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Sample records for acid spin probes

  1. Electron spin echo modulation studies of doxylstearic acid spin probes in frozen vesicles: Interaction of the spin probe with D sub 2 O and effects of cholesterol addition

    SciTech Connect

    Hiff, T.; Kevan, L. )

    1989-02-23

    Electron spin echo studies have been carried out for a series of x-doxylstearic acid (x = 5, 7, 10, 12 and 16) spin probes in frozen deuteriated aqueous solutions of phospholipid vesicles and cationic dioctadecyldimethylammonium chloride (DODAC) vesicles. Modulation effects due to interactions of the nitroxide group of the spin probes with D{sub 2}O give information about the conformations of the probes and the degree of hydration of the surfactant headgroups as well as about the degree of packing of the alkyl chain. We show that DODAC headgroups are more hydrated than choline headgroups and that the doxylstearic acid probes show a larger tendency for bending in DODAC vesicles than in phospholipid vesicles. Upon addition of cholesterol into phospholipid vesicles, the headgroups are separated and their degree of hydration increases.

  2. Intra-albumin migration of bound fatty acid probed by spin label ESR

    SciTech Connect

    Gurachevsky, Andrey . E-mail: a.gurachevsky@medinnovation.de; Shimanovitch, Ekaterina; Gurachevskaya, Tatjana; Muravsky, Vladimir

    2007-09-07

    Conventional ESR spectra of 16-doxyl-stearic acid bound to bovine and human serum albumin were recorded at different temperatures in order to investigate the status of spin-labeled fatty acid in the interior of the protein globule. A computer spectrum simulation of measured spectra, performed by non-linear least-squares fits, clearly showed two components corresponding to strongly and weakly immobilized fatty acid molecules. The two-component model was verified on spectra measured at different pH. Thermodynamic parameters of the spin probe exchange between two spin probe states were analyzed. It was concluded that at physiological conditions, fatty acid molecules permanently migrate in the globule interior between the specific binding sites and a space among albumin domains.

  3. Fatty acid binding sites of human and bovine albumins: Differences observed by spin probe ESR

    NASA Astrophysics Data System (ADS)

    Muravsky, Vladimir; Gurachevskaya, Tatjana; Berezenko, Stephen; Schnurr, Kerstin; Gurachevsky, Andrey

    2009-09-01

    Bovine and human serum albumins and recombinant human albumin, all non-covalently complexed with 5- and 16-doxyl stearic acids, were investigated by ESR spectroscopy in solution over a range of pH values (5.5-8.0) and temperatures (25-50 °C), with respect to the allocation and mobility of fatty acid (FA) molecules bound to the proteins and conformation of the binding sites. In all proteins bound FA undergo a permanent intra-albumin migration between the binding sites and inter-domain residence. Nature identity of the recombinant human albumin to its serum-derived analog was observed. However, the binding sites of bovine albumin appeared shorter in length and wider in diameter than those of human albumin. Presumably, less tightly folded domains in bovine albumin allow better penetration of water molecules in the interior of the globule that resulted in higher activation energy of FA dissociation from the binding site. Thus, the sensitive technique based on ESR non-covalent spin labeling allowed quantitative analysis and reliable comparison of the fine features of binding proteins.

  4. Vanadium-fulvic acid chemistry: conformational and binding studies by electron spin probe techniques

    NASA Astrophysics Data System (ADS)

    Templeton, G. Daniel, III; Chasteen, N. Dennis

    1980-05-01

    Two fractions of soil fulvic acid (FA) were separated by gel filtration chromatography. An observed increase in volume of the heavier fraction (FA I) with increasing pH was attributed to aggregation, intramolecular negative charge repulsions and the rupture of hydrogen bonds, which control molecular conformation. Optical absorption properties and elemental analyses of both fractions were determined. The stability constants and stoichiometries of FA complexes with vanadyl, VO 2+, at pH 5.0 and ionic strength of 0.04 M were measured by electron paramagnetic resonance (EPR) spectroscopy. EPR spectra of model VO 2+ complexes with phthalic and salicylic acids, which are the probable functional groups present in FA, are identical to those of the VO 2+-FA complexes. Aggregation of FA I occurs in the presence of VO 2+ to form a complex that can be approximated as '(VO) 2(FA I) 6'. The average site distance between vanadyl ions in this complex is shown to be greater than 1.2 nm. EPR parameters for FA I suggest binding by carboxylate groups. These parameters are compared with those of other vanadyl complexes with fulvic and humic acids reported by others. Reduction of VO 3- to VO 2+ by these materials is discussed.

  5. Spin of Planetary Probes in Atmospheric Flight

    NASA Astrophysics Data System (ADS)

    Lorenz, R. D.

    Probes that enter planetary atmospheres are often spun during entry or descent for a variety of reasons. Their spin rate histories are influenced by often subtle effects. The spin requirements, control methods and flight experience from planetary and earth entry missions are reviewed. An interaction of the probe aerodynamic wake with a drogue parachute, observed in Gemini wind tunnel tests, is discussed in connection with the anomalous spin behaviour of the Huygens probe.

  6. Probing absolute spin polarization at the nanoscale.

    PubMed

    Eltschka, Matthias; Jäck, Berthold; Assig, Maximilian; Kondrashov, Oleg V; Skvortsov, Mikhail A; Etzkorn, Markus; Ast, Christian R; Kern, Klaus

    2014-12-10

    Probing absolute values of spin polarization at the nanoscale offers insight into the fundamental mechanisms of spin-dependent transport. Employing the Zeeman splitting in superconducting tips (Meservey-Tedrow-Fulde effect), we introduce a novel spin-polarized scanning tunneling microscopy that combines the probing capability of the absolute values of spin polarization with precise control at the atomic scale. We utilize our novel approach to measure the locally resolved spin polarization of magnetic Co nanoislands on Cu(111). We find that the spin polarization is enhanced by 65% when increasing the width of the tunnel barrier by only 2.3 Å due to the different decay of the electron orbitals into vacuum.

  7. A quantum spin-probe molecular microscope

    PubMed Central

    Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L.C.L.

    2016-01-01

    Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy. PMID:27725630

  8. A quantum spin-probe molecular microscope

    NASA Astrophysics Data System (ADS)

    Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L. C. L.

    2016-10-01

    Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy.

  9. A quantum spin-probe molecular microscope.

    PubMed

    Perunicic, V S; Hill, C D; Hall, L T; Hollenberg, L C L

    2016-10-11

    Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy.

  10. Spin Polarized Electron Probes and Magnetic Nanostructures

    SciTech Connect

    D.L. Mills

    2003-10-15

    OAK B188 This report summarizes progress to date in our theoretical research program, for the period from July 1, 2002 to November 1, 2003. In addition, our research priorities for the coming year are set forth. The reporting period has been a most exciting and significant one. For the past several years, one of our principal thrust areas has been development of the theory of spin dynamics in magnetic nanostructures with emphasis on the use of spin polarized electrons as probes of short wavelength spin dynamics in such entities. Our program stimulated the first experiment which detected large wave vector spin waves in ultrathin films in 1999 through spin polarized electron loss spectroscopy (SPEELS); the publication which announced this discovery was a joint publication between a group in Halle (Germany) with our theory effort. The continued collaboration has led to the design and implementation of the new SPEELS spectrometer and we now have in hand the first detailed measurements of spin wave dispersion in an ultrathin film. A second such spectrometer is now operational in the laboratory of Prof. H. Hopster, at UC Irvine. We are thus entering a most exciting new era in the spectroscopy of spin excitations in magnetic nanostructures. During the reporting period, we have completed very important new analyses which predict key aspects of the spectra which will be uncovered by these new instruments, and the calculations continue to be developed and to expand our understanding. In addition, we have initiated a new series of theoretical studies directed toward spin dynamics of single magnetic adatoms on metal surfaces, with STM based studies of this area n mind. In the near future, these studies will continue, and we will expand our effort into new areas of spin dynamics in magnetic nanostructures.

  11. Acidic pH-induced membrane insertion of colicin A into E. coli natural lipids probed by site-directed spin labeling.

    PubMed

    Pulagam, Lakshmi Padmavathi; Steinhoff, Heinz-Jürgen

    2013-05-27

    Colicin A is a pore-forming toxin that forms a voltage-gated channel in the inner membrane of the target bacteria. The structures of the closed and open channel states of membrane-bound colicin A are not resolved. In the present site-directed spin-labeling study, the insertion-competent state of colicin A is provoked by an acidic pH jump prior to the insertion into liposomes prepared from Escherichia coli natural lipids. The membrane-bound colicin A is able to open a voltage-dependent channel as demonstrated by the efflux of tempophosphate spin label from the lumen of liposomes. The EPR spectra of spin-labeled colicin A variants in the membrane-bound closed channel state reveal a conformational equilibrium with resolved interhelical tertiary contacts. The spin label accessibility and polarity profiles suggest the amphipathic helices (H1-H7 and H10) to be located in the membrane close to the membrane-water interface and the hydrophobic hairpin (H8 and H9) to be immersed more deeply in the membrane.

  12. Spin-current probe for phase transition in an insulator

    SciTech Connect

    Qiu, Zhiyong; Li, Jia; Hou, Dazhi; Arenholz, Elke; N’Diaye, Alpha T.; Tan, Ali; Uchida, Ken-ichi; Sato, Koji; Okamoto, Satoshi; Tserkovnyak, Yaroslav; Qiu, Z. Q.; Saitoh, Eiji

    2016-08-30

    Spin fluctuation and transition have always been one of the central topics of magnetism and condensed matter science. Experimentally, the spin fluctuation is found transcribed onto scattering intensity in the neutron-scattering process, which is represented by dynamical magnetic susceptibility and maximized at phase transitions. Importantly, a neutron carries spin without electric charge, and therefore it can bring spin into a sample without being disturbed by electric energy. However, large facilities such as a nuclear reactor are necessary. Here we present that spin pumping, frequently used in nanoscale spintronic devices, provides a desktop microprobe for spin transition; spin current is a flux of spin without an electric charge and its transport reflects spin excitation. Additionally, we demonstrate detection of antiferromagnetic transition in ultra-thin CoO films via frequency-dependent spin-current transmission measurements, which provides a versatile probe for phase transition in an electric manner in minute devices.

  13. Spin-current probe for phase transition in an insulator

    NASA Astrophysics Data System (ADS)

    Qiu, Zhiyong; Li, Jia; Hou, Dazhi; Arenholz, Elke; N'diaye, Alpha T.; Tan, Ali; Uchida, Ken-Ichi; Sato, Koji; Okamoto, Satoshi; Tserkovnyak, Yaroslav; Qiu, Z. Q.; Saitoh, Eiji

    2016-08-01

    Spin fluctuation and transition have always been one of the central topics of magnetism and condensed matter science. Experimentally, the spin fluctuation is found transcribed onto scattering intensity in the neutron-scattering process, which is represented by dynamical magnetic susceptibility and maximized at phase transitions. Importantly, a neutron carries spin without electric charge, and therefore it can bring spin into a sample without being disturbed by electric energy. However, large facilities such as a nuclear reactor are necessary. Here we show that spin pumping, frequently used in nanoscale spintronic devices, provides a desktop microprobe for spin transition; spin current is a flux of spin without an electric charge and its transport reflects spin excitation. We demonstrate detection of antiferromagnetic transition in ultra-thin CoO films via frequency-dependent spin-current transmission measurements, which provides a versatile probe for phase transition in an electric manner in minute devices.

  14. Spin-current probe for phase transition in an insulator.

    PubMed

    Qiu, Zhiyong; Li, Jia; Hou, Dazhi; Arenholz, Elke; N'Diaye, Alpha T; Tan, Ali; Uchida, Ken-Ichi; Sato, Koji; Okamoto, Satoshi; Tserkovnyak, Yaroslav; Qiu, Z Q; Saitoh, Eiji

    2016-08-30

    Spin fluctuation and transition have always been one of the central topics of magnetism and condensed matter science. Experimentally, the spin fluctuation is found transcribed onto scattering intensity in the neutron-scattering process, which is represented by dynamical magnetic susceptibility and maximized at phase transitions. Importantly, a neutron carries spin without electric charge, and therefore it can bring spin into a sample without being disturbed by electric energy. However, large facilities such as a nuclear reactor are necessary. Here we show that spin pumping, frequently used in nanoscale spintronic devices, provides a desktop microprobe for spin transition; spin current is a flux of spin without an electric charge and its transport reflects spin excitation. We demonstrate detection of antiferromagnetic transition in ultra-thin CoO films via frequency-dependent spin-current transmission measurements, which provides a versatile probe for phase transition in an electric manner in minute devices.

  15. Spin-current probe for phase transition in an insulator

    PubMed Central

    Qiu, Zhiyong; Li, Jia; Hou, Dazhi; Arenholz, Elke; N'Diaye, Alpha T.; Tan, Ali; Uchida, Ken-ichi; Sato, Koji; Okamoto, Satoshi; Tserkovnyak, Yaroslav; Qiu, Z. Q.; Saitoh, Eiji

    2016-01-01

    Spin fluctuation and transition have always been one of the central topics of magnetism and condensed matter science. Experimentally, the spin fluctuation is found transcribed onto scattering intensity in the neutron-scattering process, which is represented by dynamical magnetic susceptibility and maximized at phase transitions. Importantly, a neutron carries spin without electric charge, and therefore it can bring spin into a sample without being disturbed by electric energy. However, large facilities such as a nuclear reactor are necessary. Here we show that spin pumping, frequently used in nanoscale spintronic devices, provides a desktop microprobe for spin transition; spin current is a flux of spin without an electric charge and its transport reflects spin excitation. We demonstrate detection of antiferromagnetic transition in ultra-thin CoO films via frequency-dependent spin-current transmission measurements, which provides a versatile probe for phase transition in an electric manner in minute devices. PMID:27573443

  16. Spin-current probe for phase transition in an insulator

    DOE PAGES

    Qiu, Zhiyong; Li, Jia; Hou, Dazhi; ...

    2016-08-30

    Spin fluctuation and transition have always been one of the central topics of magnetism and condensed matter science. Experimentally, the spin fluctuation is found transcribed onto scattering intensity in the neutron-scattering process, which is represented by dynamical magnetic susceptibility and maximized at phase transitions. Importantly, a neutron carries spin without electric charge, and therefore it can bring spin into a sample without being disturbed by electric energy. However, large facilities such as a nuclear reactor are necessary. Here we present that spin pumping, frequently used in nanoscale spintronic devices, provides a desktop microprobe for spin transition; spin current is amore » flux of spin without an electric charge and its transport reflects spin excitation. Additionally, we demonstrate detection of antiferromagnetic transition in ultra-thin CoO films via frequency-dependent spin-current transmission measurements, which provides a versatile probe for phase transition in an electric manner in minute devices.« less

  17. Probing spin flip scattering in ballistic nanosystems

    SciTech Connect

    Zeng, Z. M.; Feng, J. F.; Wang, Y.; Han, Prof. X. F.; Zhan, W. S.; Zhang, Xiaoguang; Zhang, Z.

    2006-01-01

    Because spin-flip scattering length is longer than the electron mean-free-path in a metal, past studies of spin-flip scattering are limited to the diffusive regime. Spin accumulation in the nanometer sized spacer layer of a magnetic double barrier tunnel junction allows the study of spin flip scattering near ballistic limit. We extract the spin-flip conductance $G_s$ of the spacer layer from magnetoresistance measurements. A linear temperature dependence of $G_s$ is found. The bias voltage dependence shows a quantum well resonance which explains the sharp reduction of the magnetoresistance. At 4.2K $G_s$ yields the mean-free-path (70nm) and the spin-flip length ($1.0$-$2.6\\mu$m).

  18. Perforated cenosphere-supported pH-sensitive spin probes

    SciTech Connect

    Fomenko, E.V.; Bobko, A.A.; Salanov, A.N.; Kirilyuk, I.A.; Grigor'ev, I.A.; Khramtsov, V.V.; Anshits, A.G.

    2008-03-15

    Porous supports with an accessible internal volume and a shell providing the diffusive migration of pH-sensitive spin probes were obtained for the first time from hollow aluminosilicate cenospheres isolated from the coal fly ash. Using the methods of scanning electron microscopy and electron spin resonance, the morphology of different porous cenosphere modifications and its influence on the diffusion of spin probes from the internal volume were studied. When supporting aqueous solutions of a radical, the characteristic diffusion time for the mesoporous structure of the support is longer by a factor of 3-5 than that for the macroporous structure. Ferrospinel in a content of 6 wt.% do not virtually affect the diffusion rate of spin probes. A constant rate of radical migration of similar to 1 {mu} mol min{sup -1}, determined by radical solubility in water, is achieved when a radical in the solid aggregate state is supported on the magnetic cenospheres.

  19. Functional nucleic acid probes and uses thereof

    DOEpatents

    Nilsen-Hamilton, Marit

    2006-10-03

    The present invention provides functional nucleic acid probes, and methods of using functional nucleic acid probes, for binding a target to carry out a desired function. The probes have at least one functional nucleic acid, at least one regulating nucleic acid, and at least one attenuator. The functional nucleic acid is maintained in an inactive state by the attenuator and activated by the regulating nucleic acid only in the presence of a regulating nucleic acid target. In its activated state the functional nucleic acid can bind to its target to carry out a desired function, such as generating a signal, cleaving a nucleic acid, or catalyzing a reaction.

  20. Microscopic understanding of spin current probed by shot noise

    NASA Astrophysics Data System (ADS)

    Arakawa, Tomonori

    much longer than the spin relaxation length. In other words, the spin currents in such a semiconducting material can be strongly out of equilibrium. In this invited talk, I will present a series of experimental work on the spin current in a (Ga,Mn)As/tunnel barrier/n-GaAs based lateral spin valve device, mainly probed by the current noise measurement. Finally I hope I will mention about our future plan to cool down the effective temperature of the spin current by using superconductivity. This work was partially supported by JSPS KAKENHI Grant Numbers 26220711, 25887037, 25103003, and 15K17680.

  1. Spin-dependent recombination probed through the dielectric polarizability

    PubMed Central

    Bayliss, Sam L.; Greenham, Neil C.; Friend, Richard H.; Bouchiat, Hélène; Chepelianskii, Alexei D

    2015-01-01

    Despite residing in an energetically and structurally disordered landscape, the spin degree of freedom remains a robust quantity in organic semiconductor materials due to the weak coupling of spin and orbital states. This enforces spin-selectivity in recombination processes which plays a crucial role in optoelectronic devices, for example, in the spin-dependent recombination of weakly bound electron-hole pairs, or charge-transfer states, which form in a photovoltaic blend. Here, we implement a detection scheme to probe the spin-selective recombination of these states through changes in their dielectric polarizability under magnetic resonance. Using this technique, we access a regime in which the usual mixing of spin-singlet and spin-triplet states due to hyperfine fields is suppressed by microwave driving. We present a quantitative model for this behaviour which allows us to estimate the spin-dependent recombination rate, and draw parallels with the Majorana–Brossel resonances observed in atomic physics experiments. PMID:26439933

  2. Nucleic acid probes in diagnostic medicine

    NASA Technical Reports Server (NTRS)

    Oberry, Phillip A.

    1991-01-01

    The need for improved diagnostic procedures is outlined and variations in probe technology are briefly reviewed. A discussion of the application of probe technology to the diagnosis of disease in animals and humans is presented. A comparison of probe versus nonprobe diagnostics and isotopic versus nonisotopic probes is made and the current state of sequence amplification is described. The current market status of nucleic acid probes is reviewed with respect to their diagnostic application in human and veterinary medicine. Representative product examples are described and information on probes being developed that offer promise as future products is discussed.

  3. Spin-probe ESR and molecular modeling studies on calcium carbonate dispersions in overbased detergent additives.

    PubMed

    Montanari, Luciano; Frigerio, Francesco

    2010-08-15

    Oil-soluble calcium carbonate colloids are used as detergent additives in lubricating oils. They are colloidal dispersions of calcium carbonate particles stabilized by different surfactants; in this study alkyl-aryl-sulfonates and sulfurized alkyl-phenates, widely used in the synthesis of these additives, are considered. The physical properties of surfactant layers surrounding the surfaces of calcium carbonate particles were analyzed by using some nitroxide spin-probes (stable free radicals) and observing the corresponding ESR spectra. The spin-probe molecules contain polar groups which tend to tether them to the carbonate particle polar surface. They can reach these surfaces only if the surfactant layers are not very compact, hence the relative amounts of spin-probe molecules accessing carbonate surfaces are an index of the compactness of surfactant core. ESR signals of spin-probe molecules dissolved in oil or "locked" near the carbonate surfaces are different because of the different molecular mobility. Through deconvolution of the ESR spectra, the fraction of spin-probes penetrating surfactant shells have been calculated, and differences were observed according to the surfactant molecular structures. Moreover, by using specially labeled spin-probes based on stearic acids, functionalized at different separations from the carboxylic acid group, it was possible to interrogate the molecular physical behavior of surfactant shells at different distances from carbonate surfaces. Molecular modeling was applied to generate some three-dimensional micellar models of the colloidal stabilizations of the stabilized carbonate particles with different molecular structures of the surfactant. The diffusion of spin-probe molecules into the surfactant shells were studied by applying a starting force to push the molecules towards the carbonate surfaces and then observing the ensuing behavior. The simulations are in accordance with the ESR data and show that the geometrical

  4. Nanometer-scale probing of spin waves using single electron spins

    NASA Astrophysics Data System (ADS)

    van der Sar, Toeno; Casola, Francesco; Walsworth, Ronald; Yacoby, Amir

    2015-05-01

    We have developed a new approach to exploring magnetic excitations in correlated-electron systems, based on single electronic spins in atom-like defects diamond known as nitrogen-vacancy (NV) color centers. We demonstrate the power of this approach by detecting spin-wave excitations in a ferromagnetic microdisc with nanoscale spatial sensitivity over a broad range of frequencies and magnetic fields. We show how spin-wave resonances can be exploited for on-chip amplification of microwave magnetic fields, allowing strongly increased spin manipulation rates and single-spin magnetometry with enhanced sensitivity. Finally, we show the possibility to detect the magnetic spin noise produced by a thin (~ 30 nm) layer of a patterned ferromagnet. For the interpretation of our results, we develop a general framework describing single-spin stray field detection in terms of a filter function sensitive mostly to spin fluctuations with wavevector ~ 1 / d , where d is the NV-ferromagnet distance. Our results pave the way towards quantitative and non-perturbative detection of spectral properties in nanomagnets, establishing NV center magnetometry as an emergent probe of collective spin dynamics in condensed matter.

  5. ESR/spin probe study of ice cream.

    PubMed

    Gillies, Duncan G; Greenley, Katherine R; Sutcliffe, Leslie H

    2006-07-12

    Spin probes based on the 1,1,3,3-tetramethylisoindolin-2-yl structure have been used, in conjunction with electron spin resonance spectroscopy (ESR), to study the physical changes occurring in ice cream during freezing and melting. The ESR measurements allowed the rotational correlation times, tau(B), of the spin probes to be determined. Two probes were used together in a given sample of ice cream, namely, 1,1,3,3-tetramethylisoindolin-2-yl (TMIO), which samples the fat phase, and the sodium salt of 1,1,3,3-tetramethylisoindolin-2-yloxyl-5-sulfonate (NaTMIOS), which samples the aqueous phase. Data from the TMIO probe showed that when ice cream is cooled, the fat phase is a mixture of solid and liquid fat until a temperature of approximately -60 degrees C is reached. The water-soluble probe NaTMIOS showed that the aqueous phase changes completely from liquid to solid within 1 degrees C of -18 degrees C. On cooling further to -24.7 degrees C and then allowing it to warm to +25.0 degrees C, the rotational correlation times of the NaTMIOS were slow to recover to their previous values. For the lipid phase, tau(B)(298) was found to be 65.7 +/- 2.0 ps and the corresponding activation enthalpy, DeltaH, was 32.5 +/- 0.9 kJ mol(-)(1): These values are typical of those expected to be found in the type of fat used to make ice cream. The water phase gave corresponding values of 32.2 +/- 0.5 ps and 24.5 +/- 0.4 kJ mol(-)(1) values, which are those expected for a sucrose concentration of 24%.

  6. Nanometre-scale probing of spin waves using single-electron spins

    PubMed Central

    van der Sar, Toeno; Casola, Francesco; Walsworth, Ronald; Yacoby, Amir

    2015-01-01

    Pushing the frontiers of condensed-matter magnetism requires the development of tools that provide real-space, few-nanometre-scale probing of correlated-electron magnetic excitations under ambient conditions. Here we present a practical approach to meet this challenge, using magnetometry based on single nitrogen-vacancy centres in diamond. We focus on spin-wave excitations in a ferromagnetic microdisc, and demonstrate local, quantitative and phase-sensitive detection of the spin-wave magnetic field at ∼50 nm from the disc. We map the magnetic-field dependence of spin-wave excitations by detecting the associated local reduction in the disc's longitudinal magnetization. In addition, we characterize the spin–noise spectrum by nitrogen-vacancy spin relaxometry, finding excellent agreement with a general analytical description of the stray fields produced by spin–spin correlations in a 2D magnetic system. These complementary measurement modalities pave the way towards imaging the local excitations of systems such as ferromagnets and antiferromagnets, skyrmions, atomically assembled quantum magnets, and spin ice. PMID:26249673

  7. A General Protocol for Temperature Calibration of MAS NMR Probes at Arbitrary Spinning Speeds

    PubMed Central

    Guan, Xudong; Stark, Ruth E.

    2010-01-01

    A protocol using 207Pb NMR of solid lead nitrate was developed to determine the temperature of magic-angle spinning (MAS) NMR probes over a range of nominal set temperatures and spinning speeds. Using BioMAS and fastMAS probes with typical sample spinning rates of 8 and 35 kHz, respectively, empirical equations were devised to predict the respective sample temperatures. These procedures provide a straightforward recipe for temperature calibration of any MAS probe. PMID:21036557

  8. Fluorescent hybridization probes for nucleic acid detection.

    PubMed

    Guo, Jia; Ju, Jingyue; Turro, Nicholas J

    2012-04-01

    Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.

  9. Noise as a Probe of Ising Spin Glass Transitions

    NASA Astrophysics Data System (ADS)

    Chen, Zhi; Yu, Clare

    2009-03-01

    Noise is ubiquitous and and is often viewed as a nuisance. However, we propose that noise can be used as a probe of the fluctuations of microscopic entities, especially in the vicinity of a phase transition. In recent work we have used simulations to show that the noise increases in the vicinity of phase transitions of ordered systems. We have recently turned our attention to noise near the phase transitions of disordered systems. In particular, we are studying the noise near Ising spin glass transitions using Monte Carlo simulations. We monitor the system as a function of temperature. At each temperature, we obtain the time series of quantities characterizing the properties of the system, i.e., the energy and magnetization. We look at different quantities, such as the noise power spectrum and the second spectrum of the noise, to analyze the fluctuations.

  10. Sealed magic angle spinning nuclear magnetic resonance probe and process for spectroscopy of hazardous samples

    SciTech Connect

    Cho, Herman M.; Washton, Nancy M.; Mueller, Karl T.; Sears, Jr., Jesse A.; Townsend, Mark R.; Ewing, James R.

    2016-06-14

    A magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) probe is described that includes double containment enclosures configured to seal and contain hazardous samples for analysis. The probe is of a modular design that ensures containment of hazardous samples during sample analysis while preserving spin speeds for superior NMR performance and convenience of operation.

  11. Spin probe dynamics of n-hexadecane in confined geometry

    NASA Astrophysics Data System (ADS)

    Lukešová, Miroslava; Švajdlenková, Helena; Sippel, Pit; Macová, Eva; Berek, Dušan; Loidl, Alois; Bartoš, Josef

    2015-02-01

    A combined study of the rotational dynamics of the stable free radical 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) and the phase behavior of n-hexadecane (n-HXD) in the bulk and the confined states in a series of silica gels (SG) by means of ESR and DSC is presented. A slow to fast motion transition of the spin probe TEMPO in the bulk n-HXD occurs at T50 G,bulk ≪ Tm,bulk, i.e., well below the melting temperature due to its trapping and localized mobility in the interlamellar gap of the crystallites [J. Bartoš, H. Švajdlenková, M. Zaleski, M. Edelmann, M. Lukešová, Physica B 430, 99 (2013)]. On the other hand, the dynamics of the TEMPO in the confined systems is strongly slowing down with T50 G (Dpore) >Tm(Dpore) and slightly increases with the pore size Dpore = 60, 100 and 300 Å of the SG's. At the same time, both the corresponding melting temperature, Tm (Dpore), and melting enthalpy, ΔHm (Dpore), decrease with Dpore together with the mutual anti-correlation between T50 G and Tm as a function of the inverse of pore diameter, 1/Dpore. Moreover, the dynamic heterogeneity of the TEMPO in the confined state below T50 G (Dpore) is closely related to the phase transformation. The strong slowing down of the spin probe motion likely results from its preferential localization at the interface layer of the matrix pore due to specific interaction of TEMPO molecules with the polar silanol groups of the SG matrix. This is supported by special study on a series of the variously filled n-HXD/SG systems, other similar experimental findings as well as by theoretical spectral argument.

  12. Probing Spatial Spin Correlations of Ultracold Gases by Quantum Noise Spectroscopy

    SciTech Connect

    Bruun, G. M.; Andersen, Brian M.; Demler, Eugene; Soerensen, Anders S.

    2009-01-23

    Spin noise spectroscopy with a single laser beam is demonstrated theoretically to provide a direct probe of the spatial correlations of cold fermionic gases. We show how the generic many-body phenomena of antibunching, pairing, antiferromagnetic, and algebraic spin liquid correlations can be revealed by measuring the spin noise as a function of laser width, temperature, and frequency.

  13. Peptide nucleic acid probes with charged photocleavable mass markers

    PubMed Central

    Ball, Rachel J; Green, Philip S; Gale, Nittaya; Langley, G John

    2010-01-01

    Halogen-labelled peptide organic acid (HPOA) monomers have been synthesised and incorporated into sequence-specific peptide nucleic acid (PNA) probes. Three different types of probe have been prepared; the unmodified PNA probe, the PNA probe with a mass marker, and the PNA probe with photocleavable mass marker. All three types of probe have been used in model studies to develop a mass spectrometry-based hybridisation assay for detection of point mutations in DNA. PMID:21687524

  14. Continuously tunable nucleic acid hybridization probes.

    PubMed

    Wu, Lucia R; Wang, Juexiao Sherry; Fang, John Z; Evans, Emily R; Pinto, Alessandro; Pekker, Irena; Boykin, Richard; Ngouenet, Celine; Webster, Philippa J; Beechem, Joseph; Zhang, David Yu

    2015-12-01

    In silico-designed nucleic acid probes and primers often do not achieve favorable specificity and sensitivity tradeoffs on the first try, and iterative empirical sequence-based optimization is needed, particularly in multiplexed assays. We present a novel, on-the-fly method of tuning probe affinity and selectivity by adjusting the stoichiometry of auxiliary species, which allows for independent and decoupled adjustment of the hybridization yield for different probes in multiplexed assays. Using this method, we achieved near-continuous tuning of probe effective free energy. To demonstrate our approach, we enforced uniform capture efficiency of 31 DNA molecules (GC content, 0-100%), maximized the signal difference for 11 pairs of single-nucleotide variants and performed tunable hybrid capture of mRNA from total RNA. Using the Nanostring nCounter platform, we applied stoichiometric tuning to simultaneously adjust yields for a 24-plex assay, and we show multiplexed quantitation of RNA sequences and variants from formalin-fixed, paraffin-embedded samples.

  15. Direct Detection of Pure ac Spin Current by X-Ray Pump-Probe Measurements

    NASA Astrophysics Data System (ADS)

    Li, J.; Shelford, L. R.; Shafer, P.; Tan, A.; Deng, J. X.; Keatley, P. S.; Hwang, C.; Arenholz, E.; van der Laan, G.; Hicken, R. J.; Qiu, Z. Q.

    2016-08-01

    Despite recent progress in spin-current research, the detection of spin current has mostly remained indirect. By synchronizing a microwave waveform with synchrotron x-ray pulses, we use the ferromagnetic resonance of the Py (Ni81Fe19 ) layer in a Py /Cu /Cu75Mn25/Cu /Co multilayer to pump a pure ac spin current into the Cu75Mn25 and Co layers, and then directly probe the spin current within the Cu75Mn25 layer and the spin dynamics of the Co layer by x-ray magnetic circular dichroism. This element-resolved pump-probe measurement unambiguously identifies the ac spin current in the Cu75Mn25 layer.

  16. Probing for compositeness, discrete time effects and Markov enviromental influences using spin polarization precession.

    NASA Astrophysics Data System (ADS)

    Wolf, Carl

    By considering a spin-one particle precession in a magnetic field, we demonstrate that if very refined measurements were made of both the precession frequency and the amplitude of spin polarization, these measurements could be used to probe for compositeness of gauge bosons, discrete time effects and possible Markov environmental effects.

  17. Concentration dependence of nitroxyl spin probes in liposomal solution: electron spin resonance and overhauser-enhanced magnetic resonance studies.

    PubMed

    Meenakumari, V; Utsumi, Hideo; Jawahar, A; Franklin Benial, A Milton

    2016-12-21

    In this work, the detailed studies of electron spin resonance (ESR) and overhauser-enhanced magnetic resonance imaging (OMRI) were carried out for permeable nitroxyl spin probe, MC-PROXYL as a function of agent concentration in liposomal solution. In order to compare the impermeable nature of nitroxyl radical, the study was also carried out only at 2 mM concentration of carboxy-PROXYL. The ESR parameters were estimated using L-band and 300 MHz ESR spectrometers. The line width broadening was measured as a function of agent concentration in liposomal solution. The estimated rotational correlation time is proportional to the agent concentration, which indicates that less mobile nature of nitroxyl spin probe in liposomal solution. The partition parameter and permeability values indicate that the diffusion of nitroxyl spin probe distribution into the lipid phase is maximum at 2 mM concentration of MC-PROXYL. The dynamic nuclear polarization (DNP) parameters such as DNP factor, longitudinal relaxivity, saturation parameter, leakage factor and coupling factor were estimated for 2 mM MC-PROXYL in 400 mM liposomal dispersion. The spin lattice relaxation time was shortened in liposomal solution, which leads to the high relaxivity. Reduction in coupling factor is due to less interaction between the electron and nuclear spins, which causes the reduction in enhancement. The leakage factor increases with increasing agent concentration. The increase in DNP enhancement was significant up to 2 mM in liposomal solution. These results paves the way for choosing optimum agent concentration and OMRI scan parameters used in intra and extra membrane water by loading the liposome vesicles with a lipid permeable nitroxyl spin probes in OMRI experiments.

  18. Directly probing spin dynamics in insulating antiferromagnets using ultrashort terahertz pulses

    SciTech Connect

    Bowlan, Pamela Renee; Trugman, Stuart Alan; Wang, X.; Dai, Yaomin; Cheong, S.-W.; Bauer, Eric Dietzgen; Taylor, Antoinette Jane; Yarotski, Dmitry Anatolievitch; Prasankumar, Rohit Prativadi

    2016-11-22

    We investigate spin dynamics in the antiferromagnetic (AFM) multiferroic TbMnO3 using opticalpump, terahertz (THz)-probe spectroscopy. Photoexcitation results in a broadband THz transmission change, with an onset time of 25 ps at 6 K that becomes faster at higher temperatures. We attribute this time constant to spin-lattice thermalization. The excellent agreement between our measurements and previous ultrafast resonant x-ray diffraction measurements on the same material confirms that our THz pulse directly probes spin order. We suggest that this could be the case in general for insulating AFM materials, if the origin of the static absorption in the THz spectral range is magnetic.

  19. Probing variations of the Rashba spin-orbit coupling at the nanometre scale

    NASA Astrophysics Data System (ADS)

    Bindel, Jan Raphael; Pezzotta, Mike; Ulrich, Jascha; Liebmann, Marcus; Sherman, Eugene Ya.; Morgenstern, Markus

    2016-10-01

    As the Rashba effect is an electrically tunable spin-orbit interaction, it could form the basis for a multitude of applications, such as spin filters, spin transistors and quantum computing using Majorana states in nanowires. Moreover, this interaction can determine the spin dephasing and antilocalization phenomena in two dimensions. However, the real space pattern of the Rashba parameter, which critically influences spin transistors using the spin-helix state and the otherwise forbidden electron backscattering in topologically protected channels, is difficult to probe. Here, we map this pattern down to nanometre length scales by measuring the spin splitting of the lowest Landau level using scanning tunnelling spectroscopy. We reveal strong fluctuations correlated with the local electrostatic potential for an InSb inversion layer with a large Rashba coefficient (~1 eV Å). This type of Rashba field mapping enables a more comprehensive understanding of its fluctuations, which might be decisive towards robust semiconductor-based spintronic devices.

  20. Spin pumping through a topological insulator probed by x-ray detected ferromagnetic resonance

    NASA Astrophysics Data System (ADS)

    Figueroa, A. I.; Baker, A. A.; Collins-McIntyre, L. J.; Hesjedal, T.; van der Laan, G.

    2016-02-01

    In the field of spintronics, the generation of a pure spin current (without macroscopic charge flow) through spin pumping of a ferromagnetic (FM) layer opens up the perspective of a new generation of dissipation-less devices. Microwave driven ferromagnetic resonance (FMR) can generate a pure spin current that enters adjacent layers, allowing for both magnetization reversal (through spin-transfer torque) and to probe spin coherence in non-magnetic materials. However, standard FMR is unable to probe multilayer dynamics directly, since the measurement averages over the contributions from the whole system. The synchrotron radiation-based technique of x-ray detected FMR (XFMR) offers an elegant solution to this drawback, giving access to element-, site-, and layer-specific dynamical measurements in heterostructures. In this work, we show how XFMR has provided unique information to understand spin pumping and spin transfer torque effects through a topological insulator (TI) layer in a pseudo-spin valve heterostructure. We demonstrate that TIs function as efficient spin sinks, while also allowing a limited dynamic coupling between ferromagnetic layers. These results shed new light on the spin dynamics of this novel class of materials, and suggest future directions for the development of room temperature TI-based spintronics.

  1. SPIN POLARIZED PHOTOELECTRON SPECTROSCOPY AS A PROBE OF MAGNETIC SYSTEMS.

    SciTech Connect

    JOHNSON, P.D.; GUNTHERODT, G.

    2006-11-01

    Spin-polarized photoelectron spectroscopy has developed into a versatile tool for the study of surface and thin film magnetism. In this chapter, we examine the methodology of the technique and its recent application to a number of different problems. We first examine the photoemission process itself followed by a detailed review of spin-polarization measurement techniques and the related experimental requirements. We review studies of spin polarized surface states, interface states and quantum well states followed by studies of the technologically important oxide systems including half-metallic transition metal oxides, ferromagnet/oxide interfaces and the antiferromagnetic cuprates that exhibit high Tc Superconductivity. We also discuss the application of high-resolution photoemission with spin resolving capabilities to the study of spin dependent self energy effects.

  2. Electrical Probing of Inherent Spin Polarization in a Topological Insulator with Electrical Gating

    NASA Astrophysics Data System (ADS)

    Lee, Joon Sue; Richardella, Anthony; Samarth, Nitin

    2015-03-01

    The hallmark of a time-reversal symmetry protected three-dimensional topological insulator is the helically spin-textured surface state. Although electrical detection of spin polarization in topological insulators has been demonstrated very recently, there have not been any electrical measurements to demonstrate the entire mapping of the spin polarization throughout the surface state. We report the electrical probing of the spin-polarized surface state using a magnetic tunnel junction as a spin detector while the chemical potential of a topological insulator (Bi,Sb)2Te3 is tuned by back gating. Hysteretic spin signals were observed as the magnetization of the detector ferromagnet (permalloy) switches with in-plane magnetic field. Changing the direction of bias current through the topological insulator channel flips the direction of the spin polarization, resulting in the reverse of sign of the detected spin signals. We demonstrate the control of the Fermi energy, which has importance not only in further understanding of the spin-momentum locking in the surface state but also in possible electrical tuning of the spin polarization for potential spin-based devices. Supported by C-SPIN & DARPA/SRC.

  3. Kit for detecting nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    2001-01-01

    A kit is provided for detecting a target nucleic acid sequence in a sample, the kit comprising: a first hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the first hybridization probe including a first complexing agent for forming a binding pair with a second complexing agent; and a second hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the first hybridization probe does not selectively hybridize, the second hybridization probe including a detectable marker; a third hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the third hybridization probe including the same detectable marker as the second hybridization probe; and a fourth hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the third hybridization probe does not selectively hybridize, the fourth hybridization probe including the first complexing agent for forming a binding pair with the second complexing agent; wherein the first and second hybridization probes are capable of simultaneously hybridizing to the target sequence and the third and fourth hybridization probes are capable of simultaneously hybridizing to the target sequence, the detectable marker is not present on the first or fourth hybridization probes and the first, second, third, and fourth hybridization probes each include a competitive nucleic acid sequence which is sufficiently complementary to a third portion of the target sequence that the competitive sequences of the first, second, third, and fourth hybridization probes compete with each other to hybridize to the third portion of the

  4. Slow molecular motion of different spin probes in a model glycerol—water matrix studied by double modulation ESR

    NASA Astrophysics Data System (ADS)

    Valić, S.; Rakvin, B.; Veksli, Z.; Pečar, S.

    1992-11-01

    The slow molecular motion of several deuterated and undeuterated spin probes differing in size and shape, embedded in a model glycerol—water matrix, have been studied by double-modulated electron spin resonance (DMESR). The DMESR spectra as a function of temperature reveal two motional regions. From the experimental linewidths of both deuterated and undeuterated spin probes in the lower temperature region and simulated data based on the variation of T1 relaxation, two different dynamics of the -CH 3 groups attached to piperidine ring were resolved. Our results indicate that the onset of the whole spin probe motion depends on the type of probe and the matrix density.

  5. Detection of atomic spin labels in a lipid bilayer using a single-spin nanodiamond probe.

    PubMed

    Kaufmann, Stefan; Simpson, David A; Hall, Liam T; Perunicic, Viktor; Senn, Philipp; Steinert, Steffen; McGuinness, Liam P; Johnson, Brett C; Ohshima, Takeshi; Caruso, Frank; Wrachtrup, Jörg; Scholten, Robert E; Mulvaney, Paul; Hollenberg, Lloyd

    2013-07-02

    Magnetic field fluctuations arising from fundamental spins are ubiquitous in nanoscale biology, and are a rich source of information about the processes that generate them. However, the ability to detect the few spins involved without averaging over large ensembles has remained elusive. Here, we demonstrate the detection of gadolinium spin labels in an artificial cell membrane under ambient conditions using a single-spin nanodiamond sensor. Changes in the spin relaxation time of the sensor located in the lipid bilayer were optically detected and found to be sensitive to near-individual (4 ± 2) proximal gadolinium atomic labels. The detection of such small numbers of spins in a model biological setting, with projected detection times of 1 s [corresponding to a sensitivity of ∼5 Gd spins per Hz(1/2)], opens a pathway for in situ nanoscale detection of dynamical processes in biology.

  6. The Spin-Plane Double Probe Electric Field Instrument for MMS

    NASA Astrophysics Data System (ADS)

    Lindqvist, P.-A.; Olsson, G.; Torbert, R. B.; King, B.; Granoff, M.; Rau, D.; Needell, G.; Turco, S.; Dors, I.; Beckman, P.; Macri, J.; Frost, C.; Salwen, J.; Eriksson, A.; Åhlén, L.; Khotyaintsev, Y. V.; Porter, J.; Lappalainen, K.; Ergun, R. E.; Wermeer, W.; Tucker, S.

    2016-03-01

    The Spin-plane double probe instrument (SDP) is part of the FIELDS instrument suite of the Magnetospheric Multiscale mission (MMS). Together with the Axial double probe instrument (ADP) and the Electron Drift Instrument (EDI), SDP will measure the 3-D electric field with an accuracy of 0.5 mV/m over the frequency range from DC to 100 kHz. SDP consists of 4 biased spherical probes extended on 60 m long wire booms 90∘ apart in the spin plane, giving a 120 m baseline for each of the two spin-plane electric field components. The mechanical and electrical design of SDP is described, together with results from ground tests and calibration of the instrument.

  7. Electron spin resonance studies on deuterated nitroxyl spin probes used in Overhauser-enhanced magnetic resonance imaging.

    PubMed

    David Jebaraj, D; Utsumi, Hideo; Milton Franklin Benial, A

    2017-01-04

    The electron spin resonance studies were carried out for 2 mm concentration of (14) N-labeled and (15) N-labeled 3-carbamoyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl, 3-carboxy-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl, 3-methoxycarbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl and their deuterated nitroxyl radicals using X-band electron spin resonance spectrometer. The electron spin resonance line shape analysis was carried out. The electron spin resonance parameters such as linewidth, Lorentzian component, signal intensity ratio, rotational correlation time, hyperfine coupling constant and g-factor were estimated. The deuterated nitroxyl radicals have narrow linewidth and an increase in Lorentzian component, compared with undeuterated nitroxyl radicals. The dynamic nuclear polarization factor was observed for all nitroxyl radicals. Upon (2) H labeling, about 70% and 40% increase in dynamic nuclear polarization factor were observed for (14) N-labeled and (15) N-labeled nitroxyl radicals, respectively. The signal intensity ratio and g-value indicate the isotropic nature of the nitroxyl radicals in pure water. Therefore, the deuterated nitroxyl radicals are suitable spin probes for in vivo/in vitro electron spin resonance and Overhauser-enhanced magnetic resonance imaging modalities. Copyright © 2017 John Wiley & Sons, Ltd.

  8. The spin Hall effect as a probe of nonlinear spin fluctuations.

    PubMed

    Wei, D H; Niimi, Y; Gu, B; Ziman, T; Maekawa, S; Otani, Y

    2012-01-01

    The spin Hall effect and its inverse have key roles in spintronic devices as they allow conversion of charge currents to and from spin currents. The conversion efficiency strongly depends on material details, such as the electronic band structure and the nature of impurities. Here we show an anomaly in the inverse spin Hall effect in weak ferromagnetic NiPd alloys near their Curie temperatures with a shape independent of material details, such as Ni concentrations. By extending Kondo's model for the anomalous Hall effect, we explain the observed anomaly as originating from the second-order nonlinear spin fluctuation of Ni moments. This brings to light an essential symmetry difference between the spin Hall effect and the anomalous Hall effect, which reflects the first-order nonlinear fluctuations of local moments. Our finding opens up a new application of the spin Hall effect, by which a minuscule magnetic moment can be detected.

  9. Diffusion studies on permeable nitroxyl spin probes through bilayer lipid membranes: A low frequency ESR study

    NASA Astrophysics Data System (ADS)

    Meenakumari, V.; Utsumi, Hideo; Ichikawa, Kazuhiro; Yamada, Ken-ichi; Hyodo, Fuminori; Jawahar, A.; Benial, A. Milton Franklin

    2015-06-01

    Electron spin resonance (ESR) studies were carried out for permeable 2mM 14N-labeled deutrated 3 Methoxy carbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl (MC-PROXYL) in pure water and 1mM, 2mM, 3mM, 4mM concentration of 14N-labeled deutrated MC-PROXYL in 400mM concentration of liposomal solution by using a 300 MHz ESR spectrometer. The ESR parameters such as linewidth, hyperfine coupling constant, g-factor, partition parameter and permeability were reported for these samples. The line broadening was observed for the nitroxyl spin probe in the liposomal solution. The line broadening indicates that the high viscous nature of the liposomal solution. The partition parameter and permeability values indicate the maximum diffusion of nitroxyl spin probes in the bilayer lipid membranes at 2 mM concentration of nitroxyl radical. This study illustrates that ESR can be used to differentiate between the intra and extra- membrane water by loading the liposome vesicles with a lipid-permeable nitroxyl spin probe. From the ESR results, the spin probe concentration was optimized as 2mM in liposomal solution for ESR phantom studies/imaging, invivo and invitro experiments.

  10. Diffusion studies on permeable nitroxyl spin probes through bilayer lipid membranes: A low frequency ESR study

    SciTech Connect

    Meenakumari, V.; Benial, A. Milton Franklin; Utsumi, Hideo; Ichikawa, Kazuhiro; Yamada, Ken-ichi; Hyodo, Fuminori; Jawahar, A.

    2015-06-24

    Electron spin resonance (ESR) studies were carried out for permeable 2mM {sup 14}N-labeled deutrated 3 Methoxy carbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl (MC-PROXYL) in pure water and 1mM, 2mM, 3mM, 4mM concentration of 14N-labeled deutrated MC-PROXYL in 400mM concentration of liposomal solution by using a 300 MHz ESR spectrometer. The ESR parameters such as linewidth, hyperfine coupling constant, g-factor, partition parameter and permeability were reported for these samples. The line broadening was observed for the nitroxyl spin probe in the liposomal solution. The line broadening indicates that the high viscous nature of the liposomal solution. The partition parameter and permeability values indicate the maximum diffusion of nitroxyl spin probes in the bilayer lipid membranes at 2 mM concentration of nitroxyl radical. This study illustrates that ESR can be used to differentiate between the intra and extra- membrane water by loading the liposome vesicles with a lipid-permeable nitroxyl spin probe. From the ESR results, the spin probe concentration was optimized as 2mM in liposomal solution for ESR phantom studies/imaging, invivo and invitro experiments.

  11. Probing the Galactic Binary Black Hole Spin with Photon Timing

    NASA Technical Reports Server (NTRS)

    Kazanas, Demosthenes

    2007-01-01

    It is generally considered that the X-ray emission in AGN and Galactic Black Hole Candidates is produced by flares above the surface of a geometrically thin optically thick accretion disk, which extends down to the Innermost Stable Circular Orbit (ISCO) of the black hole. We consider the influence of the black hole geometry on the light curves of these flares. To this end we follow a large number of photon orbits emitted impulsively in a locally isotropic fashion, at any phase of the disk orbit and examine their arrival times at infinity by an observer near the plane of the disk. We find out that the presence of the black hole spin induces a certain delay in the photon arrivals, as prograde photon orbits reach the observer on shorter (on the average) times than the retrograde ones. We form a histogram of the differences in photon time arrivals and we find that it exhibits several well defined peaks depending on the flare position and the black hole spin separated by $\\Delta t \\simeq 30 M$, where M is the black hole mass. The peaks disappear as the spin parameter goes to zero, implying that one could in principle measure the value of the black hole spin with timing measurements of sufficiently high signal to noise ratio.

  12. Probing the Galactic Binary Black Hole Spin with Photon Timing

    NASA Technical Reports Server (NTRS)

    Kazanas, Demos

    2007-01-01

    It is generally considered that the X-ray emission in AGN and Galactic Black Hole Candidates is produced by flares above the surface of a geometrically thin optically thick accretion disk, which extends down to the Innermost Stable Circular Orbit (ISCO) of the black hole. We consider the influence of the black hole geometry on the light curves of these flares. To this end we follow a large number of photon orbits emitted impulsively in a locally isotropic fashion, at any phase of the disk orbit and examine their arrival times at infinity by an observer near the plane of the disk. We find out that the presence of the black hole spin induces a certain delay in the photon arrivals, as prograde photon orbits reach the observer on shorter (on the average) times than the retrograde ones. We form a histogram of the differences in photon time arrivals and we find that it exhibits several well defined peaks depending on the flare position and the black hole spin separated by $\\Delta t\\slmeq 30 M$, where M is the black hole mass. The peaks disappear as the spin parameter goes to zero, implying that one could in principle measure the value of the black hole spin with timing measurements of sufficiently high signal to noise ratio.

  13. Highly selective detection of individual nuclear spins with rotary echo on an electron spin probe

    DOE PAGES

    Mkhitaryan, V. V.; Jelezko, F.; Dobrovitski, V. V.

    2015-10-26

    We consider an electronic spin, such as a nitrogen-vacancy center in diamond, weakly coupled to a large number of nuclear spins, and subjected to the Rabi driving with a periodically alternating phase. We show that by switching the driving phase synchronously with the precession of a given nuclear spin, the interaction to this spin is selectively enhanced, while the rest of the bath remains decoupled. The enhancement is of resonant character. The key feature of the suggested scheme is that the width of the resonance is adjustable, and can be greatly decreased by increasing the driving strength. Thus, the resonancemore » can be significantly narrowed, by a factor of 10–100 in comparison with the existing detection methods. Significant improvement in selectivity is explained analytically and confirmed by direct numerical many-spin simulations. As a result, the method can be applied to a wide range of solid-state systems.« less

  14. Current-induced spin polarization on metal surfaces probed by spin-polarized positron beam.

    PubMed

    Zhang, H J; Yamamoto, S; Fukaya, Y; Maekawa, M; Li, H; Kawasuso, A; Seki, T; Saitoh, E; Takanashi, K

    2014-04-29

    Current-induced spin polarization (CISP) on the outermost surfaces of Au, Cu, Pt, Pd, Ta, and W nanoscaled films were studied using a spin-polarized positron beam. The Au and Cu surfaces showed no significant CISP. In contrast, the Pt, Pd, Ta, and W films exhibited large CISP (3~15% per input charge current of 10(5) A/cm(2)) and the CISP of Ta and W were opposite to those of Pt and Pd. The sign of the CISP obeys the same rule in spin Hall effect suggesting that the spin-orbit coupling is mainly responsible for the CISP. The magnitude of the CISP is explained by the Rashba-Edelstein mechanism rather than the diffusive spin Hall effect. This settles a controversy, that which of these two mechanisms dominates the large CISP on metal surfaces.

  15. Highly selective detection of individual nuclear spins with rotary echo on an electron spin probe

    SciTech Connect

    Mkhitaryan, V. V.; Jelezko, F.; Dobrovitski, V. V.

    2015-10-26

    We consider an electronic spin, such as a nitrogen-vacancy center in diamond, weakly coupled to a large number of nuclear spins, and subjected to the Rabi driving with a periodically alternating phase. We show that by switching the driving phase synchronously with the precession of a given nuclear spin, the interaction to this spin is selectively enhanced, while the rest of the bath remains decoupled. The enhancement is of resonant character. The key feature of the suggested scheme is that the width of the resonance is adjustable, and can be greatly decreased by increasing the driving strength. Thus, the resonance can be significantly narrowed, by a factor of 10–100 in comparison with the existing detection methods. Significant improvement in selectivity is explained analytically and confirmed by direct numerical many-spin simulations. As a result, the method can be applied to a wide range of solid-state systems.

  16. Imaging single spin probes embedded in a conductive diamagnetic layer.

    SciTech Connect

    Messina, P.; Fradin, F.

    2009-01-01

    The detection of spin noise by means of scanning tunneling microscopy (STM) has recently been substantially improved by the work presented by Komeda and Manassen (Komeda, T.; Manassen, Y. Appl. Phys. Lett. 2008, 92, 212506). The application of this technique to molecular paramagnets requires the positioning and anchoring of paramagnetic molecules at surfaces. It also requires the possibility of tunneling high current densities into the STM-molecule-substrate tunneling junction. In this letter, we exploit the self-assembly of 1,10-phenantroline on the Au(111) surface to form a diamagnetic matrix that hosts individual molecules and dimers of diphenyl-2-picryl-hydrazyl (DPPH). STM measurements are used to characterize the molecular layer. Electron spin resonance (ESR) measurements elucidate the role of thermal annealing in the preservation of the paramagnetic nature of the DPPH molecules.

  17. 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.

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

    PubMed

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

    2015-03-01

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

  19. Two-dimensional nanoscale imaging of gadolinium spins via scanning probe relaxometry with a single spin in diamond

    NASA Astrophysics Data System (ADS)

    Pelliccione, Matthew; Myers, Bryan; Pascal, Laetitia; Das, Anand; Jayich, Ania

    2015-03-01

    Spin-labeling of molecules with paramagnetic ions is an important approach for determining molecular structure, however current ensemble techniques lack the sensitivity to detect few isolated spins. In this talk, we demonstrate two-dimensional nanoscale imaging of paramagnetic gadolinium compounds using scanning relaxometry of a single nitrogen vacancy (NV) center in diamond. Gadopentetate dimeglumine attached to an atomic force microscope tip is controllably interacted with and detected by the NV center, by virtue of the fact that the NV exhibits fast relaxation in the fluctuating magnetic field generated by electron spin flips in the gadolinium. We demonstrate a reduction in the T1 relaxation time of the NV center by over two orders of magnitude, probed with a spatial resolution of 20 nm, limited by thermal drift in ambient conditions. We discuss the importance of mitigating drift to reach truly nanoscale imaging and present progress towards cryogenic scanning magnetometry, along with utilizing chemically functionalized tips to gain greater control over the Gd distribution on the tip. Our result exhibits the viability of the technique for imaging individual spins attached to complex nanostructures or biomolecules, along with studying the magnetic dynamics of isolated spins.

  20. Zip nucleic acids are potent hydrolysis probes for quantitative PCR

    PubMed Central

    Paris, Clément; Moreau, Valérie; Deglane, Gaëlle; Voirin, Emilie; Erbacher, Patrick; Lenne-Samuel, Nathalie

    2010-01-01

    Zip nucleic acids (ZNAs) are oligonucleotides conjugated with cationic spermine units that increase affinity for their target. ZNAs were recently shown to enable specific and sensitive reactions when used as primers for polymerase chain reaction (PCR) and reverse-transcription. Here, we report their use as quantitative PCR hydrolysis probes. Ultraviolet duplex melting data demonstrate that attachment of cationic residues to the 3′ end of an oligonucleotide does not alter its ability to discriminate nucleotides nor the destabilization pattern relative to mismatch location in the oligonucleotide sequence. The stability increase provided by the cationic charges allows the use of short dual-labeled probes that significantly improve single-nucleotide polymorphism genotyping. Longer ZNA probes were shown to display reduced background fluorescence, therefore, generating greater sensitivity and signal level as compared to standard probes. ZNA probes thus provide broad flexibility in assay design and also represent an effective alternative to minor groove binder- and locked nucleic-acid-containing probes. PMID:20071749

  1. Spin-Spin Interactions in Organic Magnetoresistance Probed by Angle-Dependent Measurements

    NASA Astrophysics Data System (ADS)

    Wagemans, W.; Schellekens, A. J.; Kemper, M.; Bloom, F. L.; Bobbert, P. A.; Koopmans, B.

    2011-05-01

    The dependence of organic magnetoresistance (OMAR) on the orientation of the magnetic field has been investigated. In contrast with previous claims, a finite and systematic change in magnitude is observed when the orientation of the field is changed with respect to the sample. It is demonstrated that, to explain these effects, spin-spin interactions have to be included in the models previously suggested for OMAR. Dipole coupling and exchange coupling are introduced in combination with either an anisotropy of the orientation of the spin pairs or an anisotropy in the hyperfine fields.

  2. Magnetism of gold nanorods probed using electron spin resonance

    NASA Astrophysics Data System (ADS)

    Inagaki, Y.; Yonemura, H.; Sakai, N.; Makihara, Y.; Kawae, T.; Yamada, S.

    2016-08-01

    Electron spin resonance (ESR) spectroscopy has been performed for gold nanorods (AuNRs) of four different sizes covered with a diamagnetic stabilizing component, cetyltrimethylammonium bromide. ESR signals were detected in AuNRs except the largest one. Two smallest AuNRs showed an abrupt change in the temperature dependence of resonance field and line width at around 60 K, indicating ferromagnetic phase transition. In medium-size AuNRs, the resonance with a large shift was observed below 100 K. The resonance field shifts at the lowest temperature exhibit systematic variation with the system size, which is explained by considering magnetic anisotropy for the ferromagnetic resonance.

  3. Directly probing spin dynamics in insulating antiferromagnets using ultrashort terahertz pulses

    DOE PAGES

    Bowlan, Pamela Renee; Trugman, Stuart Alan; Wang, X.; ...

    2016-11-22

    We investigate spin dynamics in the antiferromagnetic (AFM) multiferroic TbMnO3 using opticalpump, terahertz (THz)-probe spectroscopy. Photoexcitation results in a broadband THz transmission change, with an onset time of 25 ps at 6 K that becomes faster at higher temperatures. We attribute this time constant to spin-lattice thermalization. The excellent agreement between our measurements and previous ultrafast resonant x-ray diffraction measurements on the same material confirms that our THz pulse directly probes spin order. We suggest that this could be the case in general for insulating AFM materials, if the origin of the static absorption in the THz spectral range ismore » magnetic.« less

  4. Probing quantum spin glass like system with a double quantum dot

    NASA Astrophysics Data System (ADS)

    Koh, C. Y.; Kwek, L. C.

    2016-06-01

    We study the ground state properties of a 4-qubit spin glass like (SGL) chain with probes at the end of the chain and compare our results with the non-spin glass like (NSGL) case. The SGL is modeled as a spin chain with nearest-neighbor couplings, taking on normal variates with mean J and variance Δ2. The entanglement between the probes is used to detect any discontinuity in the ground state energy spectrum. For the NSGL case, it was found that the concurrence of the probes exhibits sharp transitions whenever there are abrupt changes in the energy spectrum. In particular, for the 4-qubit case, there is a sudden change in the ground state energy at an external magnetic field B of around 0.66 (resulting in a drop in concurrence of the probes) and 1.7 (manifest as a spike). The latter spike persists for finite temperature case. For the SGL sample with sufficiently large Δ, however, the spike is absent. Thus, an absence in the spike could act as a possible signature of the presence of SGL effects. Moreover, the sudden drop in concurrence at B ≈ 0.66 does not disappear but gets smeared with increasing Δ. However, this drop can be accentuated with a smaller probe coupling. The finite temperature case is also briefly discussed.

  5. Probing photoinduced spin states in spin-crossover molecules with neutron scattering

    NASA Astrophysics Data System (ADS)

    Ridier, K.; Craig, G. A.; Damay, F.; Fennell, T.; Murrie, M.; Chaboussant, G.

    2017-03-01

    We report a neutron-scattering investigation of the spin-crossover compound [Fe (ptz) 6] (BF4)2 , which undergoes an abrupt thermal spin transition from high spin (HS), S =2 , to low spin (LS), S =0 , around 135 K. The HS magnetic state can be restored at low temperature under blue/green light irradiation. We have developed a specially designed optical setup for neutron scattering to address the magnetic properties of the light-induced HS state. By using neutron diffraction, we demonstrate that significant HS/LS ratios (of up to 60%) can be obtained with this experimental setup on a sample volume considered large (400 mg), while a complete recovery of the LS state is achieved using near-infrared light. Finally, with inelastic neutron scattering (INS) we have observed magnetic transitions arising from the photo-induced metastable HS S =2 state split by crystal-field and spin-orbit coupling. We interpret the INS data assuming a spin-only model with a zero-field splitting of the S =2 ground state. The obtained parameters are D ≈-1.28 ±0.03 meV and |E |≈0.08 ±0.03 meV. The present results show that in situ magnetic inelastic neutron-scattering investigations on a broad range of photomagnetic materials are now possible.

  6. Development of a microwave probe for the optical study of microwave-excited spin physics

    NASA Astrophysics Data System (ADS)

    Ou, Yu-Sheng; Chiu, Yi-Hsin; Adur, Rohan; Odenthal, Patrick; Kawakami, Roland; Hammel, P. Chris; Johnston-Halperin, Ezekiel

    2014-03-01

    We have developed an experimental probe that allows simultaneous broadband microwave excitation and optical excitation/detection at variable temperature and magnetic field. Specifically, we have designed a unique sample probe with a microwave stripline based sample mount that allows for direct optical access to the sample under study within a magneto- optical cryostat. This powerful combination enables optical studies of spintronic systems under microwave excitation using both CW (e.g. photo- and electro-luminescence) and time resolved (e.g. time resolved absorption/transmission and time resolved Kerr rotation, TRKR) techniques. To benchmark the capabilities of this probe we present data demonstrating simultaneous ferromagnetic resonance (FMR) and TRKR in a Fe/MgO/GaAs heterostructure. Such studies have potential applications in the study of FMR driven spin pumping and interaction of free carrier spins with native and engineered defects. MRSEC (DMR-0820414).

  7. Probing an NV Center's Nuclear Spin Environment with Coherent Population Trapping

    NASA Astrophysics Data System (ADS)

    Levonian, David; Goldman, Michael; Singh, Swati; Markