing amino acid ligands were prepared from a fac-[(99m)Tc(CO)3(H2O)3](+) precursor.The overall radiochemical yield was 94-98%. The complexes exhibited substantial in vitro and in vivo stability. The corresponding Re(I) complexes of the ligands DAPA, Asp and CysH were prepared and characterized by means of IR, NMR, and MS spectroscopic studies, as well as X-ray crystallography (for those containing D,L-DAPA and D,L-Asp). The rhenium complexes have been structurally correlated with the technetium complexes by means of HPLC studies. The reaction of Re(CO)5Cl with D,L-Asp in presence of triethylamine led to the formation of a new class of cyclic dimeric complexes formed by the OON donor atom set of the tridentate ligands. The amino carboxylate ligand system formed well defined complexes with a fac-[M(CO)3(H2O)3](+) core and shows good promise in (99m)Tc(CO)3 tracer development. PMID:23900487

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

    PubMed

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

    2012-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Gu, Qun; Jin, Helena; Dai, Kun

    2009-01-01

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

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

    PubMed

    Sato, Chihiro; Hane, Masaya; Kitajima, Ken

    2016-08-01

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

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

    PubMed

    Sato, Chihiro; Hane, Masaya; Kitajima, Ken

    2016-08-01

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

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

    PubMed Central

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

    2003-01-01

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

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

    PubMed

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

    2014-01-01

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

  16. 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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

    Schwend, Tyler; Conrad, Gary W.

    2012-01-01

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

  19. 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.

  20. 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

  1. 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.

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

    PubMed

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

    2016-05-20

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

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

    PubMed

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

    2009-06-01

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

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

    PubMed

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

    2009-01-01

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

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

    PubMed

    Yamaguchi, Masayoshi

    2016-10-01

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

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

    PubMed

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

    2007-11-01

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

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

    PubMed

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

    2011-05-25

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

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

    PubMed

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

    2006-09-01

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

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

    PubMed

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

    2012-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-11-01

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

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

    PubMed

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

    2012-12-01

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

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

    PubMed

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

    2016-07-01

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

  13. 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.

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

    PubMed

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

    2015-11-01

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

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

    PubMed

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

    2011-10-01

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

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

    PubMed Central

    Leng, Tian-dong; Xiong, Zhi-gang

    2013-01-01

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

  17. 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.

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

    PubMed Central

    2013-01-01

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

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

    PubMed

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

    2015-02-01

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

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

    PubMed

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

    2010-01-01

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

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

    PubMed

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

    2016-02-01

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

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

    PubMed

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

    2016-02-01

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

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

    PubMed

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

    2008-03-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Aschauer, Ulrich; Selloni, Annabella

    2015-07-01

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

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

    PubMed

    Aschauer, Ulrich; Selloni, Annabella

    2015-07-28

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

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

    PubMed

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

    2011-08-01

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

  9. 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.

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

    PubMed Central

    Hughes, Floyd

    1970-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Ahamed, Parbhej; Kawakami, Masaru; Furukawa, Hidemitsu

    2016-04-01

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

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

    PubMed

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

    1990-02-01

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

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

    PubMed

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

    1990-02-01

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

  14. Design of a new, multi-purpose, light-curing adhesive comprising a silane coupling agent, acidic adhesive monomers and dithiooctanoate monomers for bonding to varied metal and dental ceramic materials.

    PubMed

    Ikemura, Kunio; Tanaka, Hisaki; Fujii, Toshihide; Deguchi, Mikito; Negoro, Noriyuki; Endo, Takeshi; Kadoma, Yoshinori

    2011-01-01

    A newly designed, light-curing adhesive was investigated for its bonding effectiveness to porcelain, alumina, zirconia, Au, Au alloy, Ag alloy, Au-Ag-Pd alloy, and Ni-Cr alloy. Four experimental adhesives were prepared using varying contents of the following: a silane coupling agent [3-methacryloyloxypropyltriethoxysilane (3-MPTES)], acidic adhesive monomers [6-methacryloyloxyhexyl phosphonoacetate(6-MHPA),6-methacryloyloxyhexyl3-phosphonopropionate(6-MHPP)and 4-methacryloyloxyethoxycarbonylphthalic acid (4-MET)], and dithiooctanoate monomers [6-methacryloyloxyhexyl 6,8-dithiooctanoate (6-MHDT) and 10-methacryloyloxydecyl 6,8-dithiooctanoate (10-MDDT)]. After all adherend surfaces were sandblasted and applied with an experimental adhesive, shear bond strengths (SBSs) of a light-curing resin composite (Beautifil II, Shofu Inc., Kyoto, Japan) to the adherend materials after 2,000 times of thermal cycling were measured. For the experimental adhesive which contained 3-MPTES (30.0 wt%), 6-MHPA (1.0 wt%), 6-MHPP (1.0 wt%), 4-MET (1.0 wt%), 6-MHDT (0.5 wt%) and 10-MDDT (0.5 wt%), it consistently yielded the highest SBS for all adherend surfaces in the range of 20.8 (4.8)-30.3 (7.9) MPa, with no significant differences among all the adherend materials (p>0.05). Therefore, the newly designed, multi-purpose, light-curing adhesive was able to deliver high SBS to all the adherend materials tested.

  15. Non-aqueous liquid compositions comprising ion exchange polymers

    SciTech Connect

    Kim, Yu Seung; Lee, Kwan-Soo; Rockward, Tommy Q. T.

    2011-07-19

    Compositions, and methods of making thereof, comprising from about 1% to about 5% of a perfluorinated sulfonic acid ionomer or a hydrocarbon-based ionomer; and from about 95% to about 99% of a solvent, said solvent consisting essentially of a polyol; wherein said composition is substantially free of water and wherein said ionomer is uniformly dispersed in said solvent.

  16. Non-aqueous liquid compositions comprising ion exchange polymers

    SciTech Connect

    Kim, Yu Seung; Lee, Kwan-Soo; Rockward, Tommy Q. T.

    2013-03-12

    Compositions, and methods of making thereof, comprising from about 1% to about 5% of a perfluorinated sulfonic acid ionomer or a hydrocarbon-based ionomer; and from about 95% to about 99% of a solvent, said solvent consisting essentially of a polyol; wherein said composition is substantially free of water and wherein said ionomer is uniformly dispersed in said solvent.

  17. Cationic electrodepositable coating composition comprising lignin

    DOEpatents

    Fenn, David; Bowman, Mark P; Zawacky, Steven R; Van Buskirk, Ellor J; Kamarchik, Peter

    2013-07-30

    A cationic electrodepositable coating composition is disclosed. The present invention in directed to a cationic electrodepositable coating composition comprising a lignin-containing cationic salt resin, that comprises (A) the reaction product of: lignin, an amine, and a carbonyl compound; (B) the reaction product of lignin, epichlorohydrin, and an amine; or (C) combinations thereof.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

    Prestwich, Glenn D.

    2013-01-01

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

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

    PubMed

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

    2016-08-01

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

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

    NASA Technical Reports Server (NTRS)

    Zehe, Michael J.; Faut, Owen D.

    1990-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Zehe, Michael J.; Faut, Owen D.

    1989-01-01

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

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

    PubMed

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

    2011-03-01

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

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

    SciTech Connect

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

    2009-12-01

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

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

    PubMed

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

    2009-11-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2007-07-01

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

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

    DOEpatents

    Croteau, Rodney B.; Lange, Bernd M.

    2001-01-01

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

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2016-03-14

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

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

    PubMed

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

    2015-05-01

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

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

    PubMed

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

    2013-05-01

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

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

    PubMed

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

    2013-05-01

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

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

    PubMed

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

    2015-05-01

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

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

    PubMed

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

    2015-06-15

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

  19. Sensor devices comprising field-structured composites

    DOEpatents

    Martin, James E.; Hughes, Robert C.; Anderson, Robert A.

    2001-02-27

    A new class of sensor devices comprising field-structured conducting composites comprising a textured distribution of conducting magnetic particles is disclosed. The conducting properties of such field-structured materials can be precisely controlled during fabrication so as to exhibit a large change in electrical conductivity when subject to any environmental influence which changes the relative volume fraction. Influences which can be so detected include stress, strain, shear, temperature change, humidity, magnetic field, electromagnetic radiation, and the presence or absence of certain chemicals. This behavior can be made the basis for a wide variety of sensor devices.

  20. Non-precious metal catalysts prepared from precursor comprising cyanamide

    SciTech Connect

    Chung, Hoon Taek; Zelenay, Piotr

    2015-10-27

    Catalyst comprising graphitic carbon and methods of making thereof; said graphitic carbon comprising a metal species, a nitrogen-containing species and a sulfur containing species. A catalyst for oxygen reduction reaction for an alkaline fuel cell was prepared by heating a mixture of cyanamide, carbon black, and a salt selected from an iron sulfate salt and an iron acetate salt at a temperature of from about 700.degree. C. to about 1100.degree. C. under an inert atmosphere. Afterward, the mixture was treated with sulfuric acid at elevated temperature to remove acid soluble components, and the resultant mixture was heated again under an inert atmosphere at the same temperature as the first heat treatment step.

  1. 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.

  2. Biocatalytic material comprising multilayer enzyme coated fiber

    DOEpatents

    Kim, Jungbae [Richland, WA; Kwak, Ja Hun [Richland, WA; Grate, Jay W [West Richland, WA

    2009-11-03

    The present invention relates generally to high stability, high activity biocatalytic materials and processes for using the same. The materials comprise enzyme aggregate coatings having high biocatalytic activity and stability useful in heterogeneous environment. These new materials provide a new biocatalytic immobilized enzyme system with applications in bioconversion, bioremediation, biosensors, and biofuel cells.

  3. Synthetic thermoelectric materials comprising phononic crystals

    DOEpatents

    El-Kady, Ihab F; Olsson, Roy H; Hopkins, Patrick; Reinke, Charles; Kim, Bongsang

    2013-08-13

    Synthetic thermoelectric materials comprising phononic crystals can simultaneously have a large Seebeck coefficient, high electrical conductivity, and low thermal conductivity. Such synthetic thermoelectric materials can enable improved thermoelectric devices, such as thermoelectric generators and coolers, with improved performance. Such synthetic thermoelectric materials and devices can be fabricated using techniques that are compatible with standard microelectronics.

  4. 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

  5. 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.

  6. 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.

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

    PubMed

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

    2015-07-01

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

  8. Downhole transmission system comprising a coaxial capacitor

    DOEpatents

    Hall, David R.; Pixton, David S.; Johnson, Monte L.; Bartholomew, David B.; Hall, Jr., H. Tracy; Rawle, Michael

    2011-05-24

    A transmission system in a downhole component comprises a plurality of data transmission elements. A coaxial cable having an inner conductor and an outer conductor is disposed within a passage in the downhole component such that at least one capacitor is disposed in the passage and having a first terminal coupled to the inner conductor and a second terminal coupled to the outer conductor. Preferably the transmission element comprises an electrically conducting coil. Preferably, within the passage a connector is adapted to electrically connect the inner conductor of the coaxial cable and the lead wire. The coaxial capacitor may be disposed between and in electrically communication with the connector and the passage. In another embodiment a connector is adapted to electrical connect a first and a second portion of the inner conductor of the coaxial cable and a coaxial capacitor is in electrical communication with the connector and the passage.

  9. Nanophosphor composite scintillators comprising a polymer matrix

    DOEpatents

    Muenchausen, Ross Edward; Mckigney, Edward Allen; Gilbertson, Robert David

    2010-11-16

    An improved nanophosphor composite comprises surface modified nanophosphor particles in a solid matrix. The nanophosphor particle surface is modified with an organic ligand, or by covalently bonding a polymeric or polymeric precursor material. The surface modified nanophosphor particle is essentially charge neutral, thereby preventing agglomeration of the nanophosphor particles during formation of the composite material. The improved nanophosphor composite may be used in any conventional scintillator application, including in a radiation detector.

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  12. Fibrous composites comprising carbon nanotubes and silica

    DOEpatents

    Peng, Huisheng; Zhu, Yuntian Theodore; Peterson, Dean E.; Jia, Quanxi

    2011-10-11

    Fibrous composite comprising a plurality of carbon nanotubes; and a silica-containing moiety having one of the structures: (SiO).sub.3Si--(CH.sub.2).sub.n--NR.sub.1R.sub.2) or (SiO).sub.3Si--(CH.sub.2).sub.n--NCO; where n is from 1 to 6, and R.sub.1 and R.sub.2 are each independently H, CH.sub.3, or C.sub.2H.sub.5.

  13. 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.

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

    PubMed

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

    2015-09-28

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

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

    PubMed Central

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

    2015-01-01

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

  16. 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.

  17. 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

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

    PubMed

    Maurer, Patrick; Thomas, Vibin; Iftimie, Radu

    2011-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Maurer, Patrick; Thomas, Vibin; Iftimie, Radu

    2011-03-01

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

  20. 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.

  1. Electromagnetic radiation absorbers and modulators comprising polyaniline

    DOEpatents

    Epstein, Arthur J.; Ginder, John M.; Roe, Mitchell G.; Hajiseyedjavadi, Hamid

    1992-01-01

    A composition for absorbing electromagnetic radiation, wherein said electromagnetic radiation possesses a wavelength generally in the range of from about 1000 Angstroms to about 50 meters, wherein said composition comprises a polyaniline composition of the formula ##STR1## where y can be equal to or greater than zero, and R.sup.1 and R.sup.2 are independently selected from the group containing of H, --OCH.sub.3, --CH.sub.3, --F, --Cl, --Br, --I, NR.sup.3 .sub.2, --NHCOR.sup.3, --OH, --O.sup.-, SR.sup.3, --OCOR.sup.3, --NO.sub.2, --COOH, --COOR.sup.3, --COR.sup.3, --CHO, and --CN, where R.sup.3 is a C.sub.1 to C.sub.8 alkyl, aryl or aralkyl group.

  2. Insulating Materials Comprising Polysilazane, Methods of Forming Such Insulating Materials, and Precursor Formulations Comprising Polysilazane

    NASA Technical Reports Server (NTRS)

    Larson, Robert S. (Inventor); Fuller, Michael E. (Inventor)

    2013-01-01

    Methods of forming an insulating material comprising combining a polysilazane, a cross-linking compound, and a gas-generating compound to form a reaction mixture, and curing the reaction mixture to form a modified polysilazane. The gas-generating compound may be water, an alcohol, an amine, or combinations thereof. The cross-linking compound may be an isocyanate, an epoxy resin, or combinations thereof. The insulating material may include a matrix comprising one of a reaction product of a polysilazane and an isocyanate and a reaction product of a polysilazane and an epoxy resin. The matrix also comprises a plurality of interconnected pores produced from one of reaction of the polysilazane and the isocyanate and from reaction of the polysilazane and the epoxy resin. A precursor formulation that comprises a polysilazane, a cross-linking compound, and a gas-generating compound is also disclosed.

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

    PubMed

    Wakaki, Takayuki; Kanai, Motomu; Kuninobu, Yoichiro

    2015-04-01

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

  4. 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.

  5. 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.

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

    SciTech Connect

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

    2010-10-20

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

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

    NASA Astrophysics Data System (ADS)

    Farmanzadeh, Davood; Tabari, Leila

    2015-01-01

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

  8. Pump assembly comprising gas spring means

    SciTech Connect

    Akkerman, N.H.

    1981-10-27

    A pressure actuated, rodless pump is described for pumping fluid, preferably, from a well through a tubing string and comprises a chamber and a check valved movable piston which define a pump cavity. The chamber has a check valved outlet to the tubing string on the cavity side of the piston and a fluid inlet on the other side of the piston. The piston is connected to a spring assembly by a pull rod. The spring assembly includes a cylinder having an elastomeric bladder separating a gas filled chamber from an upper fluid chamber which is separated from a lower fluid chamber by a wall having a fluid passageway formed therein. The lower fluid chamber encloses a stationary piston and both the lower and upper fluid chambers are in fluid communication with the tubing string through a charge valve. Cyclic pressure applied to the fluid in the tubing string forces the cylinder and movable piston downward to draw fluid into the pump cavity and to force fluid from the lower fluid chamber into the upper fluid chamber to compress the gas. The charged valve functions during the pressure cycles to replace fluid lost from the lower fluid chamber past the stationary piston. 28 claims.

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

    PubMed

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

    2015-12-15

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

  10. A comparative study of the vibrational spectra of the anticancer drug melphalan and its fundamental molecules 3-phenylpropionic acid and L-phenylalanine

    NASA Astrophysics Data System (ADS)

    Badawi, Hassan M.; Khan, Ibrahim

    2016-04-01

    The structural stability and the vibrational spectra of the anticancer drug melphalan and its parent compounds 3-phenylpropionic acid and L-phenylalanine were investigated by the DFT B3LYP/6-311G** calculations. Melphalan and its fundamental compounds were predicted to exist predominantly in non-planar structures. The vibrational frequencies of the low energy structures of melphalan, 3-phenylpropionic acid, and phenylalanine were computed at the DFT B3LYP level of theory. Complete vibrational assignments of the normal modes of melphalan, 3-phenylpropionic acid, and phenylalanine were provided by combined theoretical and experimental data of the molecules. The experimental infrared spectra of phenylalanine and melphalan show a significantly different pattern of the Cdbnd O stretching mode as compared to those of normal carboxylic acids. A comparison of the 3700-2000 cm-1 infrared spectral region of the three molecules suggests the presence of similar intermolecular H-bonding in their condensed phases. The observed infrared and Raman spectra are consistent with the presence of one predominant melphalan conformation at room temperature.

  11. 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

  12. Single-molecule tracing on a fluidic microchip for quantitative detection of low-abundance nucleic acids.

    PubMed

    Wang, Tza-Huei; Peng, Yahui; Zhang, Chunyang; Wong, Pak Kin; Ho, Chih-Ming

    2005-04-20

    Here, we report a method capable of quantitative detection of low-abundance DNA/RNA molecules by incorporating confocal fluorescence spectroscopy, molecular beacons, and a molecular-confinement microfluidic reactor. By using a combination of ac and dc fields via a trio of 3-D electrodes in the microreactor, we are able to precisely direct the transport of individual molecules to a minuscule laser-focused detection volume ( approximately 1 fL). A burst of fluorescence photons is detected whenever a molecular beacon-target hybrid flows through the detection region, and the amount of targets can be directly quantified according to the number of recorded single-molecule flow-through events. This assay consumes only attomoles of molecular probes and is able to quantitatively detect subpicomolar DNA targets. A measurement time of less than 2 min is sufficient to complete the detection.

  13. Effect of propane-2-sulfonic acid octadec-9-enyl-amide on the expression of adhesion molecules in human umbilical vein endothelial cells.

    PubMed

    Chen, Cai-Xia; Yang, Li-Chao; Xu, Xu-Dong; Wei, Xiao; Gai, Ya-Ting; Peng, Lu; Guo, Han; Hao-Zhou; Wang, Yi-Qing; Jin, Xin

    2015-06-01

    Oleoylethanolamide (OEA), an endogenous agonist of PPARα, has been reported to have anti-atherosclerotic properties. However, OEA can be enzymatically hydrolyzed to oleic acid and ethanolamine and, thus, is not expected to be orally active. In the present study, we designed and synthesized an OEA analog, propane-2-sulfonic acid octadec-9-enyl-amide (N15), which is resistant to enzymatic hydrolysis. The purpose of this study was to investigate the effects of N15 on the expression of adhesion molecules in human umbilical vein endothelial cells (HUVECs). The results showed that N15 inhibited TNFα-induced production of vascular cell adhesion molecule-1 and intercellular adhesion molecule-1 and the adhesion of monocytes to TNFα-induced HUVECs. Furthermore, the protective effect of N15 on inflammation is dependent upon a PPAR-α/γ-mediated mechanism. In conclusion, N15 protects against TNFα-induced vascular endothelial inflammation. This anti-inflammatory effect of N15 is dependent on PPAR-α/γ dual targets.

  14. Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids.

    PubMed

    Aramesh, M; Shimoni, O; Fox, K; Karle, T J; Lohrmann, A; Ostrikov, K; Prawer, S; Cervenka, J

    2015-04-14

    Extracellular nucleic acids freely circulating in blood and other physiologic fluids are important biomarkers for non-invasive diagnostics and early detection of cancer and other diseases, yet difficult to detect because they exist in very low concentrations and large volumes. Here we demonstrate a new broad-range sensor platform for ultrasensitive and selective detection of circulating DNA down to the single-molecule level. The biosensor is based on a chemically functionalized nanoporous diamond-like carbon (DLC) coated alumina membrane. The few nanometer-thick, yet perfect and continuous DLC-coating confers the chemical stability and biocompatibility of the sensor, allowing its direct application in biological conditions. The selective detection is based on complementary hybridization of a fluorescently-tagged circulating cancer oncomarker (a 21-mer nucleic acid) with covalently immobilized DNA on the surface of the membrane. The captured DNAs are detected in the nanoporous structure of the sensor using confocal scanning laser microscopy. The flow-through membrane sensor demonstrates broad-range sensitivity, spanning from 10(15) molecules per cm(2) down to single molecules, which is several orders of magnitude improvement compared to the flat DNA microarrays. Our study suggests that these flow-through type nanoporous sensors represent a new powerful platform for large volume sampling and ultrasensitive detection of different chemical biomarkers. PMID:25744416

  15. Towards an understanding of the molecular mechanism of solvation of drug molecules: a thermodynamic approach by crystal lattice energy, sublimation, and solubility exemplified by hydroxybenzoic acids.

    PubMed

    Perlovich, German L; Volkova, Tatyana V; Bauer-Brandl, Annette

    2006-07-01

    Temperature dependencies of saturated vapor pressure and heat capacities for the 2-, 3-, and 4-hydroxybenzoic acids were measured and thermodynamic functions of sublimation calculated (2-hydroxybenzoic acid: DeltaG(sub) (298) = 38.5 kJ/mol; DeltaH(sub) (298) = 96.6 +/- 0.8 kJ/mol; DeltaS(sub) (298) = 191 +/- 3 J/mol . K; 3-hydroxybenzoic acid: DeltaG(sub) (298) = 50.6 kJ/mol; DeltaH(sub) (298) = 105.2 +/- 0.8 kJ/mol; DeltaS(sub) (298) = 180 +/- 2 J/mol . K; 4-hydroxybenzoic acid: DeltaG(sub) (298) = 55.0 kJ/mol; DeltaH(sub) (298) = 113.3 +/- 0.7 kJ/mol; DeltaS(sub) (298) = 193 +/- 2 J/mol . K). Analysis of crystal lattice packing energies based on geometry optimization of the molecules in the crystal using diffraction data and the program Dmol(3) was carried out. The energetic contributions of van der Waals, Coulombic, and hydrogen bond terms to the total packing energy were analyzed. The fraction of hydrogen bond energy in the packing energy increases as: 3-hydroxybenzoic (29.7%) < 2-hydroxybenzoic (34.7%) < 4-hydroxybenzoic acid (42.0%). Enthalpies of evaporation were estimated from enthalpies of sublimation and fusion. Temperature dependencies of the solubility in n-octanol and n-hexane were measured. The thermodynamic functions of solubility and solvation processes were deduced. Specific and nonspecific solvation terms were distinguished using the transfer from the "inert" n-hexane to the other solvents. The transfer of the molecules from water to n-octanol is enthalpy driven process.

  16. Flow-through Capture and in Situ Amplification Can Enable Rapid Detection of a Few Single Molecules of Nucleic Acids from Several Milliliters of Solution.

    PubMed

    Schlappi, Travis S; McCalla, Stephanie E; Schoepp, Nathan G; Ismagilov, Rustem F

    2016-08-01

    Detecting nucleic acids (NAs) at zeptomolar concentrations (few molecules per milliliter) currently requires expensive equipment and lengthy processing times to isolate and concentrate the NAs into a volume that is amenable to amplification processes, such as PCR or LAMP. Shortening the time required to concentrate NAs and integrating this procedure with amplification on-device would be invaluable to a number of analytical fields, including environmental monitoring and clinical diagnostics. Microfluidic point-of-care (POC) devices have been designed to address these needs, but they are not able to detect NAs present in zeptomolar concentrations in short time frames because they require slow flow rates and/or they are unable to handle milliliter-scale volumes. In this paper, we theoretically and experimentally investigate a flow-through capture membrane that solves this problem by capturing NAs with high sensitivity in a short time period, followed by direct detection via amplification. Theoretical predictions guided the choice of physical parameters for a chitosan-coated nylon membrane; these predictions can also be applied generally to other capture situations with different requirements. The membrane is also compatible with in situ amplification, which, by eliminating an elution step enables high sensitivity and will facilitate integration of this method into sample-to-answer detection devices. We tested a wide range of combinations of sample volumes and concentrations of DNA molecules using a capture membrane with a 2 mm radius. We show that for nucleic acid detection, this approach can concentrate and detect as few as ∼10 molecules of DNA with flow rates as high as 1 mL/min, handling samples as large as 50 mL. In a specific example, this method reliably concentrated and detected ∼25 molecules of DNA from 50 mL of sample. PMID:27429181

  17. SALDI-TOF-MS analyses of small molecules (citric acid, dexasone, vitamins E and A) using TiO2 nanocrystals as substrates.

    PubMed

    Popović, Iva A; Nešić, Maja; Vranješ, Mila; Šaponjić, Zoran; Petković, Marijana

    2016-10-01

    Surface-assisted laser desorption/ionisation time-of-flight mass spectrometry (SALDI-TOF-MS) might be the method of choice for the analysis of low mass molecules (less than m/z 500). Titanium dioxide (TiO2) nanocrystals as a substrate for SALDI-TOF-MS improve the reproducibility of the signal intensities and prevent the fragmentation of some molecules upon laser irradiation, as we have previously shown. In addition, variously shaped and sized TiO2 nanocrystals/substrates for SALDI-MS could be used for quantification of small molecules, which are otherwise difficult to detect with the assistance of organic matrices. TiO2-assisted LDI-MS spectra could be acquired with excellent reproducibility and repeatability and with low detection limit. In the current study, we analysed the spectra of dexasone, citric acid, vitamin E and vitamin A acquired with TiO2 nanocrystals of various shapes and dimensions, i.e. the colloidal TiO2 nanoparticles (TiO2 NPs), TiO2 prolate nanospheroids (TiO2 PNSs) and TiO2 nanotubes (TiO2 NTs). Various shapes and dimensions of substrates were used since these factors determine desorption and ionisation processes. The homogeneity on the target plate was compared based on signal-to-noise values of peaks of interest of analysed molecules as well as the within-day and day-to-day repeatability. In summary, the obtained results show that the applicability of individual TiO2 nanocrystals depends on the analyte. Signals which are acquired with the assistance of TiO2 PNSs have the highest sensitivity and reproducibility (the smallest standard deviation), even compared with those in the LDI mode. This implies that TiO2 PNSs could also be suitable for quantitative analyses of small molecules. PMID:27510281

  18. Synthesis and characterization of various ruthenium small molecules and metallopolymers for potential use in photovoltaic devices and luminescence properties of N-heterocyclic carbenes and trifluoro methylated tris(pyrazolyl)borate silver (I) acid-base adducts

    NASA Astrophysics Data System (ADS)

    Chitikuri, Shylaja

    This thesis with its 66 pages, 1 table, 29 figures and 47 references, deals with two major topics involving structure and properties of selected metal complexes and their use in electronic devices. The first chapter discusses the development of ruthenium-based metallopolymer and small molecular complexes toward possible utilization as active materials for solar cells. Such complexes have been found to be good "black absorbers" with solid-state absorption that spans the entire visible region into the near-infrared, representing an impressive overlap with the solar radiation that is more favorable than common molecular solar cell active materials. The second chapter includes photophysical studies of different metallo N-heterocyclic carbenes and acid-base adducts comprising fluorinated tris(pyrazolyl)borate silver(I) complexes coordinated to different solvent and aromatic molecules. These species have been investigated and found to exhibit unusual photophysical properties, including metal-free phosphorescence at room temperature with high quantum yield, multi-color emission from a single compound, and selective sensing of temperature and hazardous vapors.

  19. Solid polymer electrolyte composite membrane comprising laser micromachined porous support

    DOEpatents

    Liu, Han; LaConti, Anthony B.; Mittelsteadt, Cortney K.; McCallum, Thomas J.

    2011-01-11

    A solid polymer electrolyte composite membrane and method of manufacturing the same. According to one embodiment, the composite membrane comprises a rigid, non-electrically-conducting support, the support preferably being a sheet of polyimide having a thickness of about 7.5 to 15 microns. The support has a plurality of cylindrical pores extending perpendicularly between opposing top and bottom surfaces of the support. The pores, which preferably have a diameter of about 5 microns, are made by laser micromachining and preferably are arranged in a defined pattern, for example, with fewer pores located in areas of high membrane stress and more pores located in areas of low membrane stress. The pores are filled with a first solid polymer electrolyte, such as a perfluorosulfonic acid (PFSA) polymer. A second solid polymer electrolyte, which may be the same as or different than the first solid polymer electrolyte, may be deposited over the top and/or bottom of the first solid polymer electrolyte.

  20. Single Qdot-labeled glycosylase molecules use a wedge amino acid to probe for lesions while scanning along DNA.

    PubMed

    Dunn, Andrew R; Kad, Neil M; Nelson, Shane R; Warshaw, David M; Wallace, Susan S

    2011-09-01

    Within the base excision repair (BER) pathway, the DNA N-glycosylases are responsible for locating and removing the majority of oxidative base damages. Endonuclease III (Nth), formamidopyrimidine DNA glycosylase (Fpg) and endonuclease VIII (Nei) are members of two glycosylase families: the helix-hairpin-helix (HhH) superfamily and the Fpg/Nei family. The search mechanisms employed by these two families of glycosylases were examined using a single molecule assay to image quantum dot (Qdot)-labeled glycosylases interacting with YOYO-1 stained λ-DNA molecules suspended between 5 µm silica beads. The HhH and Fpg/Nei families were found to have a similar diffusive search mechanism described as a continuum of motion, in keeping with rotational diffusion along the DNA molecule ranging from slow, sub-diffusive to faster, unrestricted diffusion. The search mechanism for an Fpg variant, F111A, lacking a phenylalanine wedge residue no longer displayed slow, sub-diffusive motion compared to wild type, suggesting that Fpg base interrogation may be accomplished by Phe(111) insertion.

  1. Single Qdot-labeled glycosylase molecules use a wedge amino acid to probe for lesions while scanning along DNA.

    PubMed

    Dunn, Andrew R; Kad, Neil M; Nelson, Shane R; Warshaw, David M; Wallace, Susan S

    2011-09-01

    Within the base excision repair (BER) pathway, the DNA N-glycosylases are responsible for locating and removing the majority of oxidative base damages. Endonuclease III (Nth), formamidopyrimidine DNA glycosylase (Fpg) and endonuclease VIII (Nei) are members of two glycosylase families: the helix-hairpin-helix (HhH) superfamily and the Fpg/Nei family. The search mechanisms employed by these two families of glycosylases were examined using a single molecule assay to image quantum dot (Qdot)-labeled glycosylases interacting with YOYO-1 stained λ-DNA molecules suspended between 5 µm silica beads. The HhH and Fpg/Nei families were found to have a similar diffusive search mechanism described as a continuum of motion, in keeping with rotational diffusion along the DNA molecule ranging from slow, sub-diffusive to faster, unrestricted diffusion. The search mechanism for an Fpg variant, F111A, lacking a phenylalanine wedge residue no longer displayed slow, sub-diffusive motion compared to wild type, suggesting that Fpg base interrogation may be accomplished by Phe(111) insertion. PMID:21666255

  2. The sequence of rat leukosialin (W3/13 antigen) reveals a molecule with O-linked glycosylation of one third of its extracellular amino acids.

    PubMed Central

    Killeen, N; Barclay, A N; Willis, A C; Williams, A F

    1987-01-01

    Leukosialin is one of the major glycoproteins of thymocytes and T lymphocytes and is notable for a very high content of O-linked carbohydrate structures. The full protein sequence for rat leukosialin as translated from cDNA clones is now reported. The molecule contains 371 amino acids with 224 residues outside the cell, one transmembrane sequence and 124 cytoplasmic residues. Data from the peptide sequence and carbohydrate composition suggest that one in three of the extracellular amino acids may be O-glycosylated with no N-linked glycosylation sites. The cDNA sequence contained a CpG rich region in the 3' coding sequence and a large 3' non-coding region which included tandem repeats of the sequence GGAT. Images Fig. 4. PMID:2965006

  3. A Broad Anti-influenza Hybrid Small Molecule That Potently Disrupts the Interaction of Polymerase Acidic Protein-Basic Protein 1 (PA-PB1) Subunits.

    PubMed

    Massari, Serena; Nannetti, Giulio; Desantis, Jenny; Muratore, Giulia; Sabatini, Stefano; Manfroni, Giuseppe; Mercorelli, Beatrice; Cecchetti, Violetta; Palù, Giorgio; Cruciani, Gabriele; Loregian, Arianna; Goracci, Laura; Tabarrini, Oriana

    2015-05-14

    In continuing our efforts to identify small molecules able to disrupt the interaction of the polymerase acidic protein-basic protein 1 (PA-PB1) subunits of influenza virus (Flu) RNA-dependent RNA polymerase, this paper is devoted to the optimization of a dihydrotriazolopyrimidine derivative, previously identified through structure-based drug discovery. The structure modifications performed around the bicyclic core led to the identification of compounds endowed with both the ability to disrupt PA-PB1 subunits interaction and anti-Flu activity with no cytotoxicity. Very interesting results were obtained with the hybrid molecules 36 and 37, designed by merging some peculiar structural features known to impart PA-PB1 interaction inhibition, with compound 36 that emerged as the most potent PA-PB1 interaction inhibitor (IC50 = 1.1 μM) among all the small molecules reported so far. Calculations showed a very favored H-bonding between the 2-amidic carbonyl of 36 and Q408, which seems to justify its potent ability to interfere with the interaction of the polymerase subunits.

  4. A pliable electroporation patch (ep-Patch) for efficient delivery of nucleic acid molecules into animal tissues with irregular surface shapes.

    PubMed

    Wei, Zewen; Huang, Yuanyu; Zhao, Deyao; Hu, Zhiyuan; Li, Zhihong; Liang, Zicai

    2015-01-05

    Delivery of nucleic acids into animal tissues by electroporation is an appealing approach for various types of gene therapy, but efficiency of existing methodsis not satisfactory. Here we present the validation of novel electroporation patch (ep-Patch) for efficient delivery of DNA and siRNA into mouse tissues. Using micromachining technology, closely spaced gold electrodes were made on the pliable parylene substrate to form a patch-like electroporation metrics. It enabled large coverage of the target tissues and close surface contact between the tissues and electrodes, thus providing a uniform electric field to deliver nucleic acids into tissues, even beneath intact skin. Using this ep-Patch for efficiently delivery of both DNA and siRNA, non-invasive electroporation of healthy mouse muscle tissue was successfully achieved. Delivery of these nucleic acids was performed to intact tumors with satisfactory results. Silencing of tumor genes using the ep-Patch was also demonstrated on mice. This pliable electroporation patch method constitutes a novel way of in vivo delivery of siRNA and DNA to certain tissues or organs to circumvent the disadvantages of existing methodologies for in vivo delivery of nucleic acid molecules.

  5. 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.

  6. 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

  7. 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).

  8. High speed nucleic acid sequencing

    SciTech Connect

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

    2011-05-17

    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. Each type of labeled nucleotide comprises an acceptor fluorophore attached to a phosphate portion of the nucleotide such that the fluorophore is removed upon incorporation into a growing strand. Fluorescent signal is emitted via fluorescent resonance energy transfer between the donor fluorophore and the acceptor fluorophore as each nucleotide is incorporated into the growing strand. The sequence is deduced by identifying which base is being incorporated into the growing strand.

  9. Compositions Comprising Nickel-Titanium, Methods Manufacture Thereof and Articles Comprising the Same

    NASA Technical Reports Server (NTRS)

    Glennon, Glenn N. (Inventor); DellaCorte, Christopher (Inventor)

    2016-01-01

    Disclosing herein is a method for manufacturing nickel-titanium compositions. The method includes disposing a powdered composition in a mold; the powdered composition comprising nickel and titanium; the titanium being present in an amount of about 38 to about 42 wt % and the nickel being present in an amount of about 58 to about 62 wt %; sintering the powdered composition to produce a sintered preform; compacting the preform; machining the preform to form an article; heat treating the article; the annealing being conducted at a temperature of about 1650.degree. F. to about 1900.degree. F. at a pressure of about 3 Torr to about 5 Kg-f/cm.sup.2 for a time period of about 10 minutes to about 5 hours; and quenching the article.

  10. A study of functionally active amino acids involved in the interaction of HLA-A2 or HLA-A3 molecules with cytolytic T lymphocytes.

    PubMed

    Healy, F; Sire, J; Gomard, E; Yssel, H; Jordan, B; Levy, J P

    1988-10-01

    A large series of HLA-A2/HLA-A3 recombinant genes were generated by using the in vivo recombination technique. These genes have each been modified in the last two-thirds of the third exon such that one or several HLA-A2-specific substitutions have been made in the HLA-A3 gene and vice versa. The recombinant genes were transfected into the murine cell line P815 and the transfectants were used as targets for a series of 20 human CTL lines or clones specific for HLA-A2 or HLA-A3, or restricted by HLA-A2 and specific for influenza A. Several patterns of anti-HLA-A2, anti-HLA-A3, and HLA-A2-restricted anti-influenza CTL activity were observed and when uncloned cell lines were studied, a progressive selection of some clones with a similar pattern of activity was regularly found. From the comparison of these different patterns the following conclusions can be drawn: 1) In most but not all cases both domains of the class I molecule were essential for CTL recognition, but residue 152 was critically important for the majority of CTL tested; 2) amino acids 114/116 were also critical in most cases, and their position close to amino acid 152 in the tertiary structure of the molecule may have some functional significance; and 3) amino acid 161, although highly conserved, plays an unexpected but very important role in CTL function. PMID:2459213

  11. Bile acid signaling through FXR induces intracellular adhesion molecule-1 expression in mouse liver and human hepatocytes.

    PubMed

    Qin, Pu; Borges-Marcucci, Lisa A; Evans, Mark J; Harnish, Douglas C

    2005-08-01

    Previous studies have demonstrated a dramatic induction of inflammatory gene expression in livers from mice fed a high-fat, high-cholesterol diet containing cholate after 3-5 wk. To determine the contribution of cholate in mediating these inductions, C57BL/6 mice were fed a chow diet supplemented with increasing concentrations of cholic acid (CA) for 5 days. A dose-dependent induction in the hepatic levels of TNF-alpha, VCAM-1, ICAM-1, and SAA-2 mRNA were observed. As positive controls, a dose-dependent repression of cholesterol 7alpha-hydroxylase and a dose-dependent induction of small heterodimer partner (SHP) expression were also observed, suggesting that farnesoid X receptor (FXR) was activated. In addition, ICAM-1 and SHP mRNA levels were also induced in primary human hepatocytes when treated with chenodeoxycholic acid or GW4064, a FXR-selective agonist. The involvement of FXR in CA-induced inflammatory gene expression was further investigated in the human hepatic cell line HepG2. Both ICAM-1 and SHP expression were induced in a dose- and time-dependent manner by treatment with the FXR-selective agonist GW4064. Moreover, the induction of ICAM-1 by GW4064 was inhibited by the FXR antagonist guggulsterone or with transfection of FXR siRNA. Finally, the activity of FXR was mapped to a retinoic acid response element (RARE) site containing an imbedded farnesoid X response element (FXRE) on the human ICAM-1 promoter and FXR and retinoid X receptor were demonstrated to bind to this site. Finally, FXR-mediated activation of ICAM-1 could be further enhanced by TNF-alpha cotreatment in hepatocytes, suggesting a potential cooperation between cytokine and bile acid-signaling pathways during hepatic inflammatory events.

  12. 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.

  13. 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.

  14. The influence of chemisorbed molecules on mass transfer in H-ZSM-5-type zeolites and the location of Broensted acid sites

    SciTech Connect

    Caro, J.; Buelow, M. ); Kaerger, J.; Pfeifer, H. )

    1988-11-01

    Heterogeneous catalysis is one of the most important applications of zeolites. Therefore, various methods have been developed to determine the strength and concentration of Bronsted acid sites in zeolites. Among them, in the last few years, {sup 1}H MAS NMR has become a powerful tool. In addition to the accessibility of the acid sites probed by chemisorption of N-bases, the steric environment of these catalytically active sites is of importance since it imposes constraints on the geometry of the transition state. However, only a few studies have been reported on this topic. Information was obtained from quantum chemical calculations, catalytic experiments, I.R. spectroscopy, and the arrangement of guest molecules. From these investigations it has been concluded that in H-ZSM-5 the channel intersections should be preferential location centers for the Bronsted acid sites. In adsorption technology, in the use of zeolites as shape-selective adsorbents, modification of the molecular sieve properties by chemisorption of nitrogen-containing bases (N-compounds) has become a common technique. The authors have applied the NMR pulsed field gradient technique to study the influence of chemisorbed N-compounds on transport properties of molecular sieves, considering the chemisorbed compounds as transport obstacles.

  15. Alpha2,6-sialic acid on platelet endothelial cell adhesion molecule (PECAM) regulates its homophilic interactions and downstream antiapoptotic signaling.

    PubMed

    Kitazume, Shinobu; Imamaki, Rie; Ogawa, Kazuko; Komi, Yusuke; Futakawa, Satoshi; Kojima, Soichi; Hashimoto, Yasuhiro; Marth, Jamey D; Paulson, James C; Taniguchi, Naoyuki

    2010-02-26

    Antiangiogenesis therapies are now part of the standard repertoire of cancer therapies, but the mechanisms for the proliferation and survival of endothelial cells are not fully understood. Although endothelial cells are covered with a glycocalyx, little is known about how endothelial glycosylation regulates endothelial functions. Here, we show that alpha2,6-sialic acid is necessary for the cell-surface residency of platelet endothelial cell adhesion molecule (PECAM), a member of the immunoglobulin superfamily that plays multiple roles in cell adhesion, mechanical stress sensing, antiapoptosis, and angiogenesis. As a possible underlying mechanism, we found that the homophilic interactions of PECAM in endothelial cells were dependent on alpha2,6-sialic acid. We also found that the absence of alpha2,6-sialic acid down-regulated the tyrosine phosphorylation of PECAM and recruitment of Src homology 2 domain-containing protein-tyrosine phosphatase 2 and rendered the cells more prone to mitochondrion-dependent apoptosis, as evaluated using PECAM- deficient endothelial cells. The present findings open up a new possibility that modulation of glycosylation could be one of the promising strategies for regulating angiogenesis. PMID:20048157

  16. Coated silicon comprising material for protection against environmental corrosion

    NASA Technical Reports Server (NTRS)

    Hazel, Brian Thomas (Inventor)

    2009-01-01

    In accordance with an embodiment of the invention, an article is disclosed. The article comprises a gas turbine engine component substrate comprising a silicon material; and an environmental barrier coating overlying the substrate, wherein the environmental barrier coating comprises cerium oxide, and the cerium oxide reduces formation of silicate glass on the substrate upon exposure to corrodant sulfates.

  17. Oligonucleotide-conjugated thiazole orange probes as "light-up" probes for messenger ribonucleic acid molecules in living cells.

    PubMed

    Privat, E; Melvin, T; Asseline, U; Vigny, P

    2001-10-01

    "Light-up" probes, icosa-alpha-thymidylate-thiazole orange conjugates, for the in situ time-resolved detection of messenger ribonucleic acid (mRNA) in living cells are evaluated. Upon annealing with polyA in aqueous solutions, the icosa-alpha-thymidylate-thiazole orange conjugates were shown to be up to 15 times more fluorescent. Microinjection of these probes into adherent fibroblasts resulted in high yields of hybridization and fluorescent signals. Incubation of cells in the presence of these probes resulted in facile internalization of the probe and similar painting of the messenger RNA in the nuclear and cytosolic regions.

  18. Synthesis of structured lipids and etherlipids with antioxidants: combination of a selena fatty acid and a selena fatty alcohol with a carotenoic acid in glyceride molecules.

    PubMed

    Houte, H; Partali, V; Sliwka, H R; Quartey, E G

    2000-03-01

    Selenium and carotenoids show similar and complementary properties and protect against a variety of pathological processes. Mixtures of both compounds are found in nutritional supplements and are used to prevent several diseases. The synthetic connection of carotenoids with selenium in glycerols may increase the chemopreventive activity of the individual compounds. Beta-apo-8'-carotenoic acid and 7-selenacapryloic acid were esterified with glycerol to highly unsaturated stable di- and triglycerides. Intramolecular selenium:carotenoid ratios of 1:1, 2:1 and 1:2 were obtained for 1-(7-selenaoctanoyl)-3-(3beta-apo-8 -carotenoyl)-glycerol, 1,3-di-(beta-apo-8'-carotenoyl)-2-(7-selenaoctanoyl)-glycero l and 1,2-di-(7-selenaoctanoyl)-3-(beta-apo-8'-carotenoyl)-glycero l, respectively. The carotenoic acid was likewise connected to the pharmacologically interesting 11-selenalaurylglycerolether forming an alkyl-acylglyceride: 1-(11-selenadodecyl)-3-(beta-apo-8'-carotenoyl)-glycerol.

  19. The Cell Adhesion Molecule “CAR” and Sialic Acid on Human Erythrocytes Influence Adenovirus In Vivo Biodistribution

    PubMed Central

    Wodrich, Harald; Billet, Olivier; Perreau, Matthieu; Hippert, Claire; Mennechet, Franck; Schoehn, Guy; Lortat-Jacob, Hugues; Dreja, Hanna; Ibanes, Sandy; Kalatzis, Vasiliki; Wang, Jennifer P.; Finberg, Robert W.; Cusack, Stephen; Kremer, Eric J.

    2009-01-01

    Although it has been known for 50 years that adenoviruses (Ads) interact with erythrocytes ex vivo, the molecular and structural basis for this interaction, which has been serendipitously exploited for diagnostic tests, is unknown. In this study, we characterized the interaction between erythrocytes and unrelated Ad serotypes, human 5 (HAd5) and 37 (HAd37), and canine 2 (CAV-2). While these serotypes agglutinate human erythrocytes, they use different receptors, have different tropisms and/or infect different species. Using molecular, biochemical, structural and transgenic animal-based analyses, we found that the primary erythrocyte interaction domain for HAd37 is its sialic acid binding site, while CAV-2 binding depends on at least three factors: electrostatic interactions, sialic acid binding and, unexpectedly, binding to the coxsackievirus and adenovirus receptor (CAR) on human erythrocytes. We show that the presence of CAR on erythrocytes leads to prolonged in vivo blood half-life and significantly reduced liver infection when a CAR-tropic Ad is injected intravenously. This study provides i) a molecular and structural rationale for Ad–erythrocyte interactions, ii) a basis to improve vector-mediated gene transfer and iii) a mechanism that may explain the biodistribution and pathogenic inconsistencies found between human and animal models. PMID:19119424

  20. Gold Nanorods as Colorful Chromogenic Substrates for Semiquantitative Detection of Nucleic Acids, Proteins, and Small Molecules with the Naked Eye.

    PubMed

    Ma, Xiaoming; Chen, Zhitao; Kannan, Palanisamy; Lin, Zhenyu; Qiu, Bin; Guo, Longhua

    2016-03-15

    Herein, we report for the first time a colorful chromogenic substrate, which displays vivid color responses in the presence of different concentration of analytes. Our investigation reveals that the selective shortening of gold nanorods (AuNRs) could generate a series of distinct colors that covers nearly the whole visible range from 400 to 760 nm. These vivid colors can be easily distinguished by the naked eye; as a result, the accuracy of visual inspection could be greatly improved. Next, we demonstrate the utility of AuNRs as multicolor chromogenic substrate to develop a number of colorimetric immunoassay methods, e.g., multicolor enzyme-linked immunosorbent assay (ELISA), multicolor competitive ELISA, and multicolor magnetic immunoassay (MIA). These methods allow us to visually quantify the concentration of a broad range of target molecules with the naked eye, and the obtained results are highly consistent with those state-of-the-art techniques that are tested by the sophisticated apparatus. These multicolor portable and cost-effective immunoassay approaches could be potentially useful for a number of applications, for example, in-home personal healthcare, on-site environmental monitoring, and food inspection in the field.

  1. Hypothesis of Lithocoding: Origin of the Genetic Code as a "Double Jigsaw Puzzle" of Nucleobase-Containing Molecules and Amino Acids Assembled by Sequential Filling of Apatite Mineral Cellules.

    PubMed

    Skoblikow, Nikolai E; Zimin, Andrei A

    2016-05-01

    The hypothesis of direct coding, assuming the direct contact of pairs of coding molecules with amino acid side chains in hollow unit cells (cellules) of a regular crystal-structure mineral is proposed. The coding nucleobase-containing molecules in each cellule (named "lithocodon") partially shield each other; the remaining free space determines the stereochemical character of the filling side chain. Apatite-group minerals are considered as the most preferable for this type of coding (named "lithocoding"). A scheme of the cellule with certain stereometric parameters, providing for the isomeric selection of contacting molecules is proposed. We modelled the filling of cellules with molecules involved in direct coding, with the possibility of coding by their single combination for a group of stereochemically similar amino acids. The regular ordered arrangement of cellules enables the polymerization of amino acids and nucleobase-containing molecules in the same direction (named "lithotranslation") preventing the shift of coding. A table of the presumed "LithoCode" (possible and optimal lithocodon assignments for abiogenically synthesized α-amino acids involved in lithocoding and lithotranslation) is proposed. The magmatic nature of the mineral, abiogenic synthesis of organic molecules and polymerization events are considered within the framework of the proposed "volcanic scenario". PMID:27048216

  2. Order of amino acids in C-terminal cysteine-containing peptide-based chelators influences cellular processing and biodistribution of 99mTc-labeled recombinant Affibody molecules.

    PubMed

    Altai, Mohamed; Wållberg, Helena; Orlova, Anna; Rosestedt, Maria; Hosseinimehr, Seyed Jalal; Tolmachev, Vladimir; Ståhl, Stefan

    2012-05-01

    Affibody molecules constitute a novel class of molecular display selected affinity proteins based on non-immunoglobulin scaffold. Preclinical investigations and pilot clinical data have demonstrated that Affibody molecules provide high contrast imaging of tumor-associated molecular targets shortly after injection. The use of cysteine-containing peptide-based chelators at the C-terminus of recombinant Affibody molecules enabled site-specific labeling with the radionuclide 99mTc. Earlier studies have demonstrated that position, composition and the order of amino acids in peptide-based chelators influence labeling stability, cellular processing and biodistribution of Affibody molecules. To investigate the influence of the amino acid order, a series of anti-HER2 Affibody molecules, containing GSGC, GEGC and GKGC chelators have been prepared and characterized. The affinity to HER2, cellular processing of 99mTc-labeled Affibody molecules and their biodistribution were investigated. These properties were compared with that of the previously studied 99mTc-labeled Affibody molecules containing GGSC, GGEC and GGKC chelators. All variants displayed picomolar affinities to HER2. The substitution of a single amino acid in the chelator had an appreciable influence on the cellular processing of 99mTc. The biodistribution of all 99mTc-labeled Affibody molecules was in general comparable, with the main difference in uptake and retention of radioactivity in excretory organs. The hepatic accumulation of radioactivity was higher for the lysine-containing chelators and the renal retention of 99mTc was significantly affected by the amino acid composition of chelators. The order of amino acids influenced renal uptake of some conjugates at 1 h after injection, but the difference decreased at later time points. Such information can be helpful for the development of other scaffold protein-based imaging and therapeutic radiolabeled conjugates.

  3. 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.

  4. 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.

  5. 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.

  6. Folic acid deficiency increases delayed neuronal death, DNA damage, platelet endothelial cell adhesion molecule-1 immunoreactivity, and gliosis in the hippocampus after transient cerebral ischemia.

    PubMed

    Hwang, In Koo; Yoo, Ki-Yeon; Suh, Hong-Won; Kim, Young Sup; Kwon, Dae Young; Kwon, Young-Guen; Yoo, Jun-Hyun; Won, Moo-Ho

    2008-07-01

    Folic acid deficiency increases stroke risk. In the present study, we examined whether folic acid deficiency enhances neuronal damage and gliosis via oxidative stress in the gerbil hippocampus after transient forebrain ischemia. Animals were exposed to a folic acid-deficient diet (FAD) for 3 months and then subjected to occlusion of both common carotid arteries for 5 min. Exposure to an FAD increased plasma homocysteine levels by five- to eightfold compared with those of animals fed with a control diet (CD). In CD-treated animals, most neurons were dead in the hippocampal CA1 region 4 days after ischemia/reperfusion, whereas, in FAD-treated animals, this occurred 3 days after ischemia/reperfusion. Immunostaining for 8-hydroxy-2'-deoxyguanosine (8-OHdG) was performed to examine DNA damage in CA1 neurons in both groups after ischemia, and it was found that 8-OHdG immunoreactivity in both FAD and CD groups peaked at 12 hr after reperfusion, although the immunoreactivity in the FAD group was much greater than that in the CD group. Platelet endothelial cell adhesion molecule-1 (PECAM-1; a final mediator of neutrophil transendothelial migration) immunoreactivity in both groups increased with time after ischemia/reperfusion: Its immunoreactivity in the FAD group was much higher than that in the CD group 3 days after ischemia/reperfusion. In addition, reactive gliosis in the ischemic CA1 region increased with time after ischemia in both groups, but astrocytosis and microgliosis in the FAD group were more severe than in the CD group at all times after ischemia. Our results suggest that folic acid deficiency enhances neuronal damage induced by ischemia.

  7. Effects of caffeic acid phenethyl ester on matrix molecules and angiogenetic and anti-angiogenetic factors in gastric cancer cells cultured on different substrates.

    PubMed

    Kosova, F; Kurt, F O; Olmez, E; Tuğlu, I; Arı, Z

    2016-01-01

    Migration, invasion, metastasis and angiogenesis associated with cancer depend on the surrounding microenvironment. Angiogenesis, the growth of new capillaries, is a regulator of cancer growth and a useful target for cancer therapy. We examined matrix protein interactions in a gastric cancer cell culture that was treated with different doses of caffeic acid (3,4-dihydroxycinnamic acid) phenethyl ester (CAPE). We also investigated the relations among the levels of vascular endothelial growth factor (VEGF), matrix metalloproteinase-9 (MMP-9), endostatin (ES) and trombospondin-1 (TSP-1). Cytotoxity of CAPE was measured using the 3-(4,5-dmethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay. We examined the behavior of cells on laminin and collagen I coated surfaces in response to the angiogenic effect of these matrix molecules. We examined the protein alterations of these matrix molecules immunohistochemically and measured the levels of VEGF, MMP-9, ES and TSP-1 using the ELISA test. We showed that application of CAPE to the gastric cancer cell line on tissue culture plastic, laminin and collagen I significantly decreased the VEGF and MMP-9 protein levels. We found that TSP-1 levels were increased significantly in the gastric cancer cells after application of CAPE. The protein levels of gastric cancer cells also were increased significantly when tissue was cultured on laminin and collagen I. Application of CAPE to cells on laminin or collagen I coated surfaces significantly increased all of the proteins except ES. ES levels were increased on the collagen I covered surfaces, but the laminin surface decreased the levels of ES significantly. We demonstrated the beneficial effect of CAPE on a gastric cancer cell line including inhibition of proliferation and induction of some proteins that might be related to decreased angiogenesis. PMID:26523612

  8. Structure and Biophysical Properties of a Triple-Stranded Beta-Helix Comprising the Central Spike of Bacteriophage T4

    PubMed Central

    Buth, Sergey A.; Menin, Laure; Shneider, Mikhail M.; Engel, Jürgen; Boudko, Sergei P.; Leiman, Petr G.

    2015-01-01

    Gene product 5 (gp5) of bacteriophage T4 is a spike-shaped protein that functions to disrupt the membrane of the target cell during phage infection. Its C-terminal domain is a long and slender β-helix that is formed by three polypeptide chains wrapped around a common symmetry axis akin to three interdigitated corkscrews. The folding and biophysical properties of such triple-stranded β-helices, which are topologically related to amyloid fibers, represent an unsolved biophysical problem. Here, we report structural and biophysical characterization of T4 gp5 β-helix and its truncated mutants of different lengths. A soluble fragment that forms a dimer of trimers and that could comprise a minimal self-folding unit has been identified. Surprisingly, the hydrophobic core of the β-helix is small. It is located near the C-terminal end of the β-helix and contains a centrally positioned and hydrated magnesium ion. A large part of the β-helix interior comprises a large elongated cavity that binds palmitic, stearic, and oleic acids in an extended conformation suggesting that these molecules might participate in the folding of the complete β-helix. PMID:26295253

  9. Solid polymer electrolyte composite membrane comprising plasma etched porous support

    DOEpatents

    Liu, Han; LaConti, Anthony B.

    2010-10-05

    A solid polymer electrolyte composite membrane and method of manufacturing the same. According to one embodiment, the composite membrane comprises a rigid, non-electrically-conducting support, the support preferably being a sheet of polyimide having a thickness of about 7.5 to 15 microns. The support has a plurality of cylindrical pores extending perpendicularly between opposing top and bottom surfaces of the support. The pores, which preferably have a diameter of about 0.1 to 5 microns, are made by plasma etching and preferably are arranged in a defined pattern, for example, with fewer pores located in areas of high membrane stress and more pores located in areas of low membrane stress. The pores are filled with a first solid polymer electrolyte, such as a perfluorosulfonic acid (PFSA) polymer. A second solid polymer electrolyte, which may be the same as or different than the first solid polymer electrolyte, may be deposited over the top and/or bottom of the first solid polymer electrolyte.

  10. Nanopore Device for Reversible Ion and Molecule Sensing or Migration

    NASA Technical Reports Server (NTRS)

    Pourmand, Nader (Inventor); Vilozny, Boaz (Inventor); Actis, Paolo (Inventor); Seger, R. Adam (Inventor); Singaram, Bakthan (Inventor)

    2015-01-01

    Disclosed are methods and devices for detection of ion migration and binding, utilizing a nanopipette adapted for use in an electrochemical sensing circuit. The nanopipette may be functionalized on its interior bore with metal chelators for binding and sensing metal ions or other specific binding molecules such as boronic acid for binding and sensing glucose. Such a functionalized nanopipette is comprised in an electrical sensor that detects when the nanopipette selectively and reversibly binds ions or small molecules. Also disclosed is a nanoreactor, comprising a nanopipette, for controlling precipitation in aqueous solutions by voltage-directed ion migration, wherein ions may be directed out of the interior bore by a repulsing charge in the bore.

  11. Effects of sub-lethal concentrations of thyme and oregano essential oils, carvacrol, thymol, citral and trans-2-hexenal on membrane fatty acid composition and volatile molecule profile of Listeria monocytogenes, Escherichia coli and Salmonella enteritidis.

    PubMed

    Siroli, Lorenzo; Patrignani, Francesca; Gardini, Fausto; Lanciotti, Rosalba

    2015-09-01

    The aim of this work was to investigate the modifications of cell membrane fatty acid composition and volatile molecule profiles of Listeria monocytogenes, Salmonella enteritidis, Escherichia coli, during growth in the presence of different sub-lethal concentrations of thyme and oregano essential oils as well as carvacrol, thymol, trans-2-hexenal and citral. The results evidenced that the tested molecules induced noticeable modifications of membrane fatty acid profiles and volatile compounds produced during the growth. Although specific differences in relation to the species considered were identified, the tested compounds induced a marked increase of some membrane associated fatty acids, particularly unsaturated fatty acids, trans-isomers, and specific released free fatty acids. These findings can contribute to the comprehension of the stress response mechanisms used by different pathogenic microorganisms often involved in food-borne diseases in relation to the exposure to sub-lethal concentrations of natural antimicrobials. PMID:25842326

  12. 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.

  13. Oleic and docosahexaenoic acid differentially phase separate from lipid raft molecules: a comparative NMR, DSC, AFM, and detergent extraction study.

    PubMed

    Shaikh, Saame Raza; Dumaual, Alfred C; Castillo, Alicia; LoCascio, Daniel; Siddiqui, Rafat A; Stillwell, William; Wassall, Stephen R

    2004-09-01

    We have previously suggested that the omega-3 polyunsaturated fatty acid, docosahexaenoic acid (DHA) may in part function by enhancing membrane lipid phase separation into lipid rafts. Here we further tested for differences in the molecular interactions of an oleic (OA) versus DHA-containing phospholipid with sphingomyelin (SM) and cholesterol (CHOL) utilizing (2)H NMR spectroscopy, differential scanning calorimetry, atomic force microscopy, and detergent extractions in model bilayer membranes. (2)H NMR and DSC (differential scanning calorimetry) established the phase behavior of the OA-containing 1-[(2)H(31)]palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (16:0-18:1PE-d(31))/SM (1:1) and the DHA-containing 1-[(2)H(31)]palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine (16:0-22:6PE-d(31))/SM (1:1) in the absence and presence of equimolar CHOL. CHOL was observed to affect the OA-containing phosphatidylethanolamine (PE) more than the DHA-containing PE, as exemplified by >2 x greater increase in order measured for the perdeuterated palmitic chain in 16:0-18:1PE-d(31)/SM (1:1) compared to 16:0-22:6PE-d(31)/SM (1:1) bilayers in the liquid crystalline phase. Atomic force microscopy (AFM) experiments showed less lateral phase separation between 16:0-18:1PE-rich and SM/CHOL-rich raft domains in 16:0-18:1PE/SM/CHOL (1:1:1) bilayers than was observed when 16:0-22:6PE replaced 16:0-18:1PE. Differences in the molecular interaction of 16:0-18:1PE and 16:0-22:6PE with SM/CHOL were also found using biochemical detergent extractions. In the presence of equimolar SM/CHOL, 16:0-18:1PE showed decreased solubilization in comparison to 16:0-22:6PE, indicating greater phase separation with the DHA-PE. Detergent experiments were also conducted with cardiomyocytes fed radiolabeled OA or DHA. Although both OA and DHA were found to be largely detergent solubilized, the amount of OA that was found to be associated with raft-rich detergent-resistant membranes exceeded DHA by

  14. IGF-I regulates redox status in breast cancer cells by activating the amino acid transport molecule xC-.

    PubMed

    Yang, Yuzhe; Yee, Douglas

    2014-04-15

    Insulin-like growth factors (IGF) stimulate cell growth in part by increasing amino acid uptake. xCT (SLC7A11) encodes the functional subunit of the cell surface transport system xC(-), which mediates cystine uptake, a pivotal step in glutathione synthesis and cellular redox control. In this study, we show that IGF-I regulates cystine uptake and cellular redox status by activating the expression and function of xCT in estrogen receptor-positive (ER(+)) breast cancer cells by a mechanism that relies on the IGF receptor substrate-1 (IRS-1). Breast cancer cell proliferation mediated by IGF-I was suppressed by attenuating xCT expression or blocking xCT activity with the pharmacologic inhibitor sulfasalazine (SASP). Notably, SASP sensitized breast cancer cells to inhibitors of the type I IGF receptor (IGF-IR) in a manner reversed by the reactive oxygen species (ROS) scavenger N-acetyl-L-cysteine. Thus, IGF-I promoted the proliferation of ER(+) breast cancer cells by regulating xC(-) transporter function to protect cancer cells from ROS in an IRS-1-dependent manner. Our findings suggest that inhibiting xC(-) transporter function may synergize with modalities that target the IGF-IR to heighten their therapeutic effects.

  15. Nanoparticles that deliver triplex-forming peptide nucleic acid molecules correct F508del CFTR in airway epithelium.

    PubMed

    McNeer, Nicole Ali; Anandalingam, Kavitha; Fields, Rachel J; Caputo, Christina; Kopic, Sascha; Gupta, Anisha; Quijano, Elias; Polikoff, Lee; Kong, Yong; Bahal, Raman; Geibel, John P; Glazer, Peter M; Saltzman, W Mark; Egan, Marie E

    2015-04-27

    Cystic fibrosis (CF) is a lethal genetic disorder most commonly caused by the F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. It is not readily amenable to gene therapy because of its systemic nature and challenges including in vivo gene delivery and transient gene expression. Here we use triplex-forming peptide nucleic acids and donor DNA in biodegradable polymer nanoparticles to correct F508del. We confirm modification with sequencing and a functional chloride efflux assay. In vitro correction of chloride efflux occurs in up to 25% of human cells. Deep-sequencing reveals negligible off-target effects in partially homologous sites. Intranasal delivery of nanoparticles in CF mice produces changes in the nasal epithelium potential difference assay, consistent with corrected CFTR function. Also, gene correction is detected in the nasal and lung tissue. This work represents facile genome engineering in vivo with oligonucleotides using a nanoparticle system to achieve clinically relevant levels of gene editing without off-target effects.

  16. 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.

  17. Effects of Hypoxanthine Substitution in Peptide Nucleic Acids Targeting KRAS2 Oncogenic mRNA Molecules: Theory and Experiment

    PubMed Central

    Sanders, Jeffrey M.; Wampole, Matthew E.; Chen, Chang-Po; Sethi, Dalip; Singh, Amrita; Dupradeau, François-Yves; Wang, Fan; Gray, Brian D.; Thakur, Mathew L.; Wickstrom, Eric

    2013-01-01

    Genetic disorders can arise from single base substitutions in a single gene. A single base substitution for wild type guanine in the twelfth codon of KRAS2 mRNA occurs frequently to initiate lung, pancreatic, and colon cancer. We have observed single base mismatch specificity in radioimaging of mutant KRAS2 mRNA in tumors in mice by in vivo hybridization with radiolabeled peptide nucleic acid (PNA) dodecamers. We hypothesized that multi-mutant specificity could be achieved with a PNA dodecamer incorporating hypoxanthine, which can form Watson-Crick basepairs with adenine, cytosine, thymine, and uracil. Using molecular dynamics simulations and free energy calculations, we show that hypoxanthine substitutions in PNAs are tolerated in KRAS2 RNA-PNA duplexes where wild type guanine is replaced by mutant uracil or adenine in RNA. To validate our predictions, we synthesized PNA dodecamers with hypoxanthine, and then measured the thermal stability of RNA-PNA duplexes. Circular dichroism thermal melting results showed that hypoxanthine-containing PNAs are more stable in duplexes where hypoxanthine-adenine and hypoxanthine-uracil base pairs are formed than single mismatch duplexes or duplexes containing hypoxanthine-guanine opposition. PMID:23972113

  18. 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.

  19. Nucleic acids encoding antifungal polypeptides and uses thereof

    DOEpatents

    Altier, Daniel J.; Ellanskaya, I. A.; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-11-02

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include an amino acid sequence, and variants and fragments thereof, for an antipathogenic polypeptide that was isolated from a fungal fermentation broth. Nucleic acid molecules that encode the antipathogenic polypeptides of the invention, and antipathogenic domains thereof, are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  20. A single amino acid change in the cytoplasmic domain of the simian immunodeficiency virus transmembrane molecule increases envelope glycoprotein expression on infected cells.

    PubMed Central

    LaBranche, C C; Sauter, M M; Haggarty, B S; Vance, P J; Romano, J; Hart, T K; Bugelski, P J; Marsh, M; Hoxie, J A

    1995-01-01

    We have described a virus termed CP-MAC, derived from the BK28 molecular clone of simian immunodeficiency virus, that was remarkable for its ability to infect Sup-T1 cells with rapid kinetics, cell fusion, and CD4 down-modulation (C. C. LaBranche, M. M. Sauter, B. S. Haggarty, P. J. Vance, J. Romano, T. K. Hart, P. J. Bugelski, and J. A. Hoxie, J. Virol. 68:5509-5522, 1994 [Erratum 68:7665-7667]). Compared with BK28, CP-MAC exhibited a number of changes in its envelope glycoproteins, including a highly stable association between the external (SU) and transmembrane (TM) molecules, a more rapid electrophoretic mobility of TM, and, of particular interest, a marked increase in the level of envelope protein expression on the surface of infected cells. These changes were shown to be associated with 11 coding mutations in the env gene (5 in SU and 6 in TM). In this report, we demonstrate that a single amino acid mutation of a Tyr to a Cys at position 723 (Y723C) in the TM cytoplasmic domain of CP-MAC is the principal determinant for the increased expression of envelope glycoproteins on the cell surface. When introduced into the env gene of BK28, the Y723C mutation produced up to a 25-fold increase in the levels of SU and TM on chronically infected cells, as determined by fluorescence-activated cell sorter analysis with monoclonal and polyclonal antibodies. A similar effect was observed when a Tyr-to-Cys change was introduced at the analogous position (amino acid 721) in the SIVmac239 molecular clone, which, unlike BK28 does not contain a premature stop codon in its TM cytoplasmic tail. Substituting other amino acids, including Ala, Ile, and Ser, at this position produced increases in surface envelope glycoproteins that were similar to that observed for the Cys substitution, while a Tyr-to-Phe mutation produced a smaller increase. These results could not be accounted for by differences in the kinetics or efficiency of envelope glycoprotein processing or by shedding of SU

  1. Equilibrium 2H/ 1H fractionations in organic molecules. II: Linear alkanes, alkenes, ketones, carboxylic acids, esters, alcohols and ethers

    NASA Astrophysics Data System (ADS)

    Wang, Ying; Sessions, Alex L.; Nielsen, Robert J.; Goddard, William A., III

    2009-12-01

    Equilibrium 2H/ 1H fractionation factors (α eq) for various H positions in alkanes, alkenes, ketones, carboxylic acids, esters, alcohols, and ethers were calculated between 0 and 100 °C using vibrational frequencies from ab initio QM calculations (B3LYP/6-311G**). Results were then corrected using a temperature-dependent linear calibration curve based on experimental data for H α in ketones ( Wang et al., 2009). The total uncertainty in reported α eq values is estimated at 10-20‰. The effects of functional groups were found to increase the value of α eq for H next to electron-donating groups, e.g. sbnd OR, sbnd OH or sbnd O(C dbnd O)R, and to decrease the value of α eq for H next to electron-withdrawing groups, e.g. sbnd (C dbnd O)R or sbnd (C dbnd O)OR. Smaller but significant functional group effects are also observed for H β and sometimes H γ. By summing over individual H positions, we estimate the equilibrium fractionation relative to water to be -90‰ to -70‰ for n-alkanes and around -100‰ for pristane and phytane. The temperature dependence of these fractionations is very weak between 0 and 100 °C. Our estimates of α eq agree well with field data for thermally mature hydrocarbons (δ 2H values between -80‰ and -110‰ relative to water). Therefore the observed δ 2H increase of individual hydrocarbons and the disappearance of the biosynthetic δ 2H offset between n-alkyl and linear isoprenoid lipids during maturation of organic matter can be confidently attributed to H exchange towards an equilibrium state. Our results also indicate that many n-alkyl lipids are biosynthesized with δ 2H values that are close to equilibrium with water. In these cases, constant down-core δ 2H values for n-alkyl lipids cannot be reliably used to infer a lack of isotopic exchange.

  2. Compositions and methods comprising cellulase variants with reduced affinity to non-cellulosic materials

    DOEpatents

    Cascao-Pereira, Luis G.; Kaper, Thijs; Kelemen, Bradley R; Liu, Amy D.

    2012-08-07

    The present disclosure relates to cellulase variants. In particular the present disclosure relates to cellulase variants having reduced binding to non-cellulosic materials. Also described are nucleic acids encoding the cellulase, compositions comprising said cellulase, methods of identifying cellulose variants and methods of using the compositions.

  3. Non-aqueous liquid compositions comprising ion exchange polymers reference to related application

    SciTech Connect

    Kim; Yu Seung , Lee; Kwan-Soo , Rockward; Tommy Q. T.

    2012-08-07

    Compositions, and methods of making thereof, comprising from about 1% to about 5% of a perfluorinated sulfonic acid ionomer or a hydrocarbon-based ionomer; and from about 95% to about 99% of a solvent, said solvent consisting essentially of a polyol; wherein said composition is substantially free of water and wherein said ionomer is uniformly dispersed in said solvent.

  4. Compositions and methods comprising cellulase variants with reduced affinity to non-cellulosic materials

    SciTech Connect

    Cascao-Pereira, Luis G; Kaper, Thijs; Kelemen, Bradley R; Liu, Amy D

    2015-04-07

    The present disclosure relates to cellulase variants. In particular the present disclosure relates to cellulase variants having reduced binding to non-cellulosic materials. Also described are nucleic acids encoding the cellulase, compositions comprising said cellulase, methods of identifying cellulose variants and methods of using the compositions.

  5. 29 CFR 452.12 - Organizations comprised of government employees.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 2 2010-07-01 2010-07-01 false Organizations comprised of government employees. 452.12... comprised of government employees. An organization composed entirely of government employees (other than... or intermediate labor organization which has some locals of government employees not covered by...

  6. 29 CFR 452.12 - Organizations comprised of government employees.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 2 2011-07-01 2011-07-01 false Organizations comprised of government employees. 452.12... comprised of government employees. An organization composed entirely of government employees (other than... or intermediate labor organization which has some locals of government employees not covered by...

  7. Enteral n-3 fatty acids and micronutrients enhance percentage of positive neutrophil and lymphocyte adhesion molecules: a potential mediator of pressure ulcer healing in critically ill patients.

    PubMed

    Theilla, Miriam; Schwartz, Betty; Zimra, Yael; Shapiro, Haim; Anbar, Ronit; Rabizadeh, Esther; Cohen, Jonathan; Singer, Pierre

    2012-04-01

    n-3 Fatty acids are recognised as influencing both wound healing and immunity. We assessed the impact of a fish oil- and micronutrient-enriched formula (study formula) on the healing of pressure ulcers and on immune function in critically ill patients in an intensive care unit. A total of forty patients with pressure ulcers and receiving nutritional support were enrolled (intervention group, n 20, received study formula; and a control group, n 20, received an isoenergetic formula). Total and differential leucocyte count and percentage of adhesion molecule positive granulocyte and lymphocyte cells (CD11a, CD11b, CD18 and CD49b) were measured on days 0, 7 and 14. Percentage of positive lymphocytes for CD54, CD49b, CD49d and CD8 were also measured on days 0, 7 and 14. The state of pressure ulcers was assessed by using the pressure ulcer scale for healing tool score on days 7, 14 and 28 of treatment. No between-group differences in patient demographics, anthropometry or diagnostic class were observed. Patients who received the study formula showed significant increases in the percentage of positive CD18 and CD11a lymphocytes and of CD49b granulocytes as compared to controls (P < 0·05). While the severity of pressure ulcers was not significantly different between the two groups on admission, severity increased significantly over time for the control group (P < 0·05), but not for the study group. The present study suggests that a fish oil- and micronutrient-enriched formula may prevent worsening of pressure ulcers and that this effect may be mediated by an effect on adhesion molecule expression.

  8. 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…

  9. Amino acid substitution at peptide-binding pockets of HLA class I molecules increases risk of severe acute GVHD and mortality

    PubMed Central

    Wang, Tao; Haagenson, Michael; Spellman, Stephen R.; Askar, Medhat; Battiwalla, Minoo; Baxter-Lowe, Lee Ann; Bitan, Menachem; Fernandez-Viña, Marcelo; Gandhi, Manish; Jakubowski, Ann A.; Maiers, Martin; Marino, Susana R.; Marsh, Steven G. E.; Oudshoorn, Machteld; Palmer, Jeanne; Prasad, Vinod K.; Reddy, Vijay; Ringden, Olle; Saber, Wael; Santarone, Stella; Schultz, Kirk R.; Setterholm, Michelle; Trachtenberg, Elizabeth; Turner, E. Victoria; Woolfrey, Ann E.; Lee, Stephanie J.; Anasetti, Claudio

    2013-01-01

    HLA disparity has a negative impact on the outcomes of hematopoietic cell transplantation (HCT). We studied the independent impact of amino acid substitution (AAS) at peptide-binding positions 9, 99, 116, and 156, and killer immunoglobulin-like receptor binding position 77 of HLA-A, B, or C, on the risks for grade 3-4 acute graft-versus-host disease (GVHD), chronic GVHD, treatment-related mortality (TRM), relapse, and overall survival. In multivariate analysis, a mismatch at HLA-C position 116 was associated with increased risk for severe acute GVHD (hazard ratio [HR] = 1.45, 95% confidence interval [CI] = 1.15-1.82, P = .0016). Mismatch at HLA-C position 99 was associated with increased transplant-related mortality (HR = 1.37, 95% CI = 1.1-1.69, P = .0038). Mismatch at HLA-B position 9 was associated with increased chronic GVHD (HR = 2.28, 95% CI = 1.36-3.82, P = .0018). No AAS were significantly associated with outcome at HLA-A. Specific AAS pair combinations with a frequency >30 were tested for association with HCT outcomes. Cysteine to tyrosine substitution at position 99 of HLA-C was associated with increased TRM (HR = 1.78, 95% = CI 1.27-2.51, P = .0009). These results demonstrate that donor-recipient mismatch for certain peptide-binding residues of the HLA class I molecule is associated with increased risk for acute and chronic GVHD and death. PMID:23982174

  10. 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.

  11. 7. Detail view of reinforced concrete archrings comprising dam's upstream ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. Detail view of reinforced concrete arch-rings comprising dam's upstream face. Impressions of the wooden formwork used in construction are visible in the concrete. - Little Rock Creek Dam, Little Rock Creek, Littlerock, Los Angeles County, CA

  12. Immunogenic compositions comprising human immunodeficiency virus (HIV) mosaic Nef proteins

    SciTech Connect

    Korber, Bette T.; Perkins, Simon; Bhattacharya, Tanmoy; Fischer, William M.; Theiler, James; Letvin, Norman; Haynes, Barton F.; Hahn, Beatrice H.; Yusim, Karina; Kuiken, Carla

    2012-02-21

    The present invention relates to mosaic clade M HIV-1 Nef polypeptides and to compositions comprising same. The polypeptides of the invention are suitable for use in inducing an immune response to HIV-1 in a human.

  13. Method to fabricate silicon chromatographic column comprising fluid ports

    DOEpatents

    Manginell, Ronald P.; Frye-Mason, Gregory C.; Heller, Edwin J.; Adkins, Douglas R.

    2004-03-02

    A new method for fabricating a silicon chromatographic column comprising through-substrate fluid ports has been developed. This new method enables the fabrication of multi-layer interconnected stacks of silicon chromatographic columns.

  14. Neutron detectors comprising ultra-thin layers of boron powder

    SciTech Connect

    Wang, Zhehul; Morris, Christopher

    2013-07-23

    High-efficiency neutron detector substrate assemblies comprising a first conductive substrate, wherein a first side of the substrate is in direct contact with a first layer of a powder material having a thickness of from about 50 nm to about 250 nm and comprising .sup.10boron, .sup.10boron carbide or combinations thereof, and wherein a conductive material is in proximity to the first layer of powder material; and processes of making said neutron detector substrate assemblies.

  15. 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)

  16. 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)

  17. Interstellar molecules

    NASA Astrophysics Data System (ADS)

    Smith, D.

    1987-09-01

    Some 70 different molecular species have so far been detected variously in diffuse interstellar clouds, dense interstellar clouds, and circumstellar shells. Only simple (diatomic and triatomic) species exist in diffuse clouds because of the penetration of destructive UV radiations, whereas more complex (polyatomic) molecules survive in dense clouds as a result of the shielding against this UV radiation provided by dust grains. A current list of interstellar molecules is given together with a few other molecular species that have so far been detected only in circumstellar shells. Also listed are those interstellar species that contain rare isotopes of several elements. The gas phase ion chemistry is outlined via which the observed molecules are synthesized, and the process by which enrichment of the rare isotopes occurs in some interstellar molecules is described.

  18. 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.

  19. 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.

  20. 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

  1. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study.

    PubMed

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2015-09-01

    The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  2. 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

  3. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study.

    PubMed

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2015-09-01

    The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  4. 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

  5. Electrocatalytic oxidation of small organic molecules in acid medium: enhancement of activity of noble metal nanoparticles and their alloys by supporting or modifying them with metal oxides.

    PubMed

    Kulesza, Pawel J; Pieta, Izabela S; Rutkowska, Iwona A; Wadas, Anna; Marks, Diana; Klak, Karolina; Stobinski, Leszek; Cox, James A

    2013-11-01

    Different approaches to enhancement of electrocatalytic activity of noble metal nanoparticles during oxidation of small organic molecules (namely potential fuels for low-temperature fuel cells such as methanol, ethanol and formic acid) are described. A physical approach to the increase of activity of catalytic nanoparticles (e.g. platinum or palladium) involves nanostructuring to obtain highly dispersed systems of high surface area. Recently, the feasibility of enhancing activity of noble metal systems through the formation of bimetallic (e.g. PtRu, PtSn, and PdAu) or even more complex (e.g. PtRuW, PtRuSn) alloys has been demonstrated. In addition to possible changes in the electronic properties of alloys, specific interactions between metals as well as chemical reactivity of the added components have been postulated. We address and emphasize here the possibility of utilization of noble metal and alloyed nanoparticles supported on robust but reactive high surface area metal oxides (e.g. WO3, MoO3, TiO2, ZrO2, V2O5, and CeO2) in oxidative electrocatalysis. This paper concerns the way in which certain inorganic oxides and oxo species can act effectively as supports for noble metal nanoparticles or their alloys during electrocatalytic oxidation of hydrogen and representative organic fuels. Among important issues are possible changes in the morphology and dispersion, as well as specific interactions leading to the improved chemisorptive and catalytic properties in addition to the feasibility of long time operation of the discussed systems.

  6. Compositions, methods, and systems comprising fluorous-soluble polymers

    SciTech Connect

    Swager, Timothy M.; Lim, Jeewoo; Takeda, Yohei

    2015-10-13

    The present invention generally relates to compositions, methods, and systems comprising polymers that are fluorous-soluble and/or organize at interfaces between a fluorous phase and a non-fluorous phase. In some embodiments, emulsions or films are provided comprising a polymer. The polymers, emulsions, and films can be used in many applications, including for determining, treating, and/or imaging a condition and/or disease in a subject. The polymer may also be incorporated into various optoelectronic device such as photovoltaic cells, organic light-emitting diodes, organic field effect transistors, or the like. In some embodiments, the polymers comprise pi-conjugated backbones, and in some cases, are highly emissive.

  7. Thermoacoustic refrigerators and engines comprising cascading stirling thermodynamic units

    SciTech Connect

    Backhaus, Scott; Swift, Greg

    2013-06-25

    The present invention includes a thermoacoustic assembly and method for improved efficiency. The assembly has a first stage Stirling thermal unit comprising a main ambient heat exchanger, a regenerator and at least one additional heat exchanger. The first stage Stirling thermal unit is serially coupled to a first end of a quarter wavelength long coupling tube. A second stage Stirling thermal unit comprising a main ambient heat exchanger, a regenerator, and at least one additional heat exchanger, is serially coupled to a second end of the quarter wavelength long coupling tube.

  8. Non-cementitious compositions comprising vaterite and methods thereof

    SciTech Connect

    Devenney, Martin; Fernandez, Miguel; Morgan, Samuel O.

    2015-09-15

    Non-cementitious compositions and products are provided. The compositions of the invention include a carbonate additive comprising vaterite such as reactive vaterite. Additional aspects of the invention include methods of making and using the non-cementitious compositions and products.

  9. Substrate comprising a nanometer-scale projection array

    DOEpatents

    Cui, Yi; Zhu, Jia; Hsu, Ching-Mei; Connor, Stephen T; Yu, Zongfu; Fan, Shanhui; Burkhard, George

    2012-11-27

    A method for forming a substrate comprising nanometer-scale pillars or cones that project from the surface of the substrate is disclosed. The method enables control over physical characteristics of the projections including diameter, sidewall angle, and tip shape. The method further enables control over the arrangement of the projections including characteristics such as center-to-center spacing and separation distance.

  10. Reclaiming metallic material from an article comprising a non-metallic friable substrate

    DOEpatents

    Bohland, John Raphael; Anisimov, Igor Ivanovich; Dapkus, Todd James; Sasala, Richard Anthony; Smigielski, Ken Alan; Kamm, Kristin Danielle

    2000-01-01

    A method for reclaiming a metallic material from a article including a non-metallic friable substrate. The method comprising crushing the article into a plurality of pieces. An acidic solution capable of dissolving the metallic material is provided dissolving the metallic material in the acidic material to form an etchant effluent. The etchant effluent is separated from the friable substrate. A precipitation agent, capable of precipitating the metallic material, is added to the etchant effluent to precipitate out the metallic material from the etchant effluent. The metallic material is then recovered.

  11. 'Escentric' molecules.

    PubMed

    Schön, Geza

    2008-06-01

    Can a fragrance be revolutionary? In this commentary, the creation of two unusual, extravagant fine fragrances, 'escentric01' and 'molecule01', is described. In response to the fantasy components found in release notes of many recent perfume launches, both center around a single real fragrance raw material, the transparent woody aroma chemical 'Iso E Super' (1+2). The perfume 'escentric01' contains 65% of it, accompanied by Trisamber (3), red pepper, lime oil, incense and musks, while 'molecule01' consists exclusively of 'Iso E Super' (1+2). The elegant woody note lives here its own eccentric life--the revolution starts.

  12. Optical modulation of nano-gap tunnelling junctions comprising self-assembled monolayers of hemicyanine dyes.

    PubMed

    Pourhossein, Parisa; Vijayaraghavan, Ratheesh K; Meskers, Stefan C J; Chiechi, Ryan C

    2016-01-01

    Light-driven conductance switching in molecular tunnelling junctions that relies on photoisomerization is constrained by the limitations of kinetic traps and either by the sterics of rearranging atoms in a densely packed monolayer or the small absorbance of individual molecules. Here we demonstrate light-driven conductance gating; devices comprising monolayers of hemicyanine dyes trapped between two metallic nanowires exhibit higher conductance under irradiation than in the dark. The modulation of the tunnelling current occurs faster than the timescale of the measurement (∼1 min). We propose a mechanism in which a fraction of molecules enters an excited state that brings the conjugated portion of the monolayer into resonance with the electrodes. This mechanism is supported by calculations showing the delocalization of molecular orbitals near the Fermi energy in the excited and cationic states, but not the ground state and a reasonable change in conductance with respect to the effective barrier width. PMID:27272394

  13. Optical modulation of nano-gap tunnelling junctions comprising self-assembled monolayers of hemicyanine dyes

    PubMed Central

    Pourhossein, Parisa; Vijayaraghavan, Ratheesh K.; Meskers, Stefan C. J.; Chiechi, Ryan C.

    2016-01-01

    Light-driven conductance switching in molecular tunnelling junctions that relies on photoisomerization is constrained by the limitations of kinetic traps and either by the sterics of rearranging atoms in a densely packed monolayer or the small absorbance of individual molecules. Here we demonstrate light-driven conductance gating; devices comprising monolayers of hemicyanine dyes trapped between two metallic nanowires exhibit higher conductance under irradiation than in the dark. The modulation of the tunnelling current occurs faster than the timescale of the measurement (∼1 min). We propose a mechanism in which a fraction of molecules enters an excited state that brings the conjugated portion of the monolayer into resonance with the electrodes. This mechanism is supported by calculations showing the delocalization of molecular orbitals near the Fermi energy in the excited and cationic states, but not the ground state and a reasonable change in conductance with respect to the effective barrier width. PMID:27272394

  14. Formulation and method for preparing gels comprising hydrous hafnium oxide

    SciTech Connect

    Collins, Jack L; Hunt, Rodney D; Montgomery, Frederick C

    2013-08-06

    Formulations useful for preparing hydrous hafnium oxide gels contain a metal salt including hafnium, an acid, an organic base, and a complexing agent. Methods for preparing gels containing hydrous hafnium oxide include heating a formulation to a temperature sufficient to induce gel formation, where the formulation contains a metal salt including hafnium, an acid, an organic base, and a complexing agent.

  15. Elastohydrodynamics of farm-based blends comprising amphiphilic oils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vegetable oils contain non-polar hydrocarbon chains and polar ester groups (and possibly also other functional groups such as hydroxyl groups in castor oil). The presence of polar and non-polar groups within the same molecule gives vegetable oil amphiphilic character. The density, refractive index, ...

  16. Recyclable organic solar cells on substrates comprising cellulose nanocrystals (CNC)

    DOEpatents

    Kippelen, Bernard; Fuentes-Hernandez, Canek; Zhou, Yinhua; Moon, Robert; Youngblood, Jeffrey P

    2015-12-01

    Recyclable organic solar cells are disclosed herein. Systems and methods are further disclosed for producing, improving performance, and for recycling the solar cells. In certain example embodiments, the recyclable organic solar cells disclosed herein include: a first electrode; a second electrode; a photoactive layer disposed between the first electrode and the second electrode; an interlayer comprising a Lewis basic oligomer or polymer disposed between the photoactive layer and at least a portion of the first electrode or the second electrode; and a substrate disposed adjacent to the first electrode or the second electrode. The interlayer reduces the work function associated with the first or second electrode. In certain example embodiments, the substrate comprises cellulose nanocrystals that can be recycled. In certain example embodiments, one or more of the first electrode, the photoactive layer, and the second electrode may be applied by a film transfer lamination method.

  17. Attachment of second harmonic-active moiety to molecules for detection of molecules at interfaces

    DOEpatents

    Salafsky, Joshua S.; Eisenthal, Kenneth B.

    2005-10-11

    This invention provides methods of detecting molecules at an interface, which comprise labeling the molecules with a second harmonic-active moiety and detecting the labeled molecules at the interface using a surface selective technique. The invention also provides methods for detecting a molecule in a medium and for determining the orientation of a molecular species within a planar surface using a second harmonic-active moiety and a surface selective technique.

  18. High temperature battery cell comprising stress free hollow fiber bundle

    SciTech Connect

    Anand, J. N.; Revak, T. T.; Rossini, F. J.

    1985-04-16

    Thermal stressing of hollow fibers constituting the electrolyte-separator in a high temperature battery cell, and of certain other elements thereof, is avoided by suspending the assembly comprising the anolyte tank, the tube-sheet, the hollow fibers and a cathodic current collector-distributor within the casing and employing a limp connection between the collector-distributor and the cathode terminal of the cell.

  19. Influence of dietary supplementation with long-chain n-3 or n-6 polyunsaturated fatty acids on blood inflammatory cell populations and functions and on plasma soluble adhesion molecules in healthy adults.

    PubMed

    Thies, F; Miles, E A; Nebe-von-Caron, G; Powell, J R; Hurst, T L; Newsholme, E A; Calder, P C

    2001-11-01

    Greatly increasing the amounts of flaxseed oil [rich in alpha-linolenic acid (ALNA)] or fish oil (FO); [rich in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)] in the diet can decrease inflammatory cell functions and so might impair host defense. The objective of this study was to determine the effect of dietary supplementation with moderate levels of ALNA, gamma-linolenic acid (GLA), arachidonic acid (ARA), DHA, or FO on inflammatory cell numbers and functions and on circulating levels of soluble adhesion molecules. Healthy subjects aged 55 to 75 yr consumed nine capsules per day for 12 wk. The capsules contained placebo oil (an 80:20 mix of palm and sunflowerseed oils) or blends of placebo oil with oils rich in ALNA, GLA, ARA, or DHA or FO. Subjects in these groups consumed 2 g ALNA; approximately 700 mg GLA, ARA, or DHA; or 1 g EPA plus DHA (720 mg EPA + 280 mg DHA) daily from the capsules. Total fat intake from the capsules was 4 g per day. None of the treatments affected inflammatory cell numbers in the bloodstream; neutrophil and monocyte phagocytosis or respiratory burst in response to E. coli; production of tumor necrosis factor-alpha, interleukin-1beta, and interleukin-6 in response to bacterial lipopolysaccharide; or plasma concentrations of soluble intercellular adhesion molecule-1. In contrast, the ALNA and FO treatments decreased the plasma concentrations of soluble vascular cell adhesion molecule-1 (16 and 28% decrease, respectively) and soluble E-selectin (23 and 17% decrease, respectively). It is concluded that, in contrast to previous reports using higher amounts of these fatty acids, a moderate increase in consumption of long-chain n-6 or n-3 polyunsaturated fatty acids does not significantly affect inflammatory cell numbers or neutrophil and monocyte responses in humans and so would not be expected to cause immune impairment. Furthermore, we conclude that moderate levels of ALNA and FO, which could be incorporated into the diet, can

  20. 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

  1. Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond.

    PubMed

    Staniforth, Michael; Stavros, Vasilios G

    2013-11-01

    In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach.

  2. System comprising interchangeable electronic controllers and corresponding methods

    NASA Technical Reports Server (NTRS)

    Steele, Glen F. (Inventor); Salazar, George A. (Inventor)

    2009-01-01

    A system comprising an interchangeable electronic controller is provided with programming that allows the controller to adapt a behavior that is dependent upon the particular type of function performed by a system or subsystem component. The system reconfigures the controller when the controller is moved from one group of subsystem components to another. A plurality of application programs are provided by a server from which the application program for a particular electronic controller is selected. The selection is based on criteria such as a subsystem component group identifier that identifies the particular type of function associated with the system or subsystem group of components.

  3. Multilayer Electroactive Polymer Composite Material Comprising Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Ounaies, Zoubeida (Inventor); Park, Cheol (Inventor); Harrison, Joycelyn S. (Inventor); Holloway, Nancy M. (Inventor); Draughon, Gregory K. (Inventor)

    2009-01-01

    An electroactive material comprises multiple layers of electroactive composite with each layer having unique dielectric, electrical and mechanical properties that define an electromechanical operation thereof when affected by an external stimulus. For example, each layer can be (i) a 2-phase composite made from a polymer with polarizable moieties and an effective amount of carbon nanotubes incorporated in the polymer for a predetermined electromechanical operation, or (ii) a 3-phase composite having the elements of the 2-phase composite and further including a third component of micro-sized to nano-sized particles of an electroactive ceramic incorporated in the polymer matrix.

  4. Walking molecules.

    PubMed

    von Delius, Max; Leigh, David A

    2011-07-01

    Movement is intrinsic to life. Biologists have established that most forms of directed nanoscopic, microscopic and, ultimately, macroscopic movements are powered by molecular motors from the dynein, myosin and kinesin superfamilies. These motor proteins literally walk, step by step, along polymeric filaments, carrying out essential tasks such as organelle transport. In the last few years biological molecular walkers have inspired the development of artificial systems that mimic aspects of their dynamics. Several DNA-based molecular walkers have been synthesised and shown to walk directionally along a track upon sequential addition of appropriate chemical fuels. In other studies, autonomous operation--i.e. DNA-walker migration that continues as long as a complex DNA fuel is present--has been demonstrated and sophisticated tasks performed, such as moving gold nanoparticles from place-to-place and assistance in sequential chemical synthesis. Small-molecule systems, an order of magnitude smaller in each dimension and 1000× smaller in molecular weight than biological motor proteins or the walker systems constructed from DNA, have also been designed and operated such that molecular fragments can be progressively transported directionally along short molecular tracks. The small-molecule systems can be powered by light or chemical fuels. In this critical review the biological motor proteins from the kinesin, myosin and dynein families are analysed as systems from which the designers of synthetic systems can learn, ratchet concepts for transporting Brownian substrates are discussed as the mechanisms by which molecular motors need to operate, and the progress made with synthetic DNA and small-molecule walker systems reviewed (142 references). PMID:21416072

  5. Photovoltaic device comprising compositionally graded intrinsic photoactive layer

    DOEpatents

    Hoffbauer, Mark A; Williamson, Todd L

    2013-04-30

    Photovoltaic devices and methods of making photovoltaic devices comprising at least one compositionally graded photoactive layer, said method comprising providing a substrate; growing onto the substrate a uniform intrinsic photoactive layer having one surface disposed upon the substrate and an opposing second surface, said intrinsic photoactive layer consisting essentially of In.sub.1-xA.sub.xN,; wherein: i. 0.ltoreq.x.ltoreq.1; ii. A is gallium, aluminum, or combinations thereof; and iii. x is at least 0 on one surface of the intrinsic photoactive layer and is compositionally graded throughout the layer to reach a value of 1 or less on the opposing second surface of the layer; wherein said intrinsic photoactive layer is isothermally grown by means of energetic neutral atom beam lithography and epitaxy at a temperature of 600.degree. C. or less using neutral nitrogen atoms having a kinetic energy of from about 1.0 eV to about 5.0 eV, and wherein the intrinsic photoactive layer is grown at a rate of from about 5 nm/min to about 100 nm/min.

  6. High power density fuel cell comprising an array of microchannels

    DOEpatents

    Sopchak, David A; Morse, Jeffrey D; Upadhye, Ravindra S; Kotovsky, Jack; Graff, Robert T

    2014-05-06

    A phosphoric acid fuel cell according to one embodiment includes an array of microchannels defined by a porous electrolyte support structure extending between bottom and upper support layers, the microchannels including fuel and oxidant microchannels; fuel electrodes formed along some of the microchannels; and air electrodes formed along other of the microchannels. A method of making a phosphoric acid fuel cell according to one embodiment includes etching an array of microchannels in a substrate, thereby forming walls between the microchannels; processing the walls to make the walls porous, thereby forming a porous electrolyte support structure; forming anode electrodes along some of the walls; forming cathode electrodes along other of the walls; and filling the porous electrolyte support structure with a phosphoric acid electrolyte. Additional embodiments are also disclosed.

  7. An effective nanosensor for organic molecules based on water-soluble mercaptopropionic acid-capped CdTe nanocrystals with potential application in high-throughput screening and high-resolution optical microscopy.

    PubMed

    Lau, Pick-Chung; Norwood, Robert A; Mansuripur, Masud; Peyghambarian, Nasser

    2014-07-01

    Specially-treated glass substrates coated with a thin film of water soluble mercaptopropionic acid (MPA) capped CdTe nanocrystals (NCs) were prepared and found to undergo photoluminescence changes by as much as 40% when micro-droplets of organic molecules were placed in the nanometer-range proximity of the NCs. This imaging technique involving close proximity between a nano-crystal and an organic molecule is found to provide a 2 × -3 × enhanced contrast ratio over the conventional method of fluorescence imaging. Photoluminescence of NCs is recoverable upon removal of the organic molecules, therefore validating these NCs as potential all-optical organic molecular nanosensors. Upon optimization and with proper instrumentation, these nano-crystals could eventually serve as point-detectors for purposes of super-resolution optical microscopy. No solvents are required for the proposed sensing mechanism since all solutions were dried under argon flow. Fluorophores and fluorescent proteins were investigated, including fluorescein, Rhodamine 6G, and green fluorescent protein (GFP). Furthermore, NC photoluminescence changes were systematically quantified as a function of the solution pH and of the organic molecule concentration. Long duration (> 40 minutes) continuous excitation studies were conducted in order to evaluate the reliability of the proposed sensing scheme.

  8. An effective nanosensor for organic molecules based on water-soluble mercaptopropionic acid-capped CdTe nanocrystals with potential application in high-throughput screening and high-resolution optical microscopy

    PubMed Central

    Lau, Pick-Chung; Norwood, Robert A.; Mansuripur, Masud; Peyghambarian, Nasser

    2014-01-01

    Specially-treated glass substrates coated with a thin film of water soluble mercaptopropionic acid (MPA) capped CdTe nanocrystals (NCs) were prepared and found to undergo photoluminescence changes by as much as 40% when micro-droplets of organic molecules were placed in the nanometer-range proximity of the NCs. This imaging technique involving close proximity between a nano-crystal and an organic molecule is found to provide a 2 × –3 × enhanced contrast ratio over the conventional method of fluorescence imaging. Photoluminescence of NCs is recoverable upon removal of the organic molecules, therefore validating these NCs as potential all-optical organic molecular nanosensors. Upon optimization and with proper instrumentation, these nano-crystals could eventually serve as point-detectors for purposes of super-resolution optical microscopy. No solvents are required for the proposed sensing mechanism since all solutions were dried under argon flow. Fluorophores and fluorescent proteins were investigated, including fluorescein, Rhodamine 6G, and green fluorescent protein (GFP). Furthermore, NC photoluminescence changes were systematically quantified as a function of the solution pH and of the organic molecule concentration. Long duration (> 40 minutes) continuous excitation studies were conducted in order to evaluate the reliability of the proposed sensing scheme. PMID:25071975

  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. Essential fatty acids and their metabolites could function as endogenous HMG-CoA reductase and ACE enzyme inhibitors, anti-arrhythmic, anti-hypertensive, anti-atherosclerotic, anti-inflammatory, cytoprotective, and cardioprotective molecules.

    PubMed

    Das, Undurti N

    2008-01-01

    Lowering plasma low density lipoprotein-cholesterol (LDL-C), blood pressure, homocysteine, and preventing platelet aggregation using a combination of a statin, three blood pressure lowering drugs such as a thiazide, a beta blocker, and an angiotensin converting enzyme (ACE) inhibitor each at half standard dose; folic acid; and aspirin-called as polypill- was estimated to reduce cardiovascular events by approximately 80%. Essential fatty acids (EFAs) and their long-chain metabolites: gamma-linolenic acid (GLA), dihomo-GLA (DGLA), arachidonic acid, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) and other products such as prostaglandins E1 (PGE1), prostacyclin (PGI2), PGI3, lipoxins (LXs), resolvins, protectins including neuroprotectin D1 (NPD1) prevent platelet aggregation, lower blood pressure, have anti-arrhythmic action, reduce LDL-C, ameliorate the adverse actions of homocysteine, show anti-inflammatory actions, activate telomerase, and have cytoprotective properties. Thus, EFAs and their metabolites show all the classic actions expected of the "polypill". Unlike the proposed "polypill", EFAs are endogenous molecules present in almost all tissues, have no significant or few side effects, can be taken orally for long periods of time even by pregnant women, lactating mothers, and infants, children, and adults; and have been known to reduce the incidence cardiovascular diseases including stroke. In addition, various EFAs and their long-chain metabolites not only enhance nitric oxide generation but also react with nitric oxide to yield their respective nitroalkene derivatives that produce vascular relaxation, inhibit neutrophil degranulation and superoxide formation, inhibit platelet activation, and possess PPAR-gamma ligand activity and release NO, thus prevent platelet aggregation, thrombus formation, atherosclerosis, and cardiovascular diseases. Based on these evidences, I propose that a rational combination of omega-3 and omega-6 fatty acids and the

  11. Hysteresis free carbon nanotube thin film transistors comprising hydrophobic dielectrics

    NASA Astrophysics Data System (ADS)

    Lefebvre, J.; Ding, J.; Li, Z.; Cheng, F.; Du, N.; Malenfant, P. R. L.

    2015-12-01

    We present two examples of carbon nanotube network thin film transistors with strongly hydrophobic dielectrics comprising either Teflon-AF or a poly(vinylphenol)/poly(methyl silsesquioxane) (PVP/pMSSQ) blend. In the absence of encapsulation, bottom gated transistors in air ambient show no hysteresis between forward and reverse gate sweep direction. Device threshold gate voltage and On-current present excellent time dependent stability even under dielectric stress. Furthermore, threshold gate voltage for hole conduction is negative upon device encapsulation with PVP/pMSSQ enabling much improved current On/Off ratio at 0 V. This work addresses two major challenges impeding solution based fabrication of relevant thin film transistors with printable single-walled carbon nanotube channels.

  12. Rigorous calculation of nonlinear parameters in graphene-comprising waveguides

    NASA Astrophysics Data System (ADS)

    Chatzidimitriou, Dimitrios; Pitilakis, Alexandros; Kriezis, Emmanouil E.

    2015-07-01

    We describe a rigorous formalism for the calculation of the nonlinear parameter of arbitrary three-dimensional nanophotonic graphene-comprising waveguides. Graphene is naturally implemented as a zero-thickness conductive sheet, modeled solely by complex linear and nonlinear surface conductivity tensors, whose values are extracted from theoretical models. This representation is compared to the more commonly employed equivalent bulk-medium representation and is found superior. We numerically calculate the nonlinear parameters of several optical waveguide archetypes overlaid with infinite graphene monolayers, including silicon-wire and plasmonic metal-slot and metal-stripe configurations. The metal-slot configuration offers the most promising performance for Kerr-type nonlinear applications. Finally, we apply the same formalism to probe the potential of graphene nanoribbon waveguide nonlinearity in the terahertz band.

  13. Dynamical configurations of celestial systems comprised of multiple irregular bodies

    NASA Astrophysics Data System (ADS)

    Jiang, Yu; Zhang, Yun; Baoyin, Hexi; Li, Junfeng

    2016-09-01

    This manuscript considers the main features of the nonlinear dynamics of multiple irregular celestial body systems. The gravitational potential, static electric potential, and magnetic potential are considered. Based on the three established potentials, we show that three conservative values exist for this system, including a Jacobi integral. The equilibrium conditions for the system are derived and their stability analyzed. The equilibrium conditions of a celestial system comprised of n irregular bodies are reduced to 12n - 9 equations. The dynamical results are applied to simulate the motion of multiple-asteroid systems. The simulation is useful for the study of the stability of multiple irregular celestial body systems and for the design of spacecraft orbits to triple-asteroid systems discovered in the solar system. The dynamical configurations of the five triple-asteroid systems 45 Eugenia, 87 Sylvia, 93 Minerva, 216 Kleopatra, and 136617 1994CC, and the six-body system 134340 Pluto are calculated and analyzed.

  14. 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.

  15. Alcohol dose dumping: The influence of ethanol on hot-melt extruded pellets comprising solid lipids.

    PubMed

    Jedinger, N; Schrank, S; Mohr, S; Feichtinger, A; Khinast, J; Roblegg, E

    2015-05-01

    The objective of the present study was to investigate interactions between alcohol and hot-melt extruded pellets and the resulting drug release behavior. The pellets were composed of vegetable calcium stearate as matrix carrier and paracetamol or codeine phosphate as model drugs. Two solid lipids (Compritol® and Precirol®) were incorporated into the matrix to form robust/compact pellets. The drug release characteristics were a strong function of the API solubility, the addition of solid lipids, the dissolution media composition (i.e., alcohol concentration) and correspondingly, the pellet wettability. Pellets comprising paracetamol, which is highly soluble in ethanol, showed alcohol dose dumping regardless of the matrix composition. The wettability increased with increasing ethanol concentrations due to higher paracetamol solubilities yielding increased dissolution rates. For pellets containing codeine phosphate, which has a lower solubility in ethanol than in acidic media, the wettability was a function of the matrix composition. Dose dumping occurred for formulations comprising solid lipids as they showed increased wettabilities with increasing ethanol concentrations. In contrast, pellets comprising calcium stearate as single matrix component showed robustness in alcoholic media due to wettabilities that were not affected by the addition of ethanol. The results clearly indicate that the physico-chemical properties of the drug and the matrix systems are crucial for the design of ethanol-resistant dosage forms. Moreover, hydrophobic calcium stearate can be considered a suitable matrix system that minimizes the risk of ethanol-induced dose dumping for certain API's.

  16. STREPTOMYCES SPECIES COMPRISING THE BLUE-SPORE SERIES

    PubMed Central

    Trejo, W. H.; Bennett, R. E.

    1963-01-01

    Trejo, W. H. (Squibb Institute for Medical Research, New Brunswick, N.J.) and R. E. Bennett. Streptomyces species comprising the blue-spore series. J. Bacteriol. 85:676–690. 1963.—The objective of this study was to define and delimit the streptomycetes of the blue-spored (Viridochromogenes) series. The series, as defined in this study, includes 11 blue and blue-green species. The green-spored species were excluded on the basis of morphology as well as color. It was proposed that NRRL B-1511 be designated as the neotype strain of Streptomyces viridochromogenes (Krainsky) Waksman and Henrici, and that IMRU 3761 be designated as the neotype for Streptomyces cyaneus (Krassilnikov) Waksman. Evidence was presented to show that physiological criteria cannot be used to differentiate these organisms below the series level. The major characteristics of the Viridochromogenes series are blue to blue-green spores borne in spirals, and chromogenicity (melanin-positive). Reverse color and spore morphology provide a basis for separation below the series level. Images PMID:14042949

  17. Polyomavirus origin for DNA replication comprises multiple genetic elements.

    PubMed Central

    Muller, W J; Mueller, C R; Mes, A M; Hassell, J A

    1983-01-01

    To define the minimal cis-acting sequences required for polyomavirus DNA replication (ori), we constructed a number of polyomavirus-plasmid recombinants and measured their replicative capacity after transfection of a permissive mouse cell line capable of providing polyomavirus large T antigen in trans (MOP cells). Recombinant plasmids containing a 251-base-pair fragment of noncoding viral DNA replicate efficiently in MOP cells. Mutational analyses of these viral sequences revealed that they can be physically separated into two genetic elements. One of these elements, termed the core, contains an adenine-thymine-rich area, a 32-base-pair guanine-cytosine-rich palindrome, and a large T antigen binding site, and likely includes the site from which bidirectional DNA replication initiates. The other, termed beta, is located adjacent to the core near the late region and is devoid of outstanding sequence features. Surprisingly, another sequence element named alpha, located adjacent to beta but outside the borders of the 251-base-pair fragment, can functionally substitute for beta. This sequence too contains no readily recognized sequence features and possesses no obvious homology to the beta element. The three elements together occupy a contiguous noncoding stretch of DNA no more than 345 base pairs in length in the order alpha, beta, and core. These results indicate that the polyomavirus origin for DNA replication comprises multiple genetic elements. Images PMID:6312083

  18. 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.

  19. Effect of in ovo feeding of folic acid on the folate metabolism, immune function and epigenetic modification of immune effector molecules of broiler.

    PubMed

    Li, Shizhao; Zhi, Lihui; Liu, Yanli; Shen, Jing; Liu, Lei; Yao, Junhu; Yang, Xiaojun

    2016-02-14

    This study was conducted to investigate the effect of in ovo feeding (IOF) of folic acid on the folate metabolism, immune function and the involved epigenetic modification of broilers. A total of 400 (Cobb) hatching eggs were randomly divided into four groups (0, 50, 100 and 150 µg injection of folic acid at embryonic age 11 d), and chicks hatched from each treatment were randomly divided into six replicates with 12 broilers/replicate after incubation. The results indicated that, in ovo, 100- and 150-µg folic acid injections improved the hatchability. The average daily gain and feed conversion ratio increased in the 150-µg group during the late growth stage. Simultaneously, in the 100- and 150-µg groups, an increase was observed in hepatic folate content and the expression of methylenetetrahydrofolate reductase (d1 and 42) and methionine synthase reductase (d21). IgG and IgM concentrations, as well as plasma lysozyme activity of broilers, showed a marked increase along with increasing folic acid levels. The splenic expression levels of IL-2 and IL-4 were up-regulated, whereas that of IL-6 was down-regulated, in the 100- and 150-µg folic acid treatment groups. In addition, histone methylation in IL-2 and IL-4 promoters exhibited an enrichment of H3K4m2 but a loss of H3K9me2 with the increased amount of folic acid additive. In contrast, a decrease in H3K4m2 and an increase in H3K9me2 were observed in the IL-6 promoter in folic acid treatments. Furthermore, in ovo, the 150-µg folic acid injection improved the chromatin tightness of the IL-2 and IL-4 promoter regions. Our findings suggest that IOF of 150 µg of folic acid can improve the growth performance and folate metabolism of broilers, and enhance the relationship between immune function and epigenetic regulation of immune genes, which are involved with the alterations in chromatin conformation and histone methylation in their promoters. PMID:26586196

  20. 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.

  1. 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.

  2. Well acidizing compositions and methods

    SciTech Connect

    Swanson, B. L.

    1980-12-23

    Gelled acidic compositions suitable for matrix acidizing or fracture acidizing of subterranean formations are provided comprising water, a water-dispersible polymeric viscosifier such as a polymer of acrylamide, an acid, and a polyphenolic material such as lignite.

  3. Searching for new NO-donor aspirin-like molecules: a new class of nitrooxy-acyl derivatives of salicylic acid.

    PubMed

    Lazzarato, Loretta; Donnola, Monica; Rolando, Barbara; Marini, Elisabetta; Cena, Clara; Coruzzi, Gabriella; Guaita, Elena; Morini, Giuseppina; Fruttero, Roberta; Gasco, Alberto; Biondi, Stefano; Ongini, Ennio

    2008-03-27

    A new class of products in which the phenol group of salicylic acid is linked to alkanoyl moieties bearing nitrooxy functions has been synthesized and studied for their polyvalent actions. The products were stable in acid and neutral media, while they were hydrolyzed in human serum. Their half-lives were dependent upon the structure of alkanoyl moieties. The products showed anti-inflammatory activities similar to aspirin when tested in the carrageenan-induced paw edema assay in the rat. Interestingly, unlike aspirin, they showed reduced or no gastrotoxicity in a lesion model in rats at equimolar doses. A number of them were able to inhibit platelet aggregation induced by collagen in human platelet-rich plasma. All of the products were capable of relaxing rat aortic strips precontracted with phenylephrine in a concentration-dependent manner. Selected members of this new class of nonsteroidal anti-inflammatory drugs might represent possible safer alternatives to aspirin in different clinical settings.

  4. Proteins Are the Body's Worker Molecules

    MedlinePlus

    ... Each "bead" is a small molecule called an amino acid. There are 20 standard amino acids, each with its own shape, size, and properties. Proteins typically contain from 50 to 2,000 amino acids hooked end-to-end in many combinations. Each ...

  5. 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.

  6. 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.

  7. Biological Diversity Comprising Microbial Structures of Antarctic Ice Covered Lakes

    NASA Astrophysics Data System (ADS)

    Matys, E. D.

    2015-12-01

    Analysis of microbial membrane lipids is a rapid and non-selective method for evaluating the composition of microbial communities. To fully realise the diagnostic potential of these lipids, we must first understand their structural diversity, biological sources, physiological functions, and pathways of preservation. Particular environmental conditions likely prompt the production of different membrane lipid structures. Antarctica's McMurdo Dry Valleys host numerous ice-covered lakes with sharp chemical gradients that vary in illumination, geochemical structure, and benthic mat morphologies that are structured by nutrient availability and water chemistry. The lipid contents of these benthic mats have not received extensive study nor have the communities yet been thoroughly characterized. Accordingly, a combination of lipid biomarker and nucleic acid sequence data provides the means of assessing species diversity and environmental controls on the composition and diversity of membrane lipid assemblages. We investigated the richness and diversity of benthic microbial communities and accumulated organic matter in Lake Vanda of the McMurdo Dry Valleys. We have identified diverse glycolipids, aminolipids, and phospholipids in addition to many unknown compounds that may be specific to these particular environments. Light levels fluctuate seasonally, favoring low-light-tolerant cyanobacteria and specific lipid assemblages. Adaptations to nutrient limitations are reflected in contrasting intact polar lipid assemblages. For example, under P-limiting conditions, phospholipids are subsidiary to membrane-forming lipids that do not contain P (i.e. ornithine, betaine, and sulfolipids). The bacteriohopanepolyol (BHP) composition is dominated by bacteriohopanetetrol (BHT), a ubiquitous BHP, and 2-methylhopanoids. The relative abundance of 2-methylhopanoids is unprecedented and may reflect the unusual seasonal light regime of this polar environment. By establishing correlations

  8. Cycling of soluble lead flow cells comprising a honeycomb-shaped positive electrode

    NASA Astrophysics Data System (ADS)

    Oury, A.; Kirchev, A.; Bultel, Y.

    2014-10-01

    In this study, soluble lead/methanesulfonic acid flow cells comprising a 3-D honeycomb-shaped positive electrode sandwiched between two planar negative electrodes are tested under galvanostatic cycling. Two types of materials are used for the honeycomb: homemade vitreous carbon/carbon composite and graphite. The cells comprising the C/C composite substrate shows a poor cyclability with coulombic and energy efficiencies below 80% and 50%, respectively, as well as a very limited lifetime. After a few tens of cycles, the cells cannot be discharged any longer due to the emergence of overvoltages associated with the passivation of the positive electrode in the discharged states. Using the graphite-based electrode, the cyclability is considerably improved: efficiencies of 95% in charge and 75% in energy are obtained, a hundred of cycles can be achieved and no passivation is observed. The cycle life of the cell is, however, limited by lead dendrite-like formation at the negative plates. Finally, this study shows that the incorporation of fluoride ions into the electrolyte improves greatly the adhesion of PbO2 on the positive electrode surface upon cycling.

  9. Discovery of molecules for the treatment of neuropathic pain: synthesis, antiallodynic and antihyperalgesic activities of 5-(4-nitrophenyl)furoic-2-acid hydrazones.

    PubMed

    Yogeeswari, Perumal; Menon, Niloufer; Semwal, Arvind; Arjun, Muralidharan; Sriram, Dharmarajan

    2011-07-01

    Neuropathic pain is a chronic pain condition that occurs and persists in a heterogeneous group of etiologically different diseases characterized by a primary lesion or dysfunction of the peripheral or central nervous system. Current treatment options do not provide adequate relief for many patients and a significant number of the agents used have dose limiting side effects. During the course of our work on the synthesis and screening of new drugs for the treatment of neuropathic pain, we have identified 5-(4-nitrophenyl)furoic-2-acid hydrazones which showed significant antiallodynic and antihyperalgesic activities in a chronic constriction injury (CCI) model of neuropathic pain in rat. Synthesized compounds thus represent a promising lead for new drug development for the treatment of neuropathic pain. PMID:21536354

  10. New developments in hydrogen bonding acidity and basicity of small organic molecules for the prediction of physical and ADMET properties. Part 2. The universal solvation equation.

    PubMed

    Oliferenko, Polina V; Oliferenko, Alexander A; Poda, Gennadiy; Palyulin, Vladimir A; Zefirov, Nikolay S; Katritzky, Alan R

    2009-03-01

    Theoretical quantifications of hydrogen bonding (HB) basicities and acidities, originally developed for aliphatic systems (J. Chem. Inf. Comput. Sci. 2004, 44, 1042-1055), are now extended to cover aromatic, heterocyclic, anionic, cationic and zwitter-ionic molecular fragments, thus encompassing a majority of druggable chemical space. The addition of terms accounting for cavity formation, polarity, hydrophobicity, and resonance allowed us to derive a new equation able to predict accurately free energies of solvation of diverse solutes, interphase transfers, and aqueous solubilities (log S(w)). We thus provide a "universal solvation equation" (USE) available for the accurate estimation of desolvation energies in protein-ligand docking, for the prediction of many physical and ADMET properties, and for studying fluid phase equilibria.

  11. Functional N-methyl-D-aspartate receptors in O-2A glial precursor cells: a critical role in regulating polysialic acid-neural cell adhesion molecule expression and cell migration

    PubMed Central

    1996-01-01

    The capacity for long-distance migration of the oligodendrocyte precursor cell, oligodendrocyte-type 2 astrocyte (O-2A), is essential for myelin formation. To study the molecular mechanisms that control this process, we used an in vitro migration assay that uses neurohypophysial explants. We provide evidence that O-2A cells in these preparations express functional N-methyl-D-aspartate (NMDA) receptors, most likely as homomeric complexes of the NR1 subunit. We show that NMDA evokes an increase in cytosolic Ca2+ that can be blocked by the NMDA receptor antagonist AP-5 and by Mg2+. Blocking the activity of these receptors dramatically diminished O-2A cell migration from explants. We also show that NMDA receptor activity is necessary for the expression by O-2A cells of the highly sialylated polysialic acid- neural cell adhesion molecule (PSA-NCAM) that is required for their migration. Thus, glutamate or glutamate receptor ligands may regulate O- 2A cell migration by modulating expression of PSA-NCAM. These studies demonstrate how interactions between ionotropic receptors, intracellular signaling, and cell adhesion molecule expression influence cell surface properties, which in turn are critical determinants of cell migration. PMID:8978823

  12. A mixture of amino acids and other small molecules present in the serum suppresses the growth of murine and human tumors in vivo.

    PubMed

    Kulcsár, Gyula; Gaál, Dezső; Kulcsár, Péter I; Schulcz, Ákos; Czömpöly, Tamás

    2013-03-01

    Previously we have hypothesized that the small molecules which are selectively accumulated in cancer cells might participate in a non-immunological antitumor surveillance mechanism. We demonstrated earlier that a mixture of experimentally selected substances ("active mixture", AM: L-arginine, L-histidine, L-methionine, L-phenylalanine, L-tyrosine, L-tryptophan, L-ascorbate, D-biotin, pyridoxine, riboflavin, adenine, L(-)malate) possesses a selective toxic effect in vitro on a variety of tumor cell lines, and we have shown that the AM selectively induces apoptosis of cancer cells in vitro. To explore the in vivo significance of our earlier findings we examined the antitumor effect of AM in Colon 26 murine colorectal adenocarcinoma, B16 murine melanoma, MXT murine mammary carcinoma, S180 murine sarcoma, P388 murine lymphoid leukemia, HL-60 human promyeloid leukemia, PC-3 human prostate carcinoma, and HT-29 human colon carcinoma tumor models. Treatment of tumor bearing mice with AM inhibited the growth of the tumors investigated, with an inhibitory effect ranging from 40 to 69%. The AM had a comparable antitumor effect with 5-fluorouracil and cisplatin in the Colon-26 tumor model, and combined treatment with AM and 5-fluorouracil or cisplatin resulted in an enhanced tumor growth inhibitory effect. The AM induced apoptosis through the mitochondrial pathway and induced G1 arrest in PC-3 cells and increased the number of apoptotic cells in PC-3 xenografts. These findings suggest that the AM might offer an interesting perspective in the treatment of cancer and in combination with other treatments may offer hope for a more effective cancer therapy.

  13. Role of the deposition temperature on the self-assembly of the non-planar molecule benzene-1,3,5-triphosphonic acid (BTP) at the liquid-solid interface.

    PubMed

    Nguyen, Doan Chau Yen; Smykalla, Lars; Nguyen, Thi Ngoc Ha; Mehring, Michael; Hietschold, Michael

    2016-09-21

    Benzene-1,3,5-triphosphonic acid (BTP) contains three non-planar phosphonic acid groups which enable three-dimensional hydrogen bonding. Because of these versatile 3D functional groups, BTP is an interesting intermediate to design both 2D and 3D supramolecular hydrogen-bonded architectures and organic-inorganic hybrid frameworks. However, the adsorption of BTP has surprisingly not been the subject of scanning tunneling microscopy (STM) investigations so far. Here a STM study of the adsorption pattern of BTP as obtained from deposition out of a solution in undecanol on an interface to highly-oriented pyrolytic graphite (HOPG) is presented. Furthermore, the influence of the substrate temperature during the deposition from solution on the self-assembly is investigated. High-resolution STM images reveal that the BTB molecules usually form various structures by co-adsorption with undecanol and that the BTP molecules as parts of self-assembled aggregates adsorb with their benzene ring planes tilted with respect to the substrate plane. The specific supramolecular pattern and the 2D packing density of BTP can be precisely tuned by adjusting the initial substrate temperature during deposition. The experimental results are compared to corresponding model structures obtained from semi-empirical simulations and explained by the influence of temperature on the concentration at the solution-solid interface and the kinetics of the self-assembly process. Based on these results, the control of the deposition substrate temperature has been proven to be a versatile tool to control the polymorphism of molecular patterns deposited out of solutions. PMID:27530556

  14. Role of the deposition temperature on the self-assembly of the non-planar molecule benzene-1,3,5-triphosphonic acid (BTP) at the liquid-solid interface.

    PubMed

    Nguyen, Doan Chau Yen; Smykalla, Lars; Nguyen, Thi Ngoc Ha; Mehring, Michael; Hietschold, Michael

    2016-09-21

    Benzene-1,3,5-triphosphonic acid (BTP) contains three non-planar phosphonic acid groups which enable three-dimensional hydrogen bonding. Because of these versatile 3D functional groups, BTP is an interesting intermediate to design both 2D and 3D supramolecular hydrogen-bonded architectures and organic-inorganic hybrid frameworks. However, the adsorption of BTP has surprisingly not been the subject of scanning tunneling microscopy (STM) investigations so far. Here a STM study of the adsorption pattern of BTP as obtained from deposition out of a solution in undecanol on an interface to highly-oriented pyrolytic graphite (HOPG) is presented. Furthermore, the influence of the substrate temperature during the deposition from solution on the self-assembly is investigated. High-resolution STM images reveal that the BTB molecules usually form various structures by co-adsorption with undecanol and that the BTP molecules as parts of self-assembled aggregates adsorb with their benzene ring planes tilted with respect to the substrate plane. The specific supramolecular pattern and the 2D packing density of BTP can be precisely tuned by adjusting the initial substrate temperature during deposition. The experimental results are compared to corresponding model structures obtained from semi-empirical simulations and explained by the influence of temperature on the concentration at the solution-solid interface and the kinetics of the self-assembly process. Based on these results, the control of the deposition substrate temperature has been proven to be a versatile tool to control the polymorphism of molecular patterns deposited out of solutions.

  15. Glucose sensing molecules having selected fluorescent properties

    DOEpatents

    Satcher, Jr., Joe H.; Lane, Stephen M.; Darrow, Christopher B.; Cary, Douglas R.; Tran, Joe Anh

    2004-01-27

    An analyte sensing fluorescent molecule that employs intramolecular electron transfer is designed to exhibit selected fluorescent properties in the presence of analytes such as saccharides. The selected fluorescent properties include excitation wavelength, emission wavelength, fluorescence lifetime, quantum yield, photostability, solubility, and temperature or pH sensitivity. The compound comprises an aryl or a substituted phenyl boronic acid that acts as a substrate recognition component, a fluorescence switch component, and a fluorophore. The fluorophore and switch component are selected such that the value of the free energy for electron transfer is less than about 3.0 kcal mol.sup.-1. Fluorescent compounds are described that are excited at wavelengths greater than 400 nm and emit at wavelengths greater than 450 nm, which is advantageous for optical transmission through skin. The fluorophore is typically selected from transition metal-ligand complexes and thiazine, oxazine, oxazone, or oxazine-one as well as anthracene compounds. The fluorescent compound can be immobilized in a glucose permeable biocompatible polymer matrix that is implantable below the skin.

  16. Methods for analyzing nucleic acid sequences

    DOEpatents

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

    2011-05-17

    The present invention is directed to a method of sequencing a target nucleic acid. The method provides a complex comprising a polymerase enzyme, a target nucleic acid molecule, and a primer, wherein the complex is immobilized on a support Fluorescent label is attached to a terminal phosphate group of the nucleotide or nucleotide analog. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The time duration of the signal from labeled nucleotides or nucleotide analogs that become incorporated is distinguished from freely diffusing labels by a longer retention in the observation volume for the nucleotides or nucleotide analogs that become incorporated than for the freely diffusing labels.

  17. 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

  18. 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

  19. Anti-dormant mycobacterial activity and target molecule of melophlins, tetramic acid derivatives isolated from a marine sponge of Melophlus sp.

    PubMed

    Arai, Masayoshi; Yamano, Yoshi; Kamiya, Kentaro; Setiawan, Andi; Kobayashi, Motomasa

    2016-07-01

    Tuberculosis (TB), caused by Mycobacterium tuberculosis infection, is a major world health problem that is responsible for the deaths of 1.5 million people each year. In addition, the requirement for long-term therapy to cure TB complicates treatment of the disease. One of the major reasons for the extended chemotherapeutic regimens and wide epidemicity of TB is that M. tuberculosis has the ability to persist in a dormant state. We therefore established a new screening system to search for substances with activity against dormant mycobacteria using M. smegmatis and M. bovis BCG cultivated in medium containing propionate as sole carbon source to induce dormancy. Subsequently, melophlins A (1), G (2), H (3), and I (4), tetramic acid derivatives, were re-discovered from the Indonesian marine sponge of Melophlus sp. as anti-dormant mycobacterial substances. Moreover, target analysis of melophlin A indicated that it targeted the BCG1083 protein of putative exopolyphosphatase and the BCG1321c protein of diadenosine 5',5‴-P(1),P(4)-tetraphosphate phosphorylase. PMID:27193014

  20. 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

  1. 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.

  2. The Fe(III) and Ga(III) coordination chemistry of 3-(1-hydroxymethylidene) and 3-(1-hydroxydecylidene)-5-(2-hydroxyethyl)pyrrolidine-2,4-dione: novel tetramic acid degradation products of homoserine lactone bacterial quorum sensing molecules.

    PubMed

    Romano, Ariel A; Hahn, Tobias; Davis, Nicole; Lowery, Colin A; Struss, Anjali K; Janda, Kim D; Böttger, Lars H; Matzanke, Berthold F; Carrano, Carl J

    2012-02-01

    Bacteria use small diffusible molecules to exchange information in a process called quorum sensing (QS). An important class of quorum sensing molecules used by Gram-negative bacteria is the family of N-acylhomoserine lactones (HSL). It was recently discovered that a degradation product of the QS molecule 3-oxo-C(12)-homoserine lactone, the tetramic acid 3-(1-hydroxydecylidene)-5-(2-hydroxyethyl)pyrrolidine-2,4-dione, is a potent antibacterial agent, thus implying roles for QS outside of simply communication. Because these tetramic acids also appear to bind iron with appreciable affinity it was suggested that metal binding might contribute to their biological activity. Here, using a variety of spectroscopic tools, we describe the coordination chemistry of both the methylidene and decylidene tetramic acid derivatives with Fe(III) and Ga(III) and discuss the potential biological significance of such metal binding. PMID:22178671

  3. Characterization of the proteins comprising the integral matrix of Strongylocentrotus purpuratus embryonic spicules

    NASA Technical Reports Server (NTRS)

    Killian, C. E.; Wilt, F. H.

    1996-01-01

    In the present study, we enumerate and characterize the proteins that comprise the integral spicule matrix of the Strongylocentrotus purpuratus embryo. Two-dimensional gel electrophoresis of [35S]methionine radiolabeled spicule matrix proteins reveals that there are 12 strongly radiolabeled spicule matrix proteins and approximately three dozen less strongly radiolabeled spicule matrix proteins. The majority of the proteins have acidic isoelectric points; however, there are several spicule matrix proteins that have more alkaline isoelectric points. Western blotting analysis indicates that SM50 is the spicule matrix protein with the most alkaline isoelectric point. In addition, two distinct SM30 proteins are identified in embryonic spicules, and they have apparent molecular masses of approximately 43 and 46 kDa. Comparisons between embryonic spicule matrix proteins and adult spine integral matrix proteins suggest that the embryonic 43-kDa SM30 protein is an embryonic isoform of SM30. An adult 49-kDa spine matrix protein is also identified as a possible adult isoform of SM30. Analysis of the SM30 amino acid sequences indicates that a portion of SM30 proteins is very similar to the carbohydrate recognition domain of C-type lectin proteins.

  4. Attenuation of lipid peroxidation by antioxidants in rat-1 fibroblasts: comparison of the lipid peroxidation reporter molecules cis-parinaric acid and C11-BODIPY(581/591) in a biological setting.

    PubMed

    Drummen, Gregor P C; Makkinje, Miriam; Verkleij, Arie J; Op den Kamp, Jos A F; Post, Jan A

    2004-03-22

    Lipid peroxidation is a major factor in the pathogenesis of many disease states. To detect the initial stages of lipid peroxidation or evaluate antioxidant efficacy, cis-parinaric acid (cis-PnA) has been successfully used and thoroughly validated. However, cis-PnA is not very well suited for medium throughput screening of antioxidants in living cells. We recently introduced and validated a lipid peroxidation reporter molecule, C11-BODIPY(581/591). To further explore this probe, we evaluated the protective effect of 12 natural antioxidants in rat-1 fibroblasts subjected to 50 microM cumene-hydroperoxide using both probes. The same pecking order for the individual antioxidant efficacies was obtained: alpha-tocopherol approximately gamma-tocopherol > quercetin approximately lycopene > kaempferol > palm oil > hydroxy-tyrosol > > alpha-carotene = beta-carotene = lutein = tyrosol = chlorogenic acid. This validates the accuracy of the C11-BODIPY(581/591) method and shows that this assay is an accurate and highly flexible method for indexing lipid peroxidation or determining antioxidant efficacy in living cells in a medium throughput scenario. The antioxidant efficacy was compared with their one-electron reduction potential, hydrophobicity and Trolox C equivalent antioxidant capacity. Our results show that although these parameters are valuable for determining structure-function relationships, they have limited predictive value for antioxidant efficacy in vivo.

  5. Amino acid-derived 1,2-benzisothiazolinone derivatives as novel small-molecule antifungal inhibitors: identification of potential genetic targets.

    PubMed

    Alex, Deepu; Gay-Andrieu, Francoise; May, Jared; Thampi, Linta; Dou, Dengfeng; Mooney, Aileen; Groutas, William; Calderone, Richard

    2012-09-01

    We have identified four synthetic compounds (DFD-VI-15, BD-I-186, DFD-V-49, and DFD-V-66) from an amino acid-derived 1,2-benzisothiazolinone (BZT) scaffold that have reasonable MIC(50) values against a panel of fungal pathogens. These compounds have no structural similarity to existing antifungal drugs. Three of the four compounds have fungicidal activity against Candida spp., Cryptococcus neoformans, and several dermatophytes, while one is fungicidal to Aspergillus fumigatus. The kill rates of our compounds are equal to those in clinical usage. The BZT compounds remain active against azole-, polyene-, and micafungin-resistant strains of Candida spp. A genetics-based approach, along with phenotype analysis, was used to begin mode of action (MOA) studies of one of these compounds, DFD-VI-15. The genetics-based screen utilized a homozygous deletion collection of approximately 4,700 Saccharomyces cerevisiae mutants. We identified mutants that are both hypersensitive and resistant. Using FunSpec, the hypersensitive mutants and a resistant ace2 mutant clustered within a category of genes related directly or indirectly to mitochondrial functions. In Candida albicans, the functions of the Ace2p transcription factor include the regulation of glycolysis. Our model is that DFD-VI-15 targets a respiratory pathway that limits energy production. Supporting this hypothesis are phenotypic data indicating that DFD-VI-15 causes increased cell-reactive oxidants (ROS) and a decrease in mitochondrial membrane potential. Also, the same compound has activity when cells are grown in a medium containing glycerol (mitochondrial substrate) but is much less active when cells are grown anaerobically.

  6. Amino Acid-Derived 1,2-Benzisothiazolinone Derivatives as Novel Small-Molecule Antifungal Inhibitors: Identification of Potential Genetic Targets

    PubMed Central

    Alex, Deepu; Gay-Andrieu, Francoise; May, Jared; Thampi, Linta; Dou, Dengfeng; Mooney, Aileen; Groutas, William

    2012-01-01

    We have identified four synthetic compounds (DFD-VI-15, BD-I-186, DFD-V-49, and DFD-V-66) from an amino acid-derived 1,2-benzisothiazolinone (BZT) scaffold that have reasonable MIC50 values against a panel of fungal pathogens. These compounds have no structural similarity to existing antifungal drugs. Three of the four compounds have fungicidal activity against Candida spp., Cryptococcus neoformans, and several dermatophytes, while one is fungicidal to Aspergillus fumigatus. The kill rates of our compounds are equal to those in clinical usage. The BZT compounds remain active against azole-, polyene-, and micafungin-resistant strains of Candida spp. A genetics-based approach, along with phenotype analysis, was used to begin mode of action (MOA) studies of one of these compounds, DFD-VI-15. The genetics-based screen utilized a homozygous deletion collection of approximately 4,700 Saccharomyces cerevisiae mutants. We identified mutants that are both hypersensitive and resistant. Using FunSpec, the hypersensitive mutants and a resistant ace2 mutant clustered within a category of genes related directly or indirectly to mitochondrial functions. In Candida albicans, the functions of the Ace2p transcription factor include the regulation of glycolysis. Our model is that DFD-VI-15 targets a respiratory pathway that limits energy production. Supporting this hypothesis are phenotypic data indicating that DFD-VI-15 causes increased cell-reactive oxidants (ROS) and a decrease in mitochondrial membrane potential. Also, the same compound has activity when cells are grown in a medium containing glycerol (mitochondrial substrate) but is much less active when cells are grown anaerobically. PMID:22687516

  7. Amino acid-derived 1,2-benzisothiazolinone derivatives as novel small-molecule antifungal inhibitors: identification of potential genetic targets.

    PubMed

    Alex, Deepu; Gay-Andrieu, Francoise; May, Jared; Thampi, Linta; Dou, Dengfeng; Mooney, Aileen; Groutas, William; Calderone, Richard

    2012-09-01

    We have identified four synthetic compounds (DFD-VI-15, BD-I-186, DFD-V-49, and DFD-V-66) from an amino acid-derived 1,2-benzisothiazolinone (BZT) scaffold that have reasonable MIC(50) values against a panel of fungal pathogens. These compounds have no structural similarity to existing antifungal drugs. Three of the four compounds have fungicidal activity against Candida spp., Cryptococcus neoformans, and several dermatophytes, while one is fungicidal to Aspergillus fumigatus. The kill rates of our compounds are equal to those in clinical usage. The BZT compounds remain active against azole-, polyene-, and micafungin-resistant strains of Candida spp. A genetics-based approach, along with phenotype analysis, was used to begin mode of action (MOA) studies of one of these compounds, DFD-VI-15. The genetics-based screen utilized a homozygous deletion collection of approximately 4,700 Saccharomyces cerevisiae mutants. We identified mutants that are both hypersensitive and resistant. Using FunSpec, the hypersensitive mutants and a resistant ace2 mutant clustered within a category of genes related directly or indirectly to mitochondrial functions. In Candida albicans, the functions of the Ace2p transcription factor include the regulation of glycolysis. Our model is that DFD-VI-15 targets a respiratory pathway that limits energy production. Supporting this hypothesis are phenotypic data indicating that DFD-VI-15 causes increased cell-reactive oxidants (ROS) and a decrease in mitochondrial membrane potential. Also, the same compound has activity when cells are grown in a medium containing glycerol (mitochondrial substrate) but is much less active when cells are grown anaerobically. PMID:22687516

  8. Potent gene-specific inhibitory properties of mixed-backbone antisense oligonucleotides comprised of 2'-deoxy-2'-fluoro-D-arabinose and 2'-deoxyribose nucleotides.

    PubMed

    Lok, Chun-Nam; Viazovkina, Ekaterina; Min, Kyung-Lyum; Nagy, Eva; Wilds, Christopher J; Damha, Masad J; Parniak, Michael A

    2002-03-12

    Phosphorothioate deoxyribonucleotides (PS-DNA) are among the most widely used antisense inhibitors. PS-DNA exhibits desirable properties such as enhanced nuclease resistance, improved bioavailability, and the ability to induce RNase H mediated degradation of target RNA. Unfortunately, PS-DNA possesses a relatively low binding affinity for target RNA that impacts on its potency in antisense applications. We recently showed that phosphodiester-linked oligonucleotides comprised of 2'-deoxy-2'-fluoro-D-arabinonucleic acid (FANA) exhibit both high binding affinity for target RNA and the ability to elicit RNase H degradation of target RNA [Damha et al. (1998) J. Am. Chem. Soc. 120, 12976]. In the present study, we evaluated the antisense activity of phosphorothioate-linked FANA oligonucleotides (PS-FANA). Oligonucleotides comprised entirely of PS-FANA were somewhat less efficient in directing RNase H cleavage of target RNA as compared to their phosphorothioate-linked DNA counterparts, and showed only weak antisense inhibition of cellular target expression. However, mixed-backbone oligomers comprised of PS-FANA flanking a central core of PS-DNA were found to possess potent antisense activity, inhibiting specific cellular gene expression with EC(50) values of less than 5 nM. This inhibition was a true antisense effect, as indicated by the dose-dependent decrease in both target protein and target mRNA. Furthermore, the appearance of mRNA fragments was consistent with RNase H mediated cleavage of the mRNA target. We also compared a series of PS-[FANA-DNA-FANA] mixed-backbone oligomers of varying PS-DNA core sizes with the corresponding 2'-O-methyl oligonucleotide chimeras, i.e., PS-[2'meRNA-DNA-2'meRNA]. Both types of oligomers showed very similar binding affinities toward target RNA. However, the antisense potency of the 2'-O-methyl chimeric compounds was dramatically attenuated with decreasing DNA core size, whereas that of the 2'-fluoroarabino compounds was essentially

  9. 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 ...

  10. 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

  11. Inhibition of fatty acid amide hydrolase and cyclooxygenase-2 increases levels of endocannabinoid related molecules and produces analgesia via peroxisome proliferator-activated receptor-alpha in a model of inflammatory pain.

    PubMed

    Jhaveri, Maulik D; Richardson, Denise; Robinson, Ian; Garle, Michael J; Patel, Annie; Sun, Yan; Sagar, Devi R; Bennett, Andrew J; Alexander, Stephen P H; Kendall, David A; Barrett, David A; Chapman, Victoria

    2008-07-01

    The antinociceptive effects of the endocannabinoids (ECs) are enhanced by inhibiting catabolic enzymes such as fatty acid amide hydrolase (FAAH). The physiological relevance of the metabolism of ECs by other pathways, such as cyclooxygenase-2 (COX2) is less clear. To address this question we compared the effects of local inhibition of FAAH versus COX2 (URB597 and nimesulide, respectively) on inflammatory hyperalgesia and levels of endocannabinoids and related molecules in the hindpaw. Inflammatory hyperalgesia was measured following intraplantar injection of carrageenan. Effects of intraplantar injection of URB597 (25 microg and 100 microg) or nimesulide (50 microg) on hyperalgesia and hindpaw levels of anandamide (AEA), 2-arachidonoylglycerol (2AG) and N-palmitoylethanolamine (PEA) were determined. Although both doses of URB597 increased levels of AEA and 2AG in the carrageenan inflamed hindpaw, only the lower dose of URB597 attenuated hyperalgesia (P<0.05). Nimesulide attenuated both hyperalgesia and hindpaw oedema (P<0.001, P<0.01, respectively) and increased levels of PEA (P<0.05) in the hindpaw. Since both AEA and PEA are ligands for peroxisome proliferator-activated receptor-alpha (PPARalpha), the effects of the PPARalpha antagonist GW6471 on nimesulide- and URB597-mediated effects were studied. GW6471, but not a PPARgamma antagonist, blocked the inhibitory effects of nimesulide and URB597 on hyperalgesia. Our data suggest that both COX2 and FAAH play a role in the metabolism of endocannabinoids and related molecules. The finding that PPARalpha antagonism blocked the inhibitory effects of nimesulide and URB597 suggests that PPARalpha contributes to their antinociceptive effects in the carrageenan model of inflammatory hyperalgesia.

  12. 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.

  13. 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.

  14. Large birefringence and polarization holographic gratings formed in photocross-linkable polymer liquid crystals comprising bistolane mesogenic side groups

    SciTech Connect

    Emoto, Akira; Matsumoto, Taro; Shioda, Tatsutoshi; Ono, Hiroshi; Yamashita, Ayumi; Kawatsuki, Nobuhiro

    2009-10-01

    Polarization gratings with large birefringence are formed in photoreactive polymer liquid crystals with bistolane moiety and terminal cinnamic acid moiety by the use of polarized ultraviolet interference light and subsequent annealing. The polarized ultraviolet light causes the axis-selective photoreaction between the cinnamic acid groups and subsequent annealing induce the reorientation of peripheral molecules without cross-linking along the cross-linked groups. Long bistolane mesogenic moiety exhibits large birefringence in comparison with a biphenyl mesogenic moiety, the value of the induced birefringence in the bistolane mesogenic liquid crystalline (LC) polymer is strongly dependent on both the grating constant and the wavelength of the reconstruction light.

  15. Metal-air cell comprising an electrolyte with a room temperature ionic liquid and hygroscopic additive

    SciTech Connect

    Friesen, Cody A.; Krishnan, Ramkumar; Tang, Toni; Wolfe, Derek

    2014-08-19

    An electrochemical cell comprising an electrolyte comprising water and a hydrophobic ionic liquid comprising positive ions and negative ions. The electrochemical cell also includes an air electrode configured to absorb and reduce oxygen. A hydrophilic or hygroscopic additive modulates the hydrophobicity of the ionic liquid to maintain a concentration of the water in the electrolyte is between 0.001 mol % and 25 mol %.

  16. Reversible Aptamer-Au Plasmon Rulers for Secreted Single Molecules.

    PubMed

    Lee, Somin Eunice; Chen, Qian; Bhat, Ramray; Petkiewicz, Shayne; Smith, Jessica M; Ferry, Vivian E; Correia, Ana Luisa; Alivisatos, A Paul; Bissell, Mina J

    2015-07-01

    Plasmon rulers, consisting of pairs of gold nanoparticles, allow single-molecule analysis without photobleaching or blinking; however, current plasmon rulers are irreversible, restricting detection to only single events. Here, we present a reversible plasmon ruler, comprised of coupled gold nanoparticles linked by a single aptamer, capable of binding individual secreted molecules with high specificity. We show that the binding of target secreted molecules to the reversible plasmon ruler is characterized by single-molecule sensitivity, high specificity, and reversibility. Such reversible plasmon rulers should enable dynamic and adaptive live-cell measurement of secreted single molecules in their local microenvironment.

  17. Reversible Aptamer-Au Plasmon Rulers for Secreted Single Molecules

    DOE PAGES

    Lee, Somin Eunice; Chen, Qian; Bhat, Ramray; Petkiewicz, Shayne; Smith, Jessica M.; Ferry, Vivian E.; Correia, Ana Luisa; Alivisatos, A. Paul; Bissell, Mina J.

    2015-06-03

    Plasmon rulers, consisting of pairs of gold nanoparticles, allow single-molecule analysis without photobleaching or blinking; however, current plasmon rulers are irreversible, restricting detection to only single events. Here, we present a reversible plasmon ruler, comprised of coupled gold nanoparticles linked by a single aptamer, capable of binding individual secreted molecules with high specificity. We show that the binding of target secreted molecules to the reversible plasmon ruler is characterized by single-molecule sensitivity, high specificity, and reversibility. Lastly, such reversible plasmon rulers should enable dynamic and adaptive live-cell measurement of secreted single molecules in their local microenvironment.

  18. Hybridization potential of oligonucleotides comprising 3'-O-methylated altritol nucleosides.

    PubMed

    Chatelain, G; Schepers, G; Rozenski, J; Van Aerschot, Arthur

    2012-11-01

    A series of 3'-O-methylated-d-altrohexitol nucleoside analogs (MANA) was synthesized comprising all four base moieties, adenine, cytosine, uracil, and guanine. These monomers were incorporated into oligonucleotides (ONs) by automated solid phase synthesis and the thermal and thermodynamic stability of all new modified constructs were evaluated. Data were compared with results obtained for both anhydrohexitol (HNAs) and 3'-O-altrohexitol-modified ONs (ANAs). We hereby demonstrate that ONs modified with MANA monomers have an improved thermal and thermodynamic stability compared to RNA, ANA, or HNA containing ONs of which the extent depends on the number of incorporated moieties and their position in the sequence. Thermodynamic analysis afforded comparable or even improved results in comparison with the incorporation of locked nucleic acids. While the specificity of these new synthons is slightly lower compared to mismatches within RNA double strands, it is similar to the discrimination potential of other hexitol modifications (HNA and ANA) which already proved their biologic interest, highlighting the potential of MANA constructs in antisense and in siRNA applications.

  19. Characterization of a chimeric enzyme comprising feruloyl esterase and family 42 carbohydrate-binding module.

    PubMed

    Koseki, Takuya; Mochizuki, Keiji; Kisara, Hiroe; Miyanaga, Akimasa; Fushinobu, Shinya; Murayama, Tetsuya; Shiono, Yoshihito

    2010-03-01

    We engineered a chimeric enzyme (AwFaeA-CBM42) comprising of type-A feruloyl esterase from Aspergillus awamori (AwFaeA) and family 42 carbohydrate-binding module (AkCBM42) from glycoside hydrolase family 54 alpha-L-arabinofuranosidase of Aspergillus kawachii. The chimeric enzyme was successfully produced in Pichia pastoris and accumulated in the culture broth. The purified chimeric enzyme had an apparent relative molecular mass (M(r)) of 53,000. The chimeric enzyme binds to arabinoxylan; this indicates that the AkCBM42 in AwFaeA-CBM42 binds to arabinofuranose side chain moiety of arabinoxylan. The thermostability of the chimeric enzyme was greater than that of AwFaeA. No significant difference of the specific activity toward methyl ferulate was observed between the AwFaeA and chimeric enzyme, but the release of ferulic acid from insoluble arabinoxylan by the chimeric enzyme was approximately 4-fold higher than that achieved by AwFaeA alone. In addition, the chimeric enzyme and xylanase acted synergistically for the degradation of arabinoxylan. In conclusion, the findings of our study demonstrated that the components of the AwFaeA-CBM42 chimeric enzyme act synergistically to bring about the degradation of complex substrates and that the family 42 carbohydrate-binding module has potential for application in the degradation of polysaccharides.

  20. Pyrolysis and hydrolysis of mixed polymer waste comprising polyethyleneterephthalate and polyethylene to sequentially recover

    DOEpatents

    Evans, Robert J.; Chum, Helena L.

    1998-01-01

    A process of using fast pyrolysis in a carrier gas to convert a plastic waste feedstream having a mixed polymeric composition in a manner such that pyrolysis of a given polymer to its high value monomeric constituent occurs prior to pyrolysis of other plastic components therein comprising: selecting a first temperature program range to cause pyrolysis of said given polymer to its high value monomeric constituent prior to a temperature range that causes pyrolysis of other plastic components; selecting a catalyst and support for treating said feed streams with said catalyst to effect acid or base catalyzed reaction pathways to maximize yield or enhance separation of said high value monomeric constituent in said temperature program range; differentially heating said feed stream at a heat rate within the first temperature program range to provide differential pyrolysis for selective recovery of optimum quantities of the high value monomeric constituent prior to pyrolysis of other plastic components; separating the high value monomeric constituents; selecting a second higher temperature range to cause pyrolysis of a different high value monomeric constituent of said plastic waste and differentially heating the feedstream at the higher temperature program range to cause pyrolysis of the different high value monomeric constituent; and separating the different high value monomeric constituent.

  1. Amino acid analyses of R and CK chondrites

    NASA Astrophysics Data System (ADS)

    Burton, Aaron S.; McLain, Hannah; Glavin, Daniel P.; Elsila, Jamie E.; Davidson, Jemma; Miller, Kelly E.; Andronikov, Alexander V.; Lauretta, Dante; Dworkin, Jason P.

    2015-03-01

    Exogenous delivery of amino acids and other organic molecules to planetary surfaces may have played an important role in the origins of life on Earth and other solar system bodies. Previous studies have revealed the presence of indigenous amino acids in a wide range of carbon-rich meteorites, with the abundances and structural distributions differing significantly depending on parent body mineralogy and alteration conditions. Here we report on the amino acid abundances of seven type 3-6 CK chondrites and two Rumuruti (R) chondrites. Amino acid measurements were made on hot water extracts from these meteorites by ultrahigh-performance liquid chromatography with fluorescence detection and time-of-flight mass spectrometry. Of the nine meteorites analyzed, four were depleted in amino acids, and one had experienced significant amino acid contamination by terrestrial biology. The remaining four, comprised of two R and two CK chondrites, contained low levels of amino acids that were predominantly the straight chain, amino-terminal (n-ω-amino) acids β-alanine, and γ-amino-n-butyric acid. This amino acid distribution is similar to what we reported previously for thermally altered ureilites and CV and CO chondrites, and these n-ω-amino acids appear to be indigenous to the meteorites and not the result of terrestrial contamination. The amino acids may have been formed by Fischer-Tropsch-type reactions, although this hypothesis needs further testing.

  2. Electrolyte membrane, methods of manufacture thereof and articles comprising the same

    DOEpatents

    Tamaki, Ryo; Rice, Steven Thomas; Yeager, Gary William

    2013-11-05

    Disclosed herein is a method of forming an electrolyte membrane comprising forming a mixture; the mixture comprising a polyhydroxy compound, an aromatic polyhalide compound and an alkali metal hydroxide; disposing the mixture on a porous substrate; reacting the mixture to form a crosslinked proton conductor; and sulfonating the proton conductor. Disclosed herein too is an article comprising a porous substrate; and a sulfonated crosslinked proton conductor disposed within pores of the porous substrate.

  3. Electrolyte membrane, methods of manufacture thereof and articles comprising the same

    DOEpatents

    Tamaki, Ryo; Rice, Steven Thomas; Yeager, Gary William

    2012-06-12

    Disclosed herein is a method of forming an electrolyte membrane comprising forming a mixture; the mixture comprising a polyhydroxy compound, an aromatic polyhalide compound and an alkali metal hydroxide; disposing the mixture on a porous substrate; reacting the mixture to form a proton conductor; and crosslinking the proton conductor to form a cross-linked proton-conducting network. Disclosed herein too is an article comprising a porous substrate; and a crosslinked proton conductor disposed on the porous substrate.

  4. Compositions comprising a polypeptide having cellulolytic enhancing activity and a bicyclic compound and uses thereof

    DOEpatents

    Quinlan, Jason; Xu, Feng; Sweeney, Matthew

    2016-10-04

    The present invention relates to compositions comprising: a polypeptide having cellulolytic enhancing activity and a bicyclic compound. The present invention also relates to methods of using the compositions.

  5. Compositions comprising a polypeptide having cellulolytic enhancing activity and a bicycle compound and uses thereof

    SciTech Connect

    Xu, Feng; Sweeney, Matthew; Quinlan, Jason

    2015-06-16

    The present invention relates to compositions comprising: a polypeptide having cellulolytic enhancing activity and a bicyclic compound. The present invention also relates to methods of using the compositions.

  6. Compositions comprising a polypeptide having cellulolytic enhancing activity and a quinone compound and uses thereof

    DOEpatents

    Quinlan, Jason; Xu, Feng; Sweeney, Matthew

    2016-03-01

    The present invention relates to compositions comprising: a polypeptide having cellulolytic enhancing activity and a quinone compound. The present invention also relates to methods of using the compositions.

  7. Compositions comprising a polypeptide having cellulolytic enhancing activity and a heterocyclic compound and uses thereof

    DOEpatents

    Xu, Feng; Sweeney, Matthew; Quinlan, Jason

    2016-08-02

    The present invention relates to compositions comprising: a polypeptide having cellulolytic enhancing activity and a heterocyclic compound. The present invention also relates to methods of using the compositions.

  8. Compositions comprising a polypeptide having cellulolytic enhancing activity and a dioxy compound and uses thereof

    DOEpatents

    Sweeney, Matthew; Xu, Feng; Quinlan, Jason

    2016-07-19

    The present invention relates to compositions comprising: a polypeptide having cellulolytic enhancing activity and a dioxy compound. The present invention also relates to methods of using the compositions.

  9. Contraceptive efficacy of recombinant fusion protein comprising zona pellucida glycoprotein-3 fragment and gonadotropin releasing hormone.

    PubMed

    Arukha, Ananta Prasad; Minhas, Vidisha; Shrestha, Abhinav; Gupta, Satish Kumar

    2016-04-01

    Contraceptive vaccines have been used for the management of wildlife population. In the present study, we have examined the contraceptive potential of Escherichia coli-expressed recombinant fusion protein comprising of 'promiscuous' T cell epitope of tetanus toxoid [TT; amino acid (aa) residues 830-844] followed by dilysine linker (KK), dog ZP3 fragment (aa residues 307-346), triglycine spacer (GGG), T cell epitope of bovine RNase (bRNase; aa residues 94-104), GnRH, T cell epitope of circumsporozoite protein of Plasmodium falciparum (CSP; aa residues 362-383), and GnRH. SDS-PAGE analysis of the purified refolded protein revealed a dominant ∼12 kDa band, which in Western blot reacted with mouse polyclonal antibodies against dog ZP3 fragment and mouse monoclonal antibodies against GnRH. Immunization of female FvB/J mice following two booster schedule with the above recombinant protein supplemented with alum led to high antibody titres against the immunogen as well as ZP3 and GnRH as determined by ELISA. The immune sera reacted with zona pellucida of mouse oocyte and also inhibited in-vitro fertilization. The qRT-PCR studies showed decrease in the ovarian GnRH receptor in mice immunized with the recombinant fusion protein. Mating studies revealed high contraceptive efficacy of the recombinant protein as in two independent experiments, 90% of the immunized female mice failed to conceive. Following one booster immunization schedule, 50% of the immunized female mice failed to conceive. However, in adjuvanted controls, all the female mice became pregnant. To conclude, the recombinant protein described herein has a good potential to be developed as candidate contraceptive vaccine. PMID:26859695

  10. Electrode material comprising graphene-composite materials in a graphite network

    DOEpatents

    Kung, Harold H.; Lee, Jung K.

    2014-07-15

    A durable electrode material suitable for use in Li ion batteries is provided. The material is comprised of a continuous network of graphite regions integrated with, and in good electrical contact with a composite comprising graphene sheets and an electrically active material, such as silicon, wherein the electrically active material is dispersed between, and supported by, the graphene sheets.

  11. Ball bearings comprising nickel-titanium and methods of manufacture thereof

    NASA Technical Reports Server (NTRS)

    DellaCorte, Christopher (Inventor); Glennon, Glenn N. (Inventor)

    2012-01-01

    Disclosed herein is a friction reducing nickel-titanium composition. The nickel-titanium composition includes a first phase that comprises nickel and titanium in an atomic ratio of about 0.45:0.55 to about 0.55:0.45; a second phase that comprises nickel and titanium in an atomic ratio of about 0.70:0.30 to about 0.80:0.20; and a third phase that comprises nickel and titanium in an atomic ratio of about 0.52:0.48 to about 0.62:0.38. A bearing for reducing friction comprising a nickel-titanium composition comprising a first phase that comprises nickel and titanium in an atomic ratio of about 0.45:0.55 to about 0.55:0.45; a second phase that comprises nickel and titanium in an atomic ratio of about 0.70:0.30 to about 0.80:0.20; and a third phase that comprises nickel and titanium in an atomic ratio of about 0.52:0.48 to about 0.62:0.38; where the bearing is free from voids and pinholes.

  12. [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.

  13. Theoretical studies on the coupling interactions in H2SO4···HOO˙···(H2O)n (n = 0-2) clusters: toward understanding the role of water molecules in the uptake of HOO˙ radical by sulfuric acid aerosols.

    PubMed

    Li, Ping; Ma, Zhiying; Wang, Weihua; Zhai, Yazhou; Sun, Haitao; Bi, Siwei; Bu, Yuxiang

    2011-01-21

    A detailed knowledge of coupling interactions among sulfuric acid (H(2)SO(4)), the hydroperoxyl radical (HOO˙), and water molecules (H(2)O) is crucial for the better understanding of the uptake of HOO˙ radicals by sulfuric acid aerosols at different atmospheric humidities. In the present study, the equilibrium structures, binding energies, equilibrium distributions, and the nature of the coupling interactions in H(2)SO(4)···HOO˙···(H(2)O)(n) (n = 0-2) clusters have been systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, energy decomposition analyses, and ab initio molecular dynamics. Two binary, five ternary, and twelve tetramer clusters possessing multiple intermolecular H-bonds have been located on their potential energy surfaces. Two different modes for water molecules have been observed to influence the coupling interactions between H(2)SO(4) and HOO˙ through the formations of intermolecular H-bonds with or without breaking the original intermolecular H-bonds in the binary H(2)SO(4)···HOO˙ cluster. It was found that the introduction of one or two water molecules can efficiently enhance the interactions between H(2)SO(4) and HOO˙, implying the positive role of water molecules in the uptake of the HOO˙ radical by sulfuric acid aerosols. Additionally, the coupling interaction modes of the most stable clusters under study have been verified by the ab initio molecular dynamics. PMID:21052607

  14. 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)

  15. The missing organic molecules on Mars.

    PubMed

    Benner, S A; Devine, K G; Matveeva, L N; Powell, D H

    2000-03-14

    GC-MS on the Viking 1976 Mars missions did not detect organic molecules on the Martian surface, even those expected from meteorite bombardment. This result suggested that the Martian regolith might hold a potent oxidant that converts all organic molecules to carbon dioxide rapidly relative to the rate at which they arrive. This conclusion is influencing the design of Mars missions. We reexamine this conclusion in light of what is known about the oxidation of organic compounds generally and the nature of organics likely to come to Mars via meteorite. We conclude that nonvolatile salts of benzenecarboxylic acids, and perhaps oxalic and acetic acid, should be metastable intermediates of meteoritic organics under oxidizing conditions. Salts of these organic acids would have been largely invisible to GC-MS. Experiments show that one of these, benzenehexacarboxylic acid (mellitic acid), is generated by oxidation of organic matter known to come to Mars, is rather stable to further oxidation, and would not have been easily detected by the Viking experiments. Approximately 2 kg of meteorite-derived mellitic acid may have been generated per m(2) of Martian surface over 3 billion years. How much remains depends on decomposition rates under Martian conditions. As available data do not require that the surface of Mars be very strongly oxidizing, some organic molecules might be found near the surface of Mars, perhaps in amounts sufficient to be a resource. Missions should seek these and recognize that these complicate the search for organics from entirely hypothetical Martian life.

  16. The missing organic molecules on Mars

    PubMed Central

    Benner, Steven A.; Devine, Kevin G.; Matveeva, Lidia N.; Powell, David H.

    2000-01-01

    GC-MS on the Viking 1976 Mars missions did not detect organic molecules on the Martian surface, even those expected from meteorite bombardment. This result suggested that the Martian regolith might hold a potent oxidant that converts all organic molecules to carbon dioxide rapidly relative to the rate at which they arrive. This conclusion is influencing the design of Mars missions. We reexamine this conclusion in light of what is known about the oxidation of organic compounds generally and the nature of organics likely to come to Mars via meteorite. We conclude that nonvolatile salts of benzenecarboxylic acids, and perhaps oxalic and acetic acid, should be metastable intermediates of meteoritic organics under oxidizing conditions. Salts of these organic acids would have been largely invisible to GC-MS. Experiments show that one of these, benzenehexacarboxylic acid (mellitic acid), is generated by oxidation of organic matter known to come to Mars, is rather stable to further oxidation, and would not have been easily detected by the Viking experiments. Approximately 2 kg of meteorite-derived mellitic acid may have been generated per m2 of Martian surface over 3 billion years. How much remains depends on decomposition rates under Martian conditions. As available data do not require that the surface of Mars be very strongly oxidizing, some organic molecules might be found near the surface of Mars, perhaps in amounts sufficient to be a resource. Missions should seek these and recognize that these complicate the search for organics from entirely hypothetical Martian life. PMID:10706606

  17. 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.

  18. Microorganisms for producing organic acids

    DOEpatents

    Pfleger, Brian Frederick; Begemann, Matthew Brett

    2014-09-30

    Organic acid-producing microorganisms and methods of using same. The organic acid-producing microorganisms comprise modifications that reduce or ablate AcsA activity or AcsA homolog activity. The modifications increase tolerance of the microorganisms to such organic acids as 3-hydroxypropionic acid, acrylic acid, propionic acid, lactic acid, and others. Further modifications to the microorganisms increase production of such organic acids as 3-hydroxypropionic acid, lactate, and others. Methods of producing such organic acids as 3-hydroxypropionic acid, lactate, and others with the modified microorganisms are provided. Methods of using acsA or homologs thereof as counter-selectable markers are also provided.

  19. Using Remote Sensing and Radar Meteorological Data to Support Watershed Assessments Comprising Integrated Environmental Modeling

    EPA Science Inventory

    Meteorological (MET) data required by watershed assessments comprising Integrated Environmental Modeling (IEM) traditionally have been provided by land-based weather (gauge) stations, although these data may not be the most appropriate for adequate spatial and temporal resolution...

  20. Using Remote Sensing and Radar MET Data to Support Watershed Assessments Comprising IEM

    EPA Science Inventory

    Meteorological (MET) data required by watershed assessments that comprise Integrated Environmental Modeling (IEM) have traditionally been provided by land-based weather (gauge) stations; although these data may not be most appropriate for describing adequate spatial and temporal...

  1. Alignment of Carbon Nanotubes Comprising Magnetically Sensitive Metal Oxides in Nanofluids

    NASA Technical Reports Server (NTRS)

    Hong, Haiping (Inventor); Peterson, G. P. " Bud" (Inventor)

    2016-01-01

    The present invention is a nanoparticle mixture or suspension or nanofluid comprising nonmagnetically sensitive nanoparticles, magnetically sensitive nanoparticles, and surfactant(s). The present invention also relates to methods of preparing and using the same.

  2. Alignment of Carbon Nanotubes Comprising Magnetically Sensitive Metal Oxides in Nanofluids

    NASA Technical Reports Server (NTRS)

    Hong, Haiping (Inventor); Peterson, G. P. 'Bud' (Inventor)

    2014-01-01

    The present invention is a nanoparticle mixture or suspension or nanofluid comprising nonmagnetically sensitive nanoparticles, magnetically sensitive nanoparticles, and surfactant(s). The present invention also relates to methods of preparing and using the same.

  3. Nanolipoprotein particles comprising a natural rubber biosynthetic enzyme complex and related products, methods and systems

    DOEpatents

    Hoeprich, Paul D.; Whalen, Maureen

    2016-04-05

    Provided herein are nanolipoprotein particles that comprise a biosynthetic enzyme more particularly an enzyme capable of catalyzing rubber or other rubbers polymerization, and related assemblies, devices, methods and systems.

  4. Coated phosphors, methods of making them, and articles comprising the same

    DOEpatents

    Lyons, Robert Joseph

    2013-02-19

    Compositions comprising a phosphor and a compound having the formula R.sub.1R.sub.2M, wherein R.sub.1 is a substituted or unsubstituted alkyl, aryl, heteroaryl, arylalkyl, heteroarylalkyl, alkoxy, alkoxyl, acyl heterocycle, haloalkyl, oxaalkyl, or silyl; R.sub.2 is a sulfate, sulfonate, or carboxylate and M is an alkali metal or an alkaline earth metal are provided. Phosphors coated with the compound, methods of making the coated phosphors and articles comprising the compositions are provided.

  5. Conformational dynamics of peptide T molecule

    NASA Astrophysics Data System (ADS)

    Akverdieva, Gulnare; Godjayev, Niftali; Akyuz, Sevim

    2002-05-01

    Using a method of the theoretical conformational analysis, a conformational dynamics of the side chains of the amino acid residues of peptide T, a competitor of the human immuno-deficiency virus in the binding to human T cells, was investigated. For this purpose, the conformational maps of the potential surfaces were constructed over the angles of the side chains for the preferable conformations of peptide T molecule. Permissible deviations of these angles from the optimal values were determined. It has been found that the angles of the side chains of the amino acid residues involved in physiologically active fragment Thr4-Thr8 are more rigid than in the other segment of the molecule. This fact confirms the existence of such a regular structure as β-turn revealed previously in studies of the spatial structure of the peptide T molecule.

  6. 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.

  7. Asparagusic acid.

    PubMed

    Mitchell, Stephen C; Waring, Rosemary H

    2014-01-01

    Asparagusic acid (1,2-dithiolane-4-carboxylic acid) is a simple sulphur-containing 5-membered heterocyclic compound that appears unique to asparagus, though other dithiolane derivatives have been identified in non-food species. This molecule, apparently innocuous toxicologically to man, is the most probable culprit responsible for the curious excretion of odorous urine following asparagus ingestion. The presence of the two adjacent sulphur atoms leads to an enhanced chemical reactivity, endowing it with biological properties including the ability to substitute potentially for α-lipoic acid in α-keto-acid oxidation systems. This brief review collects the scattered data available in the literature concerning asparagusic acid and highlights its properties, intermediary metabolism and exploratory applications. PMID:24099657

  8. Linking ultracold polar molecules.

    PubMed

    Avdeenkov, A V; Bohn, John L

    2003-01-31

    We predict that pairs of polar molecules can be weakly bound together in an ultracold environment, provided that a dc electric field is present. The field that links the molecules together also strongly influences the basic properties of the resulting dimer, such as its binding energy and predissociation lifetime. Because of their long-range character, these dimers will be useful in disentangling cold collision dynamics of polar molecules. As an example, we estimate the microwave photoassociation yield for OH-OH cold collisions.

  9. Interlocked molecules: Aqueous assembly

    NASA Astrophysics Data System (ADS)

    Bai, Linyi; Zhao, Yanli

    2015-12-01

    The quantitative self-assembly of mechanically interlocked molecules in water, instead of organic solvents, opens up the possibility of such systems being used in a biological context where their functions can be interfaced with biomolecular systems.

  10. Single-Molecule Enzymology

    SciTech Connect

    Xie, Xiaoliang; Lu, H PETER.

    1999-06-04

    Viewing a movie of an enzyme molecule made from molecular dynamics (MD) simulation, we see incredible details of molecular motions, be it a change of the conformation or the action of a chemical reaction.

  11. 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)

  12. Micro-electro-mechanical systems phosphoric acid fuel cell

    DOEpatents

    Sopchak, David A.; Morse, Jeffrey D.; Upadhye, Ravindra S.; Kotovsky, Jack; Graff, Robert T.

    2010-08-17

    A phosphoric acid fuel cell system comprising a porous electrolyte support, a phosphoric acid electrolyte in the porous electrolyte support, a cathode electrode contacting the phosphoric acid electrolyte, and an anode electrode contacting the phosphoric acid electrolyte.

  13. Micro-electro-mechanical systems phosphoric acid fuel cell

    DOEpatents

    Sopchak, David A.; Morse, Jeffrey D.; Upadhye, Ravindra S.; Kotovsky, Jack; Graff, Robert T.

    2010-12-21

    A phosphoric acid fuel cell system comprising a porous electrolyte support, a phosphoric acid electrolyte in the porous electrolyte support, a cathode electrode contacting the phosphoric acid electrolyte, and an anode electrode contacting the phosphoric acid electrolyte.

  14. Acidic gas capture by diamines

    SciTech Connect

    Rochelle, Gary; Hilliard, Marcus

    2011-05-10

    Compositions and methods related to the removal of acidic gas. In particular, the present disclosure relates to a composition and method for the removal of acidic gas from a gas mixture using a solvent comprising a diamine (e.g., piperazine) and carbon dioxide. One example of a method may involve a method for removing acidic gas comprising contacting a gas mixture having an acidic gas with a solvent, wherein the solvent comprises piperazine in an amount of from about 4 to about 20 moles/kg of water, and carbon dioxide in an amount of from about 0.3 to about 0.9 moles per mole of piperazine.

  15. Main chain acid-degradable polymers for the delivery of bioactive materials

    DOEpatents

    Frechet, Jean M. J.; Standley, Stephany M.; Jain, Rachna; Lee, Cameron C.

    2012-03-20

    Novel main chain acid degradable polymer backbones and drug delivery systems comprised of materials capable of delivering bioactive materials to cells for use as vaccines or other therapeutic agents are described. The polymers are synthesized using monomers that contain acid-degradable linkages cleavable under mild acidic conditions. The main chain of the resulting polymers readily degrade into many small molecules at low pH, but remain relatively stable and intact at physiological pH. The new materials have the common characteristic of being able to degrade by acid hydrolysis under conditions commonly found within the endosomal or lysosomal compartments of cells thereby releasing their payload within the cell. The materials can also be used for the delivery of therapeutics to the acidic regions of tumors and other sites of inflammation.

  16. Small-molecule G-quadruplex interactions: Systematic exploration of conformational space using multiple molecular dynamics.

    PubMed

    Husby, Jarmila; Todd, Alan K; Platts, James A; Neidle, Stephen

    2013-12-01

    G-quadruplexes are higher-order four-stranded structures formed from repetitive guanine-containing tracts in nucleic acids. They comprise a core of stacked guanine-quartets linked by loops of length and sequence that vary with the context in which the quadruplex sequence occurs. Such sequences can be found in a number of genomic environments; at the telomeric ends of eukaryotic chromosomes, in promoter regions, in untranslated sequences and in open reading frames. Quadruplex formation can inhibit telomere maintenance, transcription and translation, especially when enhanced by quadruplex-binding small molecules, and quadruplex targeting is currently of considerable interest. The available experimental structural data shows that quadruplexes can have high conformational flexibility, especially in loop regions, which has hampered attempts to use high-throughput docking to find quadruplex-binding small-molecules with new scaffolds or to optimize existing ones with structure-based design methods. An approach to overcome the challenge of quadruplex conformational flexibility is presented here, which uses a combined multiple molecular dynamics and sampling approach. Two test small molecules have been used, RHPS4 and pyridostatin, which themselves have contrasting degrees of conformational flexibility.

  17. Electric circuit breaker comprising a plurality of vacuum interrupters simultaneously operated by a common operator

    DOEpatents

    Barkan, Philip; Imam, Imdad

    1980-01-01

    This circuit breaker comprises a plurality of a vacuum-type circuit interrupters, each having a movable contact rod. A common operating device for the interrupters comprises a linearly-movable operating member. The interrupters are mounted at one side of the operating member with their movable contact rods extending in a direction generally toward the operating member. Means is provided for mechanically coupling the operating member to the contact rods, and this means comprises a plurality of insulating operating rods, each connected at one end to the operating member and at its opposite end to one of the movable contact rods. The operating rods are of substantially equal length and have longitudinal axes that converge and intersect at substantially a common point.

  18. Completion and workover fluid for oil and gas wells comprising ground peanut hulls

    SciTech Connect

    Forrest, G.T.

    1993-07-20

    A method is described of carrying out operations in a bore hole extending into the subsurface formations, comprising the steps of forming a slurry comprising a liquid fluid; a sealing agent of ground peanut hulls of particles of a size distribution such that at least 30% but no more than 80% of said particles will be retained on a 100 standard sieve mesh; and a viscosifier to carry and suspend said sealing agent, and circulating said slurry in said bore hole. A dry mixture is described for mixing with a fluid to be circulated in a bore hole, comprising: a sealing agent of ground peanut hulls of particles of a size distribution such that at least 30% but no more than 80% of said particles will retained on a 100 standard sieve mesh, and a viscosifier to carry and suspend said sealing agent.

  19. Semipermeable thin-film membranes comprising siloxane, alkoxysilyl and aryloxysilyl oligomers and copolymers

    DOEpatents

    Babcock, W.C.; Friesen, D.T.

    1988-11-01

    Novel semipermeable membranes and thin film composite (TFC) gas separation membranes useful in the separation of oxygen, nitrogen, hydrogen, water vapor, methane, carbon dioxide, hydrogen sulfide, lower hydrocarbons, and other gases are disclosed. The novel semipermeable membranes comprise the polycondensation reaction product of two complementary polyfunctional compounds, each having at least two functional groups that are mutually reactive in a condensation polymerization reaction, and at least one of which is selected from siloxanes, alkoxsilyls and aryloxysilyls. The TFC membrane comprises a microporous polymeric support, the surface of which has the novel semipermeable film formed thereon, preferably by interfacial polymerization.

  20. Semipermeable thin-film membranes comprising siloxane, alkoxysilyl and aryloxysilyl oligomers and copolymers

    DOEpatents

    Babcock, Walter C.; Friesen, Dwayne T.

    1988-01-01

    Novel semiperimeable membranes and thin film composite (TFC) gas separation membranes useful in the separation of oxygen, nitrogen, hydrogen, water vapor, methane, carbon dioxide, hydrogen sulfide, lower hydrocarbons, and other gases are disclosed. The novel semipermeable membranes comprise the polycondensation reaction product of two complementary polyfunctional compounds, each having at least two functional groups that are mutually reactive in a condensation polymerization reaction, and at least one of which is selected from siloxanes, alkoxsilyls and aryloxysilyls. The TFC membrane comprises a microporous polymeric support, the surface of which has the novel semipermeable film formed thereon, preferably by interfacial polymerization.

  1. Nonlinear optical propagation in a tandem structure comprising nonlinear absorption and scattering materials

    SciTech Connect

    Wang, Kangpeng; Ju, Yongfeng; He, Jin; Zhang, Long E-mail: lzhang@siom.ac.cn; Wang, Jun E-mail: lzhang@siom.ac.cn; Chen, Yu; Blau, Werner J.

    2014-01-13

    Laser propagation in a tandem structure comprising carbon nanotubes and phthalocyanines is studied by Z-scan method. Due to the different mechanisms of the two materials, the laser beam can be attenuated with different absorptivities, by changing the sequence of light passing through each material. Numerical simulations considering the effect of path length and the change of nonlinear coefficient within each material are conducted for understanding the distribution of laser intensity in the tandem system and hence, fitting of the asymmetric Z-scan curves. The results are helpful for the design of nonlinear optical devices comprising multiple nonlinear materials and mechanisms.

  2. Catalyst system comprising a first catalyst system tethered to a supported catalyst

    DOEpatents

    Angelici, Robert J.; Gao, Hanrong

    1998-08-04

    The present invention provides new catalyst formats which comprise a supported catalyst tethered to a second and different catalyst by a suitable tethering ligand. A preferred system comprises a heterogeneous supported metal catalyst tethered to a homogeneous catalyst. This combination of homogeneous and heterogeneous catalysts has a sufficient lifetime and unusually high catalytic activity in arene hydrogenations, and potentially many other reactions as well, including, but not limited to hydroformylation, hydrosilation, olefin oxidation, isomerization, hydrocyanation, olefin metathesis, olefin polymerization, carbonylation, enantioselective catalysis and photoduplication. These catalysts are easily separated from the products, and can be reused repeatedly, making these systems very economical.

  3. Catalyst system comprising a first catalyst system tethered to a supported catalyst

    DOEpatents

    Angelici, R.J.; Gao, H.

    1998-08-04

    The present invention provides new catalyst formats which comprise a supported catalyst tethered to a second and different catalyst by a suitable tethering ligand. A preferred system comprises a heterogeneous supported metal catalyst tethered to a homogeneous catalyst. This combination of homogeneous and heterogeneous catalysts has a sufficient lifetime and unusually high catalytic activity in arene hydrogenations, and potentially many other reactions as well, including, but not limited to hydroformylation, hydrosilication, olefin oxidation, isomerization, hydrocyanidation, olefin metathesis, olefin polymerization, carbonylation, enantioselective catalysis and photoduplication. These catalysts are easily separated from the products, and can be reused repeatedly, making these systems very economical. 2 figs.

  4. Morphology and Composition of Structured, Phase-Separated Behenic Acid-Perfluorotetradecanoic Acid Monolayer Films.

    PubMed

    Rehman, Jeveria; Araghi, Hessamaddin Younesi; He, Anqiang; Paige, Matthew F

    2016-05-31

    The phase separation of immiscible surfactants in mixed monolayer films provides an approach to physically manipulate important properties of thin films, including surface morphology, microscale composition, and mechanical properties. In this work, we predict, based upon existing miscibility studies and their thermodynamic underpinnings described in the literature, the miscibility and film morphology of mixed monolayers comprised of behenic acid (C21H43COOH) and perfluorotetradecanoic acid (C13F27COOH) in various molar ratios. Predictions are tested using a combination of experimental surface characterization methods for probing miscibility and film morphology at the solid/air and air/water interfaces. Film components were immiscible and phase-separated into chemically well-defined domains under a variety of experimental conditions, with monolayer morphology consistent with initial predictions. The extensibility of these basic predictions to other systems is discussed in the context of using these works for different perfluorinated surfactant molecules. PMID:27163482

  5. How Acidic Is Carbonic Acid?

    PubMed

    Pines, Dina; Ditkovich, Julia; Mukra, Tzach; Miller, Yifat; Kiefer, Philip M; Daschakraborty, Snehasis; Hynes, James T; Pines, Ehud

    2016-03-10

    Carbonic, lactic, and pyruvic acids have been generated in aqueous solution by the transient protonation of their corresponding conjugate bases by a tailor-made photoacid, the 6-hydroxy-1-sulfonate pyrene sodium salt molecule. A particular goal is to establish the pK(a) of carbonic acid H2CO3. The on-contact proton transfer (PT) reaction rate from the optically excited photoacid to the carboxylic bases was derived, with unprecedented precision, from time-correlated single-photon-counting measurements of the fluorescence lifetime of the photoacid in the presence of the proton acceptors. The time-dependent diffusion-assisted PT rate was analyzed using the Szabo-Collins-Kimball equation with a radiation boundary condition. The on-contact PT rates were found to follow the acidity order of the carboxylic acids: the stronger was the acid, the slower was the PT reaction to its conjugate base. The pK(a) of carbonic acid was found to be 3.49 ± 0.05 using both the Marcus and Kiefer-Hynes free energy correlations. This establishes H2CO3 as being 0.37 pK(a) units stronger and about 1 pK(a) unit weaker, respectively, than the physiologically important lactic and pyruvic acids. The considerable acid strength of intact carbonic acid indicates that it is an important protonation agent under physiological conditions. PMID:26862781

  6. Newly detected molecules in dense interstellar clouds.

    PubMed

    Irvine, W M; Avery, L W; Friberg, P; Matthews, H E; Ziurys, L M

    1988-01-01

    The last year or so has seen the identification of several new interstellar molecules, including C2S, C3S, C5H, C6H, and (probably) HC2CHO in the cold, dark cloud TMC-1; and the discovery of the first interstellar phosphorous-containing molecule, PN, in the Orion "plateau" source. Further interesting results include the observations of 13C3H2 and C3HD, and the first detection of HCOOH (formic acid) in a cold cloud.

  7. 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.

  8. Thermal insulation material comprising a mixture of silk and synthetic fiber staple

    SciTech Connect

    Aldrich, W.E.

    1983-08-23

    An improved thermal insulation material is disclosed, comprising a carded web containing 30 to 80 wt. %, preferably 50 wt. % silk, the balance being crimped, hollow polyester staple or very low denier solid cross section polyester filaments. The carded web is uniformly impregnated with a thermosetting resin to form a bat which is employed as a filler for garments, sleeping bags and the like.

  9. Light source comprising a common substrate, a first led device and a second led device

    SciTech Connect

    Choong, Vi-En

    2010-02-23

    At least one stacked organic or polymeric light emitting diode (PLEDs) devices to comprise a light source is disclosed. At least one of the PLEDs includes a patterned cathode which has regions which transmit light. The patterned cathodes enable light emission from the PLEDs to combine together. The light source may be top or bottom emitting or both.

  10. Using Remote Sensing and Radar MET Data to Support Watershed Assessments Comprising IEM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Meteorological (MET) data required by watershed assessments that comprise Integrated Environmental Modeling (IEM) have traditionally been provided by land-based weather (gauge) stations; although these data may not be most appropriate for describing adequate spatial and temporal resolution if the ME...

  11. Collector surface for a microwave tube comprising a carbon-bonded carbon-fiber composite

    DOEpatents

    Lauf, Robert J.; McMillan, April D.; Johnson, Arvid C.; Moorhead, Arthur J.

    1998-01-01

    In a microwave tube, an improved collector surface coating comprises a porous carbon composite material, preferably a carbon-bonded carbon fiber composite having a bulk density less than about 2 g/cc. Installation of the coating is readily adaptable as part of the tube manufacturing process.

  12. Collector surface for a microwave tube comprising a carbon-bonded carbon-fiber composite

    DOEpatents

    Lauf, R.J.; McMillan, A.D.; Johnson, A.C.; Moorhead, A.J.

    1998-07-28

    In a microwave tube, an improved collector surface coating comprises a porous carbon composite material, preferably a carbon-bonded carbon fiber composite having a bulk density less than about 2 g/cc. Installation of the coating is readily adaptable as part of the tube manufacturing process. 4 figs.

  13. Electrolyte for an aluminum air-battery comprising an anti-foaming agent and corrosion exhibitor

    SciTech Connect

    Niksa, M.J.; Niksa, A.J.; Noscal, J.M.

    1991-09-17

    This patent describes an electrolyte for an aluminium-air battery. It comprises a caustic or saline solution; an anti-foaming agent in an amount effective to reduce the entrapment of hydrogen bubbles in the solution, the hydrogen bubbles being formed at the battery anode; and a corrosion inhibiting amount of a corrosion inhibitor.

  14. Downhole geothermal well sensors comprising a hydrogen-resistant optical fiber

    DOEpatents

    Weiss, Jonathan D.

    2005-02-08

    A new class of optical fiber based thermal sensors has been invented. The new sensors comprise hydrogen-resistant optical fibers which are able to withstand a hot, hydrogen-containing environment as is often found in the downhole well environment.

  15. High temperature battery cell comprising stress-free hollow fiber bundle

    SciTech Connect

    Anand, J.N.; Revak, T.T.; Rossini, F.J.

    1982-06-01

    Thermal stressing of hollow fibers constituting the electrolyteseparator in a high temperature battery cell, and of certain other elements thereof, is avoided by suspending the assembly comprising the anolyte tank, the tubesheet, the hollow fibers and a cathodic current collector-distributing means, within the casing and employing a limp connection between the latter means and the cathode terminal of the cell.

  16. Method of drilling with fluid comprising peanut hulls ground to a powder

    SciTech Connect

    Forrest, G.T.

    1992-02-11

    This patent describes a method of carrying out operations wherein a fluid is circulated in a well extending into the ground. It comprises: taking peanut hulls which have been ground to a powder form, adding the ground peanut hulls to a fluid, and circulating the fluid, with the ground peanut hulls added thereto, in the well.

  17. Photochemistry of interstellar molecules

    NASA Technical Reports Server (NTRS)

    Stief, L. J.

    1971-01-01

    The photochemistry of two diatomic and eight polyatomic molecules is discussed quantitatively. For an interstellar molecule, the lifetime against photodecomposition depends upon the absorption cross section, the quantum yield or probability of dissociation following photon absorption, and the interstellar radiation field. The constant energy density of Habing is used for the unobserved regions of interstellar radiation field, and the field in obscuring clouds is estimated by combining the constant flux with the observed interstellar extinction curve covering the visible and ultraviolet regions. Lifetimes against photodecomposition in the unobscured regions and as a function of increasing optical thickness in obscuring clouds are calculated for the ten species. The results show that, except for CO, all the molecules have comparable lifetimes of less than one hundred years. Thus they can exist only in dense clouds and can never have been exposed to the unobscured radiation. The calculations further show that the lifetimes in clouds of moderate opacity are of the order of one million years.

  18. 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.

  19. Atomic branching in molecules

    NASA Astrophysics Data System (ADS)

    Estrada, Ernesto; Rodríguez-Velázquez, Juan A.; Randić, Milan

    A graph theoretic measure of extended atomic branching is defined that accounts for the effects of all atoms in the molecule, giving higher weight to the nearest neighbors. It is based on the counting of all substructures in which an atom takes part in a molecule. We prove a theorem that permits the exact calculation of this measure based on the eigenvalues and eigenvectors of the adjacency matrix of the graph representing a molecule. The definition of this measure within the context of the Hückel molecular orbital (HMO) and its calculation for benzenoid hydrocarbons are also studied. We show that the extended atomic branching can be defined using any real symmetric matrix, as well as any Hermitian (self-adjoint) matrix, which permits its calculation in topological, geometrical, and quantum chemical contexts.

  20. 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.

  1. Single Molecule Manipulation

    NASA Astrophysics Data System (ADS)

    Kiang, Ching-Hwa

    2011-10-01

    Single-molecule manipulation studies open a door for a close-up investigation of complex biological interactions at the molecular level. In these studies, single biomolecules are pulled while their force response is being monitored. The process is often nonequilibrium, and interpretation of the results has been challenging. We used the atomic force microscope to pull proteins and DNA, and determined the equilibrium properties of the molecules using the recently derived nonequilibrium work theorem. I will present applications of the technique in areas ranging from fundamental biological problems such as DNA mechanics, to complex medical processes such as the mechanical activation of von Willebrand Factor, a key protein in blood coagulation.

  2. Plasmonic nanostructures: artificial molecules.

    PubMed

    Wang, Hui; Brandl, Daniel W; Nordlander, Peter; Halas, Naomi J

    2007-01-01

    This Account describes a new paradigm for the relationship between the geometry of metallic nanostructures and their optical properties. While the interaction of light with metallic nanoparticles is determined by their collective electronic or plasmon response, a compelling analogy exists between plasmon resonances of metallic nanoparticles and wave functions of simple atoms and molecules. Based on this insight, an entire family of plasmonic nanostructures, artificial molecules, has been developed whose optical properties can be understood within this picture: nanoparticles (nanoshells, nanoeggs, nanomatryushkas, nanorice), multi-nanoparticle assemblies (dimers, trimers, quadrumers), and a nanoparticle-over-metallic film, an electromagnetic analog of the spinless Anderson model. PMID:17226945

  3. In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes[OPEN

    PubMed Central

    Husbands, Aman Y.; Aggarwal, Vasudha; Ha, Taekjip; Timmermans, Marja C.P.

    2016-01-01

    Deciphering complex biological processes markedly benefits from approaches that directly assess the underlying biomolecular interactions. Most commonly used approaches to monitor protein-protein interactions typically provide nonquantitative readouts that lack statistical power and do not yield information on the heterogeneity or stoichiometry of protein complexes. Single-molecule pull-down (SiMPull) uses single-molecule fluorescence detection to mitigate these disadvantages and can quantitatively interrogate interactions between proteins and other compounds, such as nucleic acids, small molecule ligands, and lipids. Here, we establish SiMPull in plants using the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) and LITTLE ZIPPER (ZPR) interaction as proof-of-principle. Colocalization analysis of fluorophore-tagged HD-ZIPIII and ZPR proteins provides strong statistical evidence of complex formation. In addition, we use SiMPull to directly quantify YFP and mCherry maturation probabilities, showing these differ substantially from values obtained in mammalian systems. Leveraging these probabilities, in conjunction with fluorophore photobleaching assays on over 2000 individual complexes, we determined HD-ZIPIII:ZPR stoichiometry. Intriguingly, these complexes appear as heterotetramers, comprising two HD-ZIPIII and two ZPR molecules, rather than heterodimers as described in the current model. This surprising result raises new questions about the regulation of these key developmental factors and is illustrative of the unique contribution SiMPull is poised to make to in planta protein interaction studies. PMID:27385814

  4. In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes.

    PubMed

    Husbands, Aman Y; Aggarwal, Vasudha; Ha, Taekjip; Timmermans, Marja C P

    2016-08-01

    Deciphering complex biological processes markedly benefits from approaches that directly assess the underlying biomolecular interactions. Most commonly used approaches to monitor protein-protein interactions typically provide nonquantitative readouts that lack statistical power and do not yield information on the heterogeneity or stoichiometry of protein complexes. Single-molecule pull-down (SiMPull) uses single-molecule fluorescence detection to mitigate these disadvantages and can quantitatively interrogate interactions between proteins and other compounds, such as nucleic acids, small molecule ligands, and lipids. Here, we establish SiMPull in plants using the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) and LITTLE ZIPPER (ZPR) interaction as proof-of-principle. Colocalization analysis of fluorophore-tagged HD-ZIPIII and ZPR proteins provides strong statistical evidence of complex formation. In addition, we use SiMPull to directly quantify YFP and mCherry maturation probabilities, showing these differ substantially from values obtained in mammalian systems. Leveraging these probabilities, in conjunction with fluorophore photobleaching assays on over 2000 individual complexes, we determined HD-ZIPIII:ZPR stoichiometry. Intriguingly, these complexes appear as heterotetramers, comprising two HD-ZIPIII and two ZPR molecules, rather than heterodimers as described in the current model. This surprising result raises new questions about the regulation of these key developmental factors and is illustrative of the unique contribution SiMPull is poised to make to in planta protein interaction studies.

  5. Spin transport in molecules studied by Fe3O4/molecule nanoparticles

    NASA Astrophysics Data System (ADS)

    Yue, F. J.; Wang, S.; Wu, D.

    2013-05-01

    In this work, we synthesize single molecular layer coated Fe3O4 nanoparticles to form the network of the molecular junction spin valves. The Fe3O4 nanoparticles chemically bond with molecules without any physically absorbed molecules, leading to one monolayer molecule coated on nanoparticles. The magnetoresistance (MR) of cold-pressed Fe3O4/oleic acid nanoparticles is more than two times larger than bare Fe3O4 nanoparticles, indicating weaker spin scattering in molecules. Furthermore, the MR ratio is as high as ˜21 % at room temperature for Fe3O4/alkane molecule nanoparticles. Interestingly, even though the resistance spans about two decades as the alkane molecular length varies from 0.7 to 2.5 nm, the MR ratio stays approximately constant. This molecular length independent spin valve MR, originated from the weaker hyperfine interaction strength of the σ-electrons in alkane molecules, entails room-temperature spin-conserving transport in molecular materials. Using the size of ˜500 nm Fe3O4 nanoparticles, a large MR is achieved in a relatively low magnetic field. This feature opens a door for the development of future spin-based molecular electronics. Moreover, spin injection at the interface of Fe3O4/stearic acid molecule is investigated in a comparative study between Fe3O4 nanoparticles chemically bonded (ChemNPs) and physically absorbed (PhyNPs) molecules. A MR of 12 % at room temperature is observed in ChemNPs, in sharp contrast to the zero MR ratio in PhyNPs, reflecting that the chemical bonding is crucial for spin injection. These results show that the hybrid nanoparticles provide a simple approach to study the spin transport in molecules.

  6. Single Molecule Conductance of Oligothiophene Derivatives

    NASA Astrophysics Data System (ADS)

    Dell, Emma J.

    to sample similar conformers. This work demonstrates that the conductance of bithiophene displays a strong dependence on the conformational fluctuations accessible within a given junction configuration, and that the symmetry of such small molecules can significantly influence their conductance behavior. Next, the single-molecule conductance of a family of oligothiophenes comprising one to six thiophene units was measured. An anomalous behavior was found: the peak of the conductance histogram distribution did not follow a clear exponential decay with increasing number of thiophene units in the chain. The electronic properties of the materials were characterized by optical spectroscopy and electrochemistry to gain an understanding of the factors affecting the conductance of these molecules. Different conformers in the junction were postulated to be a contributing factor to the anomalous trend in the observed conductance as a function of molecule length. Then, the electronic properties of the thiophene-1,1-dioxide unit were investigated. These motifs have become synthetically accessible in the last decade, due to Rozen's unprecedentedly potent oxidizing reagent - HOF˙CH 3CN - which has been shown to be powerful yet selective enough to oxidize thiophenes in various environments. The resulting thiophene-1,1-dioxides show great promise for electronic devices. The oxidation chemistry of thiophenes was expanded and tuning of the frontier energy levels was demonstrated through combining electron poor and electron rich units. Finally, charge carriers in single-molecule junctions were shown to be tunable within a family of molecules containing these thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed in order to increase electron affinity, maintain delocalized frontier orbitals, while significantly decreasing the transport gap. Through thermopower measurements, the dominant charge carriers were shown to change from holes to electrons as the number of

  7. Boric acid catalyzed chemoselective esterification of alpha-hydroxycarboxylic acids.

    PubMed

    Houston, Todd A; Wilkinson, Brendan L; Blanchfield, Joanne T

    2004-03-01

    Boric acid catalyzes the selective esterification of alpha-hydroxycarboxylic acids without causing significant esterification to occur with other carboxylic acids. The procedure is simple, high-yielding, and applicable to the esterification of alpha-hydroxy carboxylates in the presence of other carboxylic acids including beta-hydroxyacids within the same molecule. [reaction: see text

  8. Production, Quality Control, Stability and Pharmacotoxicity of a Malaria Vaccine Comprising Three Highly Similar PfAMA1 Protein Molecules to Overcome Antigenic Variation

    PubMed Central

    Houard, Sophie; Havelange, Nicolas; Drossard, Jürgen; Mertens, Hubert; Croon, Alexander; Kastilan, Robin; Byrne, Richard; van der Werff, Nicole; van der Eijk, Marjolein; Thomas, Alan W.; Kocken, Clemens H. M.; Remarque, Edmond J.

    2016-01-01

    Plasmodium falciparum apical membrane antigen 1 (PfAMA1) is a leading asexual blood stage vaccine candidate for malaria. In preparation for clinical trials, three Diversity Covering (DiCo) PfAMA1 ectodomain proteins, designed to overcome the intrinsic polymorphism that is present in PfAMA1, were produced under Good Manufacturing Practice (GMP) in Pichia pastoris. Using identical methodology, the 3 strains were cultivated in 70-L scale fed-batch fermentations and PfAMA1-DiCos were purified by two chromatography steps, an ultrafiltration/diafiltration procedure and size exclusion chromatography, resulting in highly pure (>95%) PfAMA1-DiCo1, PfAMA1 DiCo2 and PfAMA1 DiCo3, with final yields of 1.8, 1.9 and 1.3 gram, respectively. N-terminal determinations showed that approximately 50% of each of the proteins lost 12 residues from their N-terminus, in accordance with SDS-PAGE (2 main bands) and MS-data. Under reducing conditions a site of limited proteolytic cleavage within a disulphide bonded region became evident. The three proteins quantitatively bound to the mAb 4G2 that recognizes a conformational epitope, suggesting proper folding of the proteins. The lyophilized Drug Product (1:1:1 mixture of PfAMA1-DiCo1, DiCo2, DiCo3) fulfilled all pre-set release criteria (appearance, dissolution rate, identity, purity, protein content, moisture content, sub-visible particles, immuno-potency (after reconstitution with adjuvant), abnormal toxicity, sterility and endotoxin), was stable in accelerated and real-time stability studies at -20°C for over 24 months. When formulated with adjuvants selected for clinical phase I evaluation, the Drug Product did not show adverse effect in a repeated-dose toxicity study in rabbits. The Drug Product has entered a phase Ia/Ib clinical trial. PMID:27695087

  9. 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.

  10. 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…

  11. Halley's polymeric organic molecules

    NASA Technical Reports Server (NTRS)

    Huebner, W. F.; Boice, D. C.; Korth, A.

    1989-01-01

    The detection of polymeric organic compounds in the mass spectrum of Comet Halley obtained with the Positive Ion Cluster Composition analyzer on Giotto are examined. It is found that, in addition to polyoxymethylene, other polymers and complex molecules may exist in the comet. It is suggested that polymerized hydrogen cyanide may be a source for the observed CN and NH2 jets.

  12. 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…

  13. OMG: Open Molecule Generator

    PubMed Central

    2012-01-01

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck. PMID:22985496

  14. OMG: Open Molecule Generator.

    PubMed

    Peironcely, Julio E; Rojas-Chertó, Miguel; Fichera, Davide; Reijmers, Theo; Coulier, Leon; Faulon, Jean-Loup; Hankemeier, Thomas

    2012-01-01

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck. PMID:22985496

  15. 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.

  16. Influence of the water molecules near surface of viral protein on virus activation process

    NASA Astrophysics Data System (ADS)

    Shepelenko, S. O.; Salnikov, A. S.; Rak, S. V.; Goncharova, E. P.; Ryzhikov, A. B.

    2009-06-01

    The infection of a cell with influenza virus comprises the stages of receptor binding to the cell membrane, endocytosis of virus particle, and fusion of the virus envelope and cell endosome membrane, which is determined by the conformational changes in hemagglutinin, a virus envelope protein, caused by pH decrease within the endosome. The pH value that induces conformation rearrangements of hemagglutinin molecule considerably varies for different influenza virus strains, first and foremost, due to the differences in amino acid structure of the corresponding proteins. The main goal of this study was to construct a model making it possible to assess the critical pH value characterizing the fusogenic activity of influenza virus hemagglutinin from the data on hemagglutinin structure and experimental verification of this model. Under this model, we assume that when the electrostatic force between interacting hemagglutinin molecules in the virus envelop exceeds a certain value, the hemagglutinin HA1 subunits are arranged so that they form a cavity sufficient for penetration of water molecules. This event leads to an irreversible hydration of the inner fragments of hemagglutinin molecule in a trimer and to the completion of conformational changes. The geometry of electrostatic field in hemagglutinin trimer was calculated taking into account the polarization effects near the interface of two dielectrics, aqueous medium and protein macromolecule. The critical pH values for the conformational changes in hemagglutinin were measured by the erythrocyte hemolysis induced by influenza virus particles when decreasing pH. The critical pH value conditionally separating the pH range into the regions with and without the conformational changes was calculated for several influenza virus H1N1 and H3N2 strains based on the data on the amino acid structure of the corresponding hemagglutinin molecules. Comparison of the theoretical and experimental values of critical pH values for

  17. Novel, electrolyte solutions comprising fully inorganic salts with high anodic stability for rechargeable magnesium batteries

    SciTech Connect

    Doe, RE; Han, R; Hwang, J; Gmitter, AJ; Shterenberg, I; Yoo, HD; Pour, N; Aurbach, D

    2014-01-01

    Herein the first inorganic magnesium salt solution capable of highly reversible magnesium electrodeposition is presented. Synthesized by acid-base reaction of MgCl2 and Lewis acidic compounds such as AlCl3, this salt class demonstrates upwards of 99% Coulombic efficiency, deposition overpotential of <200 mV, and anodic stability of 3.1 V.

  18. Method and device for fabricating dispersion fuel comprising fission product collection spaces

    DOEpatents

    Shaber, Eric L; Fielding, Randall S

    2015-05-05

    A method of fabricating a nuclear fuel comprising a fissile material, one or more hollow microballoons, a phenolic resin, and metal matrix. The fissile material, phenolic resin and the one or more hollow microballoons are combined. The combined fissile material, phenolic resin and the hollow microballoons are heated sufficiently to form at least some fissile material carbides creating a nuclear fuel particle. The resulting nuclear fuel particle comprises one or more fission product collection spaces. In a preferred embodiment, the fissile material, phenolic resin and the one or more hollow microballoons are combined by forming the fissile material into microspheres. The fissile material microspheres are then overcoated with the phenolic resin and microballoon. In another preferred embodiment, the fissile material, phenolic resin and the one or more hollow microballoons are combined by overcoating the microballoon with the fissile material, and phenolic resin.

  19. Lateral acoustic wave resonator comprising a suspended membrane of low damping resonator material

    DOEpatents

    Olsson, Roy H.; El-Kady; , Ihab F.; Ziaei-Moayyed, Maryam; Branch; , Darren W.; Su; Mehmet F.,; Reinke; Charles M.,

    2013-09-03

    A very high-Q, low insertion loss resonator can be achieved by storing many overtone cycles of a lateral acoustic wave (i.e., Lamb wave) in a lithographically defined suspended membrane comprising a low damping resonator material, such as silicon carbide. The high-Q resonator can sets up a Fabry-Perot cavity in a low-damping resonator material using high-reflectivity acoustic end mirrors, which can comprise phononic crystals. The lateral overtone acoustic wave resonator can be electrically transduced by piezoelectric couplers. The resonator Q can be increased without increasing the impedance or insertion loss by storing many cycles or wavelengths in the high-Q resonator material, with much lower damping than the piezoelectric transducer material.

  20. Spiralian phylogenomics supports the resurrection of Bryozoa comprising Ectoprocta and Entoprocta.

    PubMed

    Hausdorf, Bernhard; Helmkampf, Martin; Meyer, Achim; Witek, Alexander; Herlyn, Holger; Bruchhaus, Iris; Hankeln, Thomas; Struck, Torsten H; Lieb, Bernhard

    2007-12-01

    Phylogenetic analyses based on 79 ribosomal proteins of 38 metazoans, partly derived from 6 new expressed sequence tag projects for Ectoprocta, Entoprocta, Sipuncula, Annelida, and Acanthocephala, indicate the monophyly of Bryozoa comprising Ectoprocta and Entoprocta, 2 taxa that have been separated for more than a century based on seemingly profound morphological differences. Our results also show that bryozoans are more closely related to Neotrochozoa, including molluscs and annelids, than to Syndermata, the latter comprising Rotifera and Acanthocephala. Furthermore, we find evidence for the position of Sipuncula within Annelida. These findings suggest that classical developmental and morphological key characters such as cleavage pattern, coelomic cavities, gut architecture, and body segmentation are subject to greater evolutionary plasticity than traditionally assumed.

  1. A Bilayered Structure Comprised of Functionalized Carbon Nanotubes for Desalination by Membrane Distillation.

    PubMed

    Bhadra, Madhuleena; Roy, Sagar; Mitra, Somenath

    2016-08-01

    The development of a novel carbon nanotube (CNT) immobilized membrane comprised of a double-layer structure is presented for water desalination by membrane distillation. The bilayered structure is comprised of CNTs functionalized with a hydrophobic octadecyl amine group on the feed side and carboxylated CNTs on the permeate side. The latter is more hydrophilic. The hydrophobic CNTs provide higher water vapor permeation, while the hydrophilic CNTs facilitate the condensation of water vapor. Together, these led to superior performance, and flux in a direct contact membrane distillation mode was found to be as high as 121 kg/m(2)h at 80 °C. The bilayered membrane represented an enhancement of 70% over the unmodified membrane and 37% over a membrane which had a monolayered structure where only the feed side was CNT-modified. PMID:27387851

  2. Energy storage systems having an electrode comprising Li.sub.xS.sub.y

    DOEpatents

    Xiao, Jie; Zhang, Jiguang; Graff, Gordon L.; Liu, Jun; Wang, Wei; Zheng, Jianming; Xu, Wu; Shao, Yuyan; Yang, Zhenguo

    2016-08-02

    Improved lithium-sulfur energy storage systems can utilizes Li.sub.xS.sub.y as a component in an electrode of the system. For example, the energy storage system can include a first electrode current collector, a second electrode current collector, and an ion-permeable separator separating the first and second electrode current collectors. A second electrode is arranged between the second electrode current collector and the separator. A first electrode is arranged between the first electrode current collector and the separator and comprises a first condensed-phase fluid comprising Li.sub.xS.sub.y. The energy storage system can be arranged such that the first electrode functions as a positive or a negative electrode.

  3. A Bilayered Structure Comprised of Functionalized Carbon Nanotubes for Desalination by Membrane Distillation.

    PubMed

    Bhadra, Madhuleena; Roy, Sagar; Mitra, Somenath

    2016-08-01

    The development of a novel carbon nanotube (CNT) immobilized membrane comprised of a double-layer structure is presented for water desalination by membrane distillation. The bilayered structure is comprised of CNTs functionalized with a hydrophobic octadecyl amine group on the feed side and carboxylated CNTs on the permeate side. The latter is more hydrophilic. The hydrophobic CNTs provide higher water vapor permeation, while the hydrophilic CNTs facilitate the condensation of water vapor. Together, these led to superior performance, and flux in a direct contact membrane distillation mode was found to be as high as 121 kg/m(2)h at 80 °C. The bilayered membrane represented an enhancement of 70% over the unmodified membrane and 37% over a membrane which had a monolayered structure where only the feed side was CNT-modified.

  4. 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

  5. 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

  6. Article comprising a garment or other textile structure for use in controlling body temperature

    DOEpatents

    Butzer, Melissa J.

    2000-01-01

    There is disclosed an article for use in cooling body temperature which comprises a garment having a coat and pant, with each having a body section adapted to receive a portion of the torso of the wearer and extensions from the body section to receive the wearer's limbs. The garment includes a system for circulating temperature controlling fluid from a suitable source through patches removably received in pockets in each of body section and extensions.

  7. Unidirectional resonance modes supported by secondary islands in a microcavity comprised of two half-ellipses

    SciTech Connect

    Lee, Jinhyung; Rim, Sunghwan; Cho, Jinhang; Kim, Chil-Min

    2011-03-15

    We propose a simple and robust mechanism to achieve unidirectional emission in a microcavity comprised of two half-ellipses. The microcavity has two geometrical parameters, two eccentricities, which permit a control of the directional emissions. For the microcavity with two small eccentricities, the positions of secondary islands near primary islands in the survival probability distributions determine the directionality of emissions. We obtain the optimized values of the eccentricities for unidirectional emission.

  8. A reconfigurable on-line learning spiking neuromorphic processor comprising 256 neurons and 128K synapses

    PubMed Central

    Qiao, Ning; Mostafa, Hesham; Corradi, Federico; Osswald, Marc; Stefanini, Fabio; Sumislawska, Dora; Indiveri, Giacomo

    2015-01-01

    Implementing compact, low-power artificial neural processing systems with real-time on-line learning abilities is still an open challenge. In this paper we present a full-custom mixed-signal VLSI device with neuromorphic learning circuits that emulate the biophysics of real spiking neurons and dynamic synapses for exploring the properties of computational neuroscience models and for building brain-inspired computing systems. The proposed architecture allows the on-chip configuration of a wide range of network connectivities, including recurrent and deep networks, with short-term and long-term plasticity. The device comprises 128 K analog synapse and 256 neuron circuits with biologically plausible dynamics and bi-stable spike-based plasticity mechanisms that endow it with on-line learning abilities. In addition to the analog circuits, the device comprises also asynchronous digital logic circuits for setting different synapse and neuron properties as well as different network configurations. This prototype device, fabricated using a 180 nm 1P6M CMOS process, occupies an area of 51.4 mm2, and consumes approximately 4 mW for typical experiments, for example involving attractor networks. Here we describe the details of the overall architecture and of the individual circuits and present experimental results that showcase its potential. By supporting a wide range of cortical-like computational modules comprising plasticity mechanisms, this device will enable the realization of intelligent autonomous systems with on-line learning capabilities. PMID:25972778

  9. Sturgeon and Paddlefish Saggital Otoliths are Comprised of the Calcium Carbonate Polymorphs Vaterite and Calcite

    DOE PAGES

    Prachell, B. M.; Chakoumakos, Bryan C.; Feygenson, Mikhail; Whitledge, Gregory; Koenigs, Ryan; Bruch, Ronald

    2016-07-27

    The otoliths of modern fishes are most commonly comprised of the metastable aragonite polymorph of calcium carbonate (CaCO3); however, sturgeons have otoliths reportedly comprised of the least stable of the three most-common polymorphs, vaterite. In this study, we used neutron diffraction to characterize CaCO3 polymorph composition of lake sturgeon and paddlefish otoliths. Based on previous summaries of CaCO3 composition over fish evolutionary history, we hypothesized that sturgeon and paddlefish otoliths would have similar polymorph composition. We found that despite previous reports of sturgeon otoliths being comprised entirely of vaterite, that all otoliths we examined in this study also had amore » calcite fraction that ranged from 17.9+ 6.0 wt. % to 35.9 + 2.9 wt. %. We also conducted a grinding experiment that demonstrated that calcite fractions were due to biological variation and not an artifact of polymorph transformation during preparation. Our study provides the initial characterization of the polymorph composition of the otoliths of lake sturgeon, and paddlefish and also provides the first-ever report of otoliths of Acipenserids as having a calcite fraction.« less

  10. Langmuir Films of Chiral Molecules on Mercury

    SciTech Connect

    Tamam, L.; Menahem, T; Mastai, Y; Sloutskin, E; Yefet, S; Deustch, M

    2009-01-01

    Homo- and heterochiral Langmuir films of a chiral derivative of stearic acid are studied in situ on the surface of liquid mercury as a function of surface coverage by surface tensiometry and surface-specific synchrotron X-ray diffraction and reflectivity. A transition from a phase of surface-parallel molecules to a phase of standing-up molecules is found. The former shows no surface-parallel long-range order. The standing-up phase of both homochiral and heterochiral compositions exhibit long-range order. However, the former has an oblique unit cell with parallel molecular planes, and the later has a centered rectangular unit cell with a herringbone molecular packing. For both cases, the standing-up molecules are tilted by 44 from the surface normal and pack at a density of 19.5 Angstroms2/molecule in the plane normal to the molecular long axis. Important differences are found, and discussed, between this behavior and that of a Langmuir film of the nonchiral stearic acid on mercury.

  11. Single-molecule electrophoresis

    SciTech Connect

    Castro, A.; Shera, E.B.

    1995-09-15

    A novel method for the detection and identification of single molecules in solution has been devised, computer simulated, and experimentally achieved. The technique involves the determination of electrophoretic velocities by measuring the time required for individual molecules to travel a fixed distance between two laser beams. Computer simulations of the process were performed before-hand in order to estimate the experimental feasibility of the method and to determine the optimum values for the various experimental parameters. Examples of the use of the technique for the ultrasensitive detection and identification of rhodamine-6G, a mixture of DNA restriction fragments, and a mixture of proteins in aqueous solution are presented. 20 refs., 8 figs.

  12. Cometary Parent Molecules

    NASA Astrophysics Data System (ADS)

    Feldman, Paul

    1990-12-01

    We propose to use HRS observations of a suitable target-of-opportunity comet to study two outstanding problems related to the composition of the volatile component of the cometary nucleus. These problems concern two species, CO and S2, which have been observed in the cometary coma and identified as "parent" molecules sublimating directly from the nucleus. Both of these molecules have their principal fluorescent emissions in the vaccuum ultraviolet. The high spectral resolution will allow the determination of the rotational temperature of CO, which is diagnostic of the source temperature and the excitation mechanism of the observed emission. The determination of the abundance of both CO and S2 in the primarily water ice of the nucleus can serve to constrain current models of comet formation in the primordial solar nebula.

  13. Small molecule annotation for the Protein Data Bank.

    PubMed

    Sen, Sanchayita; Young, Jasmine; Berrisford, John M; Chen, Minyu; Conroy, Matthew J; Dutta, Shuchismita; Di Costanzo, Luigi; Gao, Guanghua; Ghosh, Sutapa; Hudson, Brian P; Igarashi, Reiko; Kengaku, Yumiko; Liang, Yuhe; Peisach, Ezra; Persikova, Irina; Mukhopadhyay, Abhik; Narayanan, Buvaneswari Coimbatore; Sahni, Gaurav; Sato, Junko; Sekharan, Monica; Shao, Chenghua; Tan, Lihua; Zhuravleva, Marina A

    2014-01-01

    The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors.

  14. Small molecule annotation for the Protein Data Bank.

    PubMed

    Sen, Sanchayita; Young, Jasmine; Berrisford, John M; Chen, Minyu; Conroy, Matthew J; Dutta, Shuchismita; Di Costanzo, Luigi; Gao, Guanghua; Ghosh, Sutapa; Hudson, Brian P; Igarashi, Reiko; Kengaku, Yumiko; Liang, Yuhe; Peisach, Ezra; Persikova, Irina; Mukhopadhyay, Abhik; Narayanan, Buvaneswari Coimbatore; Sahni, Gaurav; Sato, Junko; Sekharan, Monica; Shao, Chenghua; Tan, Lihua; Zhuravleva, Marina A

    2014-01-01

    The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors. PMID:25425036

  15. 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.

  16. 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)

  17. Synthesis of acid addition salt of delta-aminolevulinic acid from 5-bromo levulinic acid esters

    DOEpatents

    Moens, Luc

    2003-06-24

    A process of preparing an acid addition salt of delta-aminolevulinc acid comprising: a) dissolving a lower alkyl 5-bromolevulinate and hexamethylenetetramine in a solvent selected from the group consisting of water, ethyl acetate, chloroform, acetone, ethanol, tetrahydrofuran and acetonitrile, to form a quaternary ammonium salt of the lower alkyl 5-bromolevulinate; and b) hydrolyzing the quaternary ammonium salt with an inorganic acid to form an acid addition salt of delta-aminolevulinic acid.

  18. Molecules as magnetic probes of starspots

    NASA Astrophysics Data System (ADS)

    Afram, N.; Berdyugina, S. V.

    2015-04-01

    Context. Stellar dynamo processes can be explored by measuring the magnetic field. This is usually obtained using the atomic and molecular Zeeman effect in spectral lines. While the atomic Zeeman effect can only access warmer regions, the use of molecular lines is of advantage for studying cool objects. The molecules MgH, TiO, CaH, and FeH are suited to probe stellar magnetic fields, each one for a different range of spectral types, by considering the signal that is obtained from modeling various spectral types. Aims: We have analyzed the usefulness of different molecules (MgH, TiO, CaH, and FeH) as diagnostic tools for studying stellar magnetism on active G-K-M dwarfs. We investigate the temperature range in which the selected molecules can serve as indicators for magnetic fields on highly active cool stars and present synthetic Stokes profiles for the modeled spectral type. Methods: We modeled a star with a spot size of 10% of the stellar disk and a spot comprising either only longitudinal or only transverse magnetic fields and estimated the strengths of the polarization Stokes V and Q signals for the molecules MgH, TiO, CaH, and FeH. We combined various photosphere and spot models according to realistic scenarios. Results: In G dwarfs, the molecules MgH and FeH show overall the strongest Stokes V and Q signals from the starspot, whereas FeH has a stronger Stokes V signal in all G dwarfs with a spot temperature of 3800 K. In K dwarfs, CaH signals are generally stronger, and the TiO signature is most prominent in M dwarfs. Conclusions: Modeling synthetic polarization signals from starspots for a range of G-K-M dwarfs leads to differences in the prominence of various molecular signatures in different wavelength regions, which helps to efficiently select targets and exposure times for observations.

  19. Preparation and evaluation of novel chiral stationary phases based on quinine derivatives comprising crown ether moieties.

    PubMed

    Wang, Dongqiang; Zhao, Jianchao; Wu, Haixia; Wu, Haibo; Cai, Jianfeng; Ke, Yanxiong; Liang, Xinmiao

    2015-01-01

    The C9-position of quinine was modified by meta- or para-substituted benzo-18-crown-6, and immobilized on 3-mercaptopropyl-modified silica gel through the radical thiol-ene addition reaction. These two chiral stationary phases were evaluated by chiral acids, amino acids, and chiral primary amines. The crown ether moiety on the quinine anion exchanger provided a ligand-exchange site for primary amino groups, which played an important role in the retention and enantioselectivity for chiral compounds containing primary amine groups. These two stationary phases showed good selectivity for some amino acids. The complex interaction between crown ether and protonated primary amino group was investigated by the addition of inorganic salts such as LiCl, NH4Cl, NaCl, and KCl to the mobile phase. The resolution results showed that the simultaneous interactions between two function moieties (quinine and crown ether) and amino acids were important for the chiral separation.

  20. Calculations of distance distributions and probabilities of binding by ligands between parallel plane membranes comprising receptors

    NASA Astrophysics Data System (ADS)

    Plante, Ianik; Devroye, Luc; Cucinotta, Francis A.

    2014-03-01

    Cell communication through biochemical signaling pathways is a key determinant of tissue responses to radiation. Several molecules, such as the transforming growth factor β (TGFβ), are implicated in radiation-induced signaling between cells. Brownian Dynamics (BD) algorithms have recently been used to simulate the interaction of ligands with receptors and to elucidate signal transduction and autocrine loops in ligand-receptors systems. In this paper, we discuss the simulation of particle diffusion and binding kinetics in a space bounded by two parallel plane membranes, using an exact algorithm to sample the propagator (Green’s function) of a particle located between 2 membranes. We also show that the simulation results are independent of the number of time steps used, in accordance with time discretization equations. These simulations could be used to simulate the motion and binding of ligand molecules in a cell culture, and possibly in neuronal synapses.

  1. Isomerization reactions on single adsorbed molecules.

    PubMed

    Morgenstern, Karina

    2009-02-17

    Molecular switches occur throughout nature. In one prominent example, light induces the isomerization of retinal from the compact 11-cis form to the elongated all-trans form, a conversion that triggers the transformation of light into a neural impulse in the eye. Applying these natural principles to synthetic systems offers a promising way to construct smaller and faster nanoelectronic devices. In such systems, electronic switches are essential components for storage and logical operations. The development of molecular switches on the single-molecule level would represent a major step toward incorporating molecules as building units into nanoelectronic circuits. Molecular switches must be both reversible and bistable. To meet these requirements, a molecule must have at least two different thermally stable forms and a way to repeatedly interconvert between those forms based on changes in light, heat, pressure, magnetic or electric fields, pH, mechanical forces, or electric currents. The conversion should be connected to a measurable change in electronic, optical, magnetic, or mechanical properties. Because isomers can differ significantly in physical and chemical properties, isomerization could serve as a molecular switching mechanism. Integration of molecular switches into larger circuits will probably require arranging them on surfaces, which will require a better understanding of isomerization reactions in these environments. In this Account, we describe our scanning tunneling microscopy studies of the isomerization of individual molecules adsorbed on metal surfaces. Investigating chlorobenzene and azobenzene derivatives on the fcc(111) faces of Ag, Cu, and Au, we explored the influence of substituents and the substrate on the excitation mechanism of the isomerization reaction induced by inelastically tunneling electrons. We achieved an irreversible configurational (cis-trans) isomerization of individual 4-dimethyl-amino-azobenzene-4-sulfonic acid molecules on Au

  2. Quantum correlations and entanglement in a model comprised of a short chain of nonlinear oscillators

    NASA Astrophysics Data System (ADS)

    Kalaga, J. K.; Kowalewska-Kudłaszyk, A.; Leoński, W.; Barasiński, A.

    2016-09-01

    We discuss a model comprised of a chain of three Kerr-like nonlinear oscillators pumped by two modes of external coherent field. We show that the system can be treated as nonlinear quantum scissors and behave as a three-qubit model. For such situation, different types of tripartite entangled states can be generated, even when damping effects are present in the system. Some amount of such entanglement can survive even in a long-time limit. The flow of bipartite entanglement between subsystems of the model and relations among first-order correlations, second-order correlations, and the entanglement are discussed.

  3. The Electrical Properties for Phenolic Isocyanate-Modified Bisphenol-Based Epoxy Resins Comprising Benzoate Group.

    PubMed

    Lee, Eun Yong; Chae, Il Seok; Park, Dongkyung; Suh, Hongsuk; Kang, Sang Wook

    2016-03-01

    Epoxy resin has been required to have a low dielectric constant (D(k)), low dissipation factor (Df), low coefficient of thermal expansion (CTE), low water absorption, high mechanical, and high adhesion properties for various applications. A series of novel phenolic isocyanate-modified bisphenol-based epoxy resins comprising benzoate group were prepared for practical electronic packaging applications. The developed epoxy resins showed highly reduced dielectric constants (D(k)-3.00 at 1 GHz) and low dissipation values (Df-0.014 at 1 GHz) as well as enhanced thermal properties. PMID:27455751

  4. The Electrical Properties for Phenolic Isocyanate-Modified Bisphenol-Based Epoxy Resins Comprising Benzoate Group.

    PubMed

    Lee, Eun Yong; Chae, Il Seok; Park, Dongkyung; Suh, Hongsuk; Kang, Sang Wook

    2016-03-01

    Epoxy resin has been required to have a low dielectric constant (D(k)), low dissipation factor (Df), low coefficient of thermal expansion (CTE), low water absorption, high mechanical, and high adhesion properties for various applications. A series of novel phenolic isocyanate-modified bisphenol-based epoxy resins comprising benzoate group were prepared for practical electronic packaging applications. The developed epoxy resins showed highly reduced dielectric constants (D(k)-3.00 at 1 GHz) and low dissipation values (Df-0.014 at 1 GHz) as well as enhanced thermal properties.

  5. Yb:FAP and related materials, laser gain medium comprising same, and laser systems using same

    DOEpatents

    Krupke, William F.; Payne, Stephen A.; Chase, Lloyd L.; Smith, Larry K.

    1994-01-01

    An ytterbium doped laser material remarkably superior to all others, including Yb:YAG, comprises Ytterbium doped apatite (Yb:Ca.sub.5 (PO.sub.4).sub.3 F) or Yb:FAP, or ytterbium doped crystals that are structurally related to FAP. The new laser material is used in laser systems pumped by diode pump sources having an output near 0.905 microns or 0.98 microns, such as InGaAs and AlInGaAs, or other narrowband pump sources near 0.905 microns or 0.98 microns. The laser systems are operated in either the conventional or ground state depletion mode.

  6. Electrical characterization of MIM capacitor comprises an adamantane film at room temperature

    NASA Astrophysics Data System (ADS)

    Tiwari, Rajanish N.; Yoshimura, Masamichi

    2016-06-01

    We fabricated a new metal-insulator-metal capacitor at room temperature, comprising a ˜90 nm thin low-k adamantane film on a Si substrate. The surface morphology of deposited organic film was investigated by using scanning electron microscopy and Raman spectroscopy, which is confirmed that the adamantane thin film was uniformly distributed on the Si surface. The adamantane film exhibits a low leakage current density of 7.4 x 10-7 A/cm2 at 13.5 V, better capacitance density of 2.14 fF/μm2 at 100 KHz.

  7. Enhancement of thermal stability of porous bodies comprised of stainless steel or an alloy

    DOEpatents

    Bischoff, Brian L.; Sutton, Theodore G.; Judkins, Roddie R.; Armstrong, Timothy R.; Adcock, Kenneth D.

    2010-11-09

    A method for treating a porous item constructed of metal powder, such as a powder made of Series 400 stainless steel, involves a step of preheating the porous item to a temperature of between about 700 and 900.degree. C. degrees in an oxidizing atmosphere and then sintering the body in an inert or reducing atmosphere at a temperature which is slightly below the melting temperature of the metal which comprises the porous item. The thermal stability of the resulting item is enhanced by this method so that the item retains its porosity and metallic characteristics, such as ductility, at higher (e.g. near-melting) temperatures.

  8. Laboratory studies of astrophysical molecules

    NASA Astrophysics Data System (ADS)

    Wang, Haiyan

    There is growing evidence that the molecules necessary for the evolution of life on earth arrived from the interstellar medium. The study of these molecules is therefore of great current interest. Two major types of signals from interstellar space, so-called unidentified interstellar infrared emission bands and the diffuse interstellar absorption bands, have intrigued and puzzled astrochemists for decades. This work has been concentrated on how to contribute to an understanding of the origins of these perplexing signals from space and help identify other molecules that may exist in outer space. Matrix isolation spectroscopy (infrared and ultraviolet-visible) combined with theoretical calculations has been employed throughout this research. Fourier transform infrared absorption spectroscopic measurements, aided by theoretical calculations and 13 C-isotope shifts, have led to the identification of eight heretofore unknown C n S m clusters: C 2 S, C 6 S, C 7 S, C 7 S 2 , C 9 S 2 , C 11 S 2 , C 13 S 2 , and C 15 S 2 . Infrared absorption studies of xenon polycarbon clusters aid in understanding the special electronic structure and reactivity of carbon clusters, which might be associated with the formation mechanism of Buckyball (C 60 ). Reaction of C3 with benzene and ammonia might be involved in the formation of more complex molecular structures, including polycyclic aromatic hydrocarbons (PAHs) and biomolecules such as the amino acids. High resolution vibrational and electronic spectra of neutral dibenzo [b,def]chrysene and its ions in 12 K argon matrices have been recorded. Spectral assignments were supported by high level theoretical calculations. A mixture of the neutral and ionic infrared spectra of dibenzo[b,def]chrysene resembles the unidentified IR bands in the reflection nebula NGC 7023. Anharmonic frequency calculations for neutral and cationic naphthalene, phenanthrene and anthracene using density functional theory have been carried out for the first time

  9. Acetic Acid Can Catalyze Succinimide Formation from Aspartic Acid Residues by a Concerted Bond Reorganization Mechanism: A Computational Study

    PubMed Central

    Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

    2015-01-01

    Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism. PMID:25588215

  10. 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

  11. Neutron Nucleic Acid Crystallography.

    PubMed

    Chatake, Toshiyuki

    2016-01-01

    The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination. PMID:26227050

  12. Neutron Nucleic Acid Crystallography.

    PubMed

    Chatake, Toshiyuki

    2016-01-01

    The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

  13. Pyrolysis and hydrolysis of mixed polymer waste comprising polyethylene-terephthalate and polyethylene to sequentially recover [monomers

    DOEpatents

    Evans, R.J.; Chum, H.L.

    1998-10-13

    A process is described for using fast pyrolysis in a carrier gas to convert a plastic waste feed stream having a mixed polymeric composition in a manner such that pyrolysis of a given polymer to its high value monomeric constituent occurs prior to pyrolysis of other plastic components therein comprising: selecting a first temperature program range to cause pyrolysis of said given polymer to its high value monomeric constituent prior to a temperature range that causes pyrolysis of other plastic components; selecting a catalyst and support for treating said feed streams with said catalyst to effect acid or base catalyzed reaction pathways to maximize yield or enhance separation of said high value monomeric constituent in said temperature program range; differentially heating said feed stream at a heat rate within the first temperature program range to provide differential pyrolysis for selective recovery of optimum quantities of the high value monomeric constituent prior to pyrolysis of other plastic components; separating the high value monomeric constituents; selecting a second higher temperature range to cause pyrolysis of a different high value monomeric constituent of said plastic waste and differentially heating the feed stream at the higher temperature program range to cause pyrolysis of the different high value monomeric constituent; and separating the different high value monomeric constituent. 83 figs.

  14. Hepatoprotective Activity of Herbal Composition SAL, a Standardize Blend Comprised of Schisandra chinensis, Artemisia capillaris, and Aloe barbadensis

    PubMed Central

    Yimam, Mesfin; Jiao, Ping; Moore, Breanna; Hong, Mei; Cleveland, Sabrina; Chu, Min; Jia, Qi; Lee, Young-Chul; Kim, Hyun-Jin; Nam, Jeong-Bum; Kim, Mi-Ran; Hyun, Eu-Jin; Jung, Gayoung; Do, Seon Gil

    2016-01-01

    Some botanicals have been reported to possess antioxidative activities acting as scavengers of free radicals rendering their usage in herbal medicine. Here we describe the potential use of “SAL,” a standardized blend comprised of three extracts from Schisandra chinensis, Artemisia capillaris, and Aloe barbadensis, in mitigating chemically induced acute liver toxicities. Acetaminophen and carbon tetrachloride induced acute liver toxicity models in mice were utilized. Hepatic functional tests from serum collected at T24 and hepatic glutathione and superoxide dismutases from liver homogenates were evaluated. Histopathology analysis and merit of blending 3 standardized extracts were also confirmed. Statistically significant and dose-correlated inhibitions in serum ALT ranging from 52.5% (p = 0.004) to 34.6% (p = 0.05) in the APAP and 46.3% (p < 0.001) to 29.9% (p = 0.02) in the CCl4 models were observed for SAL administered at doses of 400–250 mg/kg. Moreover, SAL resulted in up to 60.6% and 80.2% reductions in serums AST and bile acid, respectively. The composition replenished depleted hepatic glutathione in association with an increase of hepatic superoxide dismutase. Unexpected synergistic protection from liver damage was also observed. Therefore, the composition SAL could be potentially utilized as an effective hepatic-detoxification agent for the protection from liver damage. PMID:27066270

  15. Hepatoprotective Activity of Herbal Composition SAL, a Standardize Blend Comprised of Schisandra chinensis, Artemisia capillaris, and Aloe barbadensis.

    PubMed

    Yimam, Mesfin; Jiao, Ping; Moore, Breanna; Hong, Mei; Cleveland, Sabrina; Chu, Min; Jia, Qi; Lee, Young-Chul; Kim, Hyun-Jin; Nam, Jeong-Bum; Kim, Mi-Ran; Hyun, Eu-Jin; Jung, Gayoung; Do, Seon Gil

    2016-01-01

    Some botanicals have been reported to possess antioxidative activities acting as scavengers of free radicals rendering their usage in herbal medicine. Here we describe the potential use of "SAL," a standardized blend comprised of three extracts from Schisandra chinensis, Artemisia capillaris, and Aloe barbadensis, in mitigating chemically induced acute liver toxicities. Acetaminophen and carbon tetrachloride induced acute liver toxicity models in mice were utilized. Hepatic functional tests from serum collected at T24 and hepatic glutathione and superoxide dismutases from liver homogenates were evaluated. Histopathology analysis and merit of blending 3 standardized extracts were also confirmed. Statistically significant and dose-correlated inhibitions in serum ALT ranging from 52.5% (p = 0.004) to 34.6% (p = 0.05) in the APAP and 46.3% (p < 0.001) to 29.9% (p = 0.02) in the CCl4 models were observed for SAL administered at doses of 400-250 mg/kg. Moreover, SAL resulted in up to 60.6% and 80.2% reductions in serums AST and bile acid, respectively. The composition replenished depleted hepatic glutathione in association with an increase of hepatic superoxide dismutase. Unexpected synergistic protection from liver damage was also observed. Therefore, the composition SAL could be potentially utilized as an effective hepatic-detoxification agent for the protection from liver damage. PMID:27066270

  16. Small human islets comprised of more β-cells with higher insulin content than large islets

    PubMed Central

    Farhat, Bilal; Almelkar, Akshay; Ramachandran, Karthik; Williams, S. Janette; Huang, Han-Hung; Zamierowksi, David; Novikova, Lesya; Stehno-Bittel, Lisa

    2013-01-01

    For the past 30 y, data have suggested that unique islet populations exist, based on morphology and glucose sensitivity. Yet little has been done to determine the mechanism of these functional differences. The purpose of this study was to determine whether human islets were comprised functionally unique populations, and to elucidate a possible mechanism. Islets or pancreatic sections from 29 human donors were analyzed. Islets were isolated and measured for insulin secretion, cell composition and organization, insulin and glucagon granule density and insulin content. Insulin secretion was significantly greater in small compared with large islets. In sectioned human pancreata, β-cells comprised a higher proportion of the total endocrine cells in small islets (63%) than large islets (39%). A higher percentage of β-cells in small islets contacted blood vessels (44%) compared with large islets (31%). Total insulin content of isolated human islets was significantly greater in the small (1323 ± 512 μIU/IE) compared with large islets (126 ± 48 μIU/IE). There was less immunostaining for insulin in the large islets from human pancreatic sections, especially in the core of the islet, compared with small islets. The results suggest that differences in insulin secretion between large and small islets may be due to a higher percentage of β-cells in small islets with more β-cells in contact with blood vessels and a higher concentration of insulin/β-cell in small islets. PMID:23648896

  17. Emergent ferroelectricity in disordered tri-color multilayer structure comprised of ferromagnetic manganites

    NASA Astrophysics Data System (ADS)

    Niu, Li-Wei; Chen, Chang-Le; Dong, Xiang-Lei; Xing, Hui; Luo, Bing-Cheng; Jin, Ke-Xin

    2016-10-01

    Multiferroic materials, showing the coexistence and coupling of ferroelectric and magnetic orders, are of great technological and fundamental importance. However, the limitation of single phase multiferroics with robust magnetization and polarization hinders the magnetoelectric effect from being applied practically. Magnetic frustration, which can induce ferroelectricity, gives rise to multiferroic behavior. In this paper, we attempt to construct an artificial magnetically frustrated structure comprised of manganites to induce ferroelectricity. A disordered stacking of manganites is expected to result in frustration at interfaces. We report here that a tri-color multilayer structure comprised of non-ferroelectric La0.9Ca0.1MnO3(A)/Pr0.85Ca0.15MnO3(B)/Pr0.85Sr0.15MnO3(C) layers with the disordered arrangement of ABC-ACB-CAB-CBA-BAC-BCA is prepared to form magnetoelectric multiferroics. The multilayer film exhibits evidence of ferroelectricity at room temperature, thus presenting a candidate for multiferroics. Project supported by the National Natural Science Foundation of China (Grant Nos. 61471301, 61078057, 51172183, 51402240, and 51471134), the Specialized Research Fund for the Doctoral Program of Higher Education, China (Grant No. 20126102110045), the Natural Science Foundation of Shaanxi Province, China (Grant No. 2015JQ5125), and the Fundamental Research Funds for the Central Universities, China (Grant No. 3102015ZY078).

  18. 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.

  19. 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.

  20. In vivo unnatural amino acid expression in the methylotrophic yeast Pichia pastoris

    DOEpatents

    Young, Travis [San Diego, CA; Schultz, Peter G [La Jolla, CA

    2014-02-11

    The invention provides orthogonal translation systems for the production of polypeptides comprising unnatural amino acids in methyltrophic yeast such as Pichia pastoris. Methods for producing polypeptides comprising unnatural amino acids in methyltrophic yeast such as Pichia pastoris are also provided.

  1. 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)

  2. Melatonin: a multitasking molecule.

    PubMed

    Reiter, Russel J; Tan, Dun-Xian; Fuentes-Broto, Lorena

    2010-01-01

    Melatonin (N-acetyl-5-methoxytryptamine) has revealed itself as an ubiquitously distributed and functionally diverse molecule. The mechanisms that control its synthesis within the pineal gland have been well characterized and the retinal and biological clock processes that modulate the circadian production of melatonin in the pineal gland are rapidly being unravelled. A feature that characterizes melatonin is the variety of mechanisms it employs to modulate the physiology and molecular biology of cells. While many of these actions are mediated by well-characterized, G-protein coupled melatonin receptors in cellular membranes, other actions of the indole seem to involve its interaction with orphan nuclear receptors and with molecules, for example calmodulin, in the cytosol. Additionally, by virtue of its ability to detoxify free radicals and related oxygen derivatives, melatonin influences the molecular physiology of cells via receptor-independent means. These uncommonly complex processes often make it difficult to determine specifically how melatonin functions to exert its obvious actions. What is apparent, however, is that the actions of melatonin contribute to improved cellular and organismal physiology. In view of this and its virtual absence of toxicity, melatonin may well find applications in both human and veterinary medicine.

  3. Corannulene-Helicene Hybrids: Chiral π-Systems Comprising Both Bowl and Helical Motifs.

    PubMed

    Fujikawa, Takao; Preda, Dorin V; Segawa, Yasutomo; Itami, Kenichiro; Scott, Lawrence T

    2016-08-19

    Two distinct structural elements that render π-systems nonplanar, i.e., geodesic curvature and helical motifs, have been combined into new polyarenes that contain both features. The resultant corannulene-[n]helicenes (n = 5, 6) show unique molecular dynamics in their enantiomerization processes, including inversion motions of both the bowl and the helix. Optical resolution of a corannulene-based skeletally chiral molecule was also achieved for the first time, and the influence of the bowl-motif annulation on the chiroptical properties was investigated. PMID:27490184

  4. 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.

  5. Ankyrin-binding activity of nervous system cell adhesion molecules expressed in adult brain.

    PubMed

    Davis, J Q; Bennett, V

    1993-01-01

    A family of ankyrin-binding glycoproteins have been identified in adult rat brain that include alternatively spliced products of the same pre-mRNA. A composite sequence of ankyrin-binding glycoprotein (ABGP) shares 72% amino acid sequence identity with chicken neurofascin, a membrane-spanning neural cell adhesion molecule in the Ig super-family expressed in embryonic brain. ABGP polypeptides and ankyrin associate as pure proteins in a 1:1 molar stoichiometry at a site located in the predicted cytoplasmic domain. ABGP polypeptides are expressed late in postnatal development to approximately the same levels as ankyrin, and comprise a significant fraction of brain membrane proteins. Immunofluorescence studies have shown that ABGP polypeptides are co-localized with ankyrinB. Major differences in developmental expression have been reported for neurofascin in embryos compared with the late postnatal expression of ABGP, suggesting that ABGP and neurofascin represent products of gene duplication events that have subsequently evolved in parallel with distinct roles. Predicted cytoplasmic domains of rat ABGP and chicken neurofascin are nearly identical to each other and closely related to a group of nervous system cell adhesion molecules with variable extracellular domains, including L1, Nr-CAM and Ng-CAM of vertebrates, and neuroglian of Drosophila. A hypothesis to be evaluated is that ankyrin-binding activity is shared by all of these proteins.

  6. The interaction of fluorescent Pyronin Y molecules with monodisperse silver nanoparticles in chloroform

    NASA Astrophysics Data System (ADS)

    Şenol, Ayşe Merve; Metin, Önder; Acar, Murat; Onganer, Yavuz; Meral, Kadem

    2016-01-01

    The interaction of fluorescent Pyronin Y (PyY) molecules with monodisperse silver nanoparticles (Ag NPs) in chloroform was studied by using UV-Vis, steady-state and time-resolved fluorescence spectroscopies. Monodisperse Ag NPs were synthesized by using a surfactant assisted organic solution phase protocol comprising the tandem thermal decomposition and reduction of silver (I) acetate in oleic acid and oleylamine at 180 °C. The average particle size of Ag NPs was determined to be ˜3 nm by transmission electron microcopy (TEM) and their X-ray diffraction (XRD) pattern revealed the face centered cubic crystal phase. Afterward, PyY and monodisperse Ag NPs were interacted in chloroform via sonication at various time periods. The obtained spectroscopic results revealed that the photophysical properties of PyY molecules were dramatically changed after their interaction with Ag NPs in chloroform. It was determined that the amount of Ag NPs and PyY has the major effects on the photophysical properties of the dye.

  7. 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.

  8. Fabrication and Characterization of Cylindrical Light Diffusers Comprised of Shape Memory Polymer

    SciTech Connect

    Small IV, W; Buckley, P R; Wilson, T S; Loge, J M; Maitland, K D; Maitland, D J

    2007-01-29

    We have developed a technique for constructing light diffusing devices comprised of a flexible shape memory polymer (SMP) cylindrical diffuser attached to the tip of an optical fiber. Devices were fabricated by casting an SMP rod over the cleaved tip of an optical fiber and media blasting the SMP rod to create a light diffusing surface. The axial and polar emission profiles and circumferential (azimuthal) uniformity were characterized for various blasting pressures, nozzle-to-sample distances, and nozzle translation speeds. The diffusers were generally strongly forward-directed and consistently withstood over 8 W of incident infrared laser light without suffering damage when immersed in water. These devices are suitable for various endoluminal and interstitial biomedical applications.

  9. Transgenic Carrot Expressing Fusion Protein Comprising M. tuberculosis Antigens Induces Immune Response in Mice

    PubMed Central

    Permyakova, Natalia V.; Zagorskaya, Alla A.; Belavin, Pavel A.; Uvarova, Elena A.; Nosareva, Olesya V.; Nesterov, Andrey E.; Novikovskaya, Anna A.; Zav'yalov, Evgeniy L.; Moshkin, Mikhail P.; Deineko, Elena V.

    2015-01-01

    Tuberculosis remains one of the major infectious diseases, which continues to pose a major global health problem. Transgenic plants may serve as bioreactors to produce heterologous proteins including antibodies, antigens, and hormones. In the present study, a genetic construct has been designed that comprises the Mycobacterium tuberculosis genes cfp10, esat6 and dIFN gene, which encode deltaferon, a recombinant analog of the human γ-interferon designed for expression in plant tissues. This construct was transferred to the carrot (Daucus carota L.) genome by Agrobacterium-mediated transformation. This study demonstrates that the fusion protein CFP10-ESAT6-dIFN is synthesized in the transgenic carrot storage roots. The protein is able to induce both humoral and cell-mediated immune responses in laboratory animals (mice) when administered either orally or by injection. It should be emphasized that M. tuberculosis antigens contained in the fusion protein have no cytotoxic effect on peripheral blood mononuclear cells. PMID:25949997

  10. Charge generation layers comprising transition metal-oxide/organic interfaces. Electronic structure and charge generation mechanism

    SciTech Connect

    Meyer, Jens; Kröger, M.; Hamwi, S.; Gnam, F.; Riedl, T.; Kowalsky, W.; Kahn, Antoine

    2010-01-01

    The energetics of an archetype charge generation layer (CGL) architecture comprising of 4,4' ,4 '' -tris(N -carbazolyl)triphenylamine (TCTA), tungsten oxide (WO3 ) , and bathophenanthroline (BPhen) n-doped with cesium carbonate (Cs2 CO3 ) are determined by ultraviolet and inverse photoemissionspectroscopy. We show that the charge generation process occurs at the interface between the hole-transport material (TCTA) and WO3 and not, as commonly assumed, at the interface between WO3 and the n-doped electron-transport material (BPhen:Cs2 CO3 ) . However, the n-doped layer is also essential to the realization of an efficient CGL structure. The charge generation mechanism occurs via electron transfer from the TCTA highest occupied molecular orbital level to the transition metal-oxide conduction band.

  11. Highly bendable bilayer-type photo-actuators comprising of reduced graphene oxide dispersed in hydrogels

    PubMed Central

    Kim, Dowan; Lee, Heon Sang; Yoon, Jinhwan

    2016-01-01

    To avoid the problem of reduced graphene oxide (rGO) restacking in aqueous solution, the preparation of light-responsive poly(N-isopropylacrylamide) incorporating rGO (PNIPAm/rGO) was achieved by the chemical reduction of GO dispersed in the hydrogel matrix. Due to the enhanced photothermal efficiency of the rGO, the prepared PNIPAm/rGO underwent large volume reductions in response to irradiation by visible light of modest intensity. With respect to potential applications, bilayer-type photo-actuators comprising a PNIPAm/rGO active layer and poly(acrylamide) passive layer were fabricated; these achieved a full bending motion upon visible-light exposure. Adjusting the swelling ratio of each layer in the initial state yielded bidirectional photo-actuators that showed the active motion of turning inside out. Furthermore, we demonstrated that the fabricated actuation system would exhibit controlled bending motion in response to solar radiation. PMID:26865239

  12. Photovoltaic devices comprising cadmium stannate transparent conducting films and method for making

    DOEpatents

    Wu, Xuanzhi; Coutts, Timothy J.; Sheldon, Peter; Rose, Douglas H.

    1999-01-01

    A photovoltaic device having a substrate, a layer of Cd.sub.2 SnO.sub.4 disposed on said substrate as a front contact, a thin film comprising two or more layers of semiconductor materials disposed on said layer of Cd.sub.2 SnO.sub.4, and an electrically conductive film disposed on said thin film of semiconductor materials to form a rear electrical contact to said thin film. The device is formed by RF sputter coating a Cd.sub.2 SnO.sub.4 layer onto a substrate, depositing a thin film of semiconductor materials onto the layer of Cd.sub.2 SnO.sub.4, and depositing an electrically conductive film onto the thin film of semiconductor materials.

  13. Photovoltaic devices comprising cadmium stannate transparent conducting films and method for making

    DOEpatents

    Wu, X.; Coutts, T.J.; Sheldon, P.; Rose, D.H.

    1999-07-13

    A photovoltaic device is disclosed having a substrate, a layer of Cd[sub 2]SnO[sub 4] disposed on said substrate as a front contact, a thin film comprising two or more layers of semiconductor materials disposed on said layer of Cd[sub 2]SnO[sub 4], and an electrically conductive film disposed on said thin film of semiconductor materials to form a rear electrical contact to said thin film. The device is formed by RF sputter coating a Cd[sub 2]SnO[sub 4] layer onto a substrate, depositing a thin film of semiconductor materials onto the layer of Cd[sub 2]SnO[sub 4], and depositing an electrically conductive film onto the thin film of semiconductor materials. 10 figs.

  14. Contact Radius and the Insulator-Metal Transition in Films Comprised of Touching Semiconductor Nanocrystals.

    PubMed

    Lanigan, Deanna; Thimsen, Elijah

    2016-07-26

    Nanocrystal assemblies are being explored for a number of optoelectronic applications such as transparent conductors, photovoltaic solar cells, and electrochromic windows. Majority carrier transport is important for these applications, yet it remains relatively poorly understood in films comprised of touching nanocrystals. Specifically, the underlying structural parameters expected to determine the transport mechanism have not been fully elucidated. In this report, we demonstrate experimentally that the contact radius, between touching heavily doped ZnO nanocrystals, controls the electron transport mechanism. Spherical nanocrystals are considered, which are connected by a circular area. The radius of this circular area is the contact radius. For nanocrystals that have local majority carrier concentration above the Mott transition, there is a critical contact radius. If the contact radius between nanocrystals is less than the critical value, then the transport mechanism is variable range hopping. If the contact radius is greater than the critical value, the films display behavior consistent with metallic electron transport. PMID:27398597

  15. Mobile encapsulated bodies comprising fat necrosis and fibrous tissue in the abdominal cavity of cows.

    PubMed

    Herzog, K; Burgdorf, W; Hewicker-Trautwein, M

    2010-11-01

    The microscopical features of 18 samples of fat necrosis and/or fibrous tissue removed from the abdominal cavity during laparotomy from 15 cows were studied. The nodular, ivory-coloured mobile structures were free-floating in the abdominal cavity, were not attached to any abdominal tissues or organs, and were completely surrounded by a fibrous capsule. Abdominal fat necrosis (bovine lipomatosis) was not observed in any animal. The structures comprised either necrotic fat, fibrous tissue or varying proportions of both. Focal calcification and mild inflammatory cell infiltration and accumulations of haemosiderin were also present. Microscopically, the lesions resembled encapsulated fat necrosis occurring in human subcutaneous tissue. The mechanisms of development of these mobile encapsulated bodies in cows is unknown and it is not clear how, in the absence of a blood supply, there can be inflammatory cell infiltration, calcification and proliferation of fibroblasts.

  16. Precise percolation thresholds of two-dimensional random systems comprising overlapping ellipses

    NASA Astrophysics Data System (ADS)

    Li, Jiantong; Östling, Mikael

    2016-11-01

    This work explores the percolation thresholds of continuum systems consisting of randomly-oriented overlapping ellipses. High-precision percolation thresholds for various homogeneous ellipse systems with different aspect ratios are obtained from extensive Monte Carlo simulations based on the incorporation of Vieillard-Baron's contact function of two identical ellipses with our efficient algorithm for continuum percolation. In addition, we generalize Vieillard-Baron's contact function from identical ellipses to unequal ellipses, and extend the Monte Carlo algorithm to heterogeneous ellipse systems where the ellipses have different dimensions and/or aspect ratios. Based on the concept of modified excluded area, a general law is verified for precise prediction of percolation threshold for many heterogeneous ellipse systems. In particular, the study of heterogeneous ellipse systems gains insight into the apparent percolation threshold symmetry observed earlier in systems comprising unequal circles (Consiglio et al., 2004).

  17. Dynamical Casimir–Polder force on a partially dressed atom in a cavity comprising a dielectric

    SciTech Connect

    Yang, H.; Zheng, T.Y. Zhang, X.; Shao, X.Q.; Pan, S.M.

    2014-05-15

    We put a two-level atom into a cavity comprising a dielectric with output coupling. An analytical expression of the dynamical Casimir–Polder force in such a system is obtained when the system starts from a partially dressed state. And the effects of several relevant parameters of the system on the time-dependent force are also discussed. -- Highlights: •We get the dynamical CP force on a partially dressed atom in a dielectric cavity. •The force in this cavity is larger than that in infinite dielectric space. •The force is not symmetric with respect to the center of the cavity. •The oscillating time of the force increases with the cavity size.

  18. Melt-castable energetic compounds comprising oxadiazoles and methods of production thereof

    SciTech Connect

    Pagoria, Philip F; Zhang, Mao X

    2013-11-12

    In one embodiment, a melt-castable energetic material comprises at least one of: 3,5-bis(4-nitro-1,2,5-oxadiazol-3-yl)-1,2,4-oxadiazole (DNFO), and 3-(4-amino-1,2,5-oxadiazol-3-yl)-5-(4-nitro-1,2,5-oxadiazol-3-yl)-1,2- ,4-oxadiazole (ANFO). In another embodiment, a method for forming a melt-castable energetic material includes reacting 3,5-bis(4-amino-1,2,5-oxadiazol-3-yl)-1,2,4-oxadiazole (DAFO) with oxygen or an oxygen-containing compound to form a mixture of at least: DNFO, and ANFO.

  19. Yb:FAP and related materials, laser gain medium comprising same, and laser systems using same

    DOEpatents

    Krupke, W.F.; Payne, S.A.; Chase, L.L.; Smith, L.K.

    1994-01-18

    An ytterbium doped laser material remarkably superior to all others, including Yb:YAG, comprises ytterbium doped apatite (Yb:Ca[sub 5](PO[sub 4])[sub 3]F) or Yb:FAP, or ytterbium doped crystals that are structurally related to FAP. The new laser material is used in laser systems pumped by diode pump sources having an output near 0.905 microns or 0.98 microns, such as InGaAs and AlInGaAs, or other narrowband pump sources near 0.905 microns or 0.98 microns. The laser systems are operated in either the conventional or ground state depletion mode. 9 figures.

  20. Highly bendable bilayer-type photo-actuators comprising of reduced graphene oxide dispersed in hydrogels

    NASA Astrophysics Data System (ADS)

    Kim, Dowan; Lee, Heon Sang; Yoon, Jinhwan

    2016-02-01

    To avoid the problem of reduced graphene oxide (rGO) restacking in aqueous solution, the preparation of light-responsive poly(N-isopropylacrylamide) incorporating rGO (PNIPAm/rGO) was achieved by the chemical reduction of GO dispersed in the hydrogel matrix. Due to the enhanced photothermal efficiency of the rGO, the prepared PNIPAm/rGO underwent large volume reductions in response to irradiation by visible light of modest intensity. With respect to potential applications, bilayer-type photo-actuators comprising a PNIPAm/rGO active layer and poly(acrylamide) passive layer were fabricated; these achieved a full bending motion upon visible-light exposure. Adjusting the swelling ratio of each layer in the initial state yielded bidirectional photo-actuators that showed the active motion of turning inside out. Furthermore, we demonstrated that the fabricated actuation system would exhibit controlled bending motion in response to solar radiation.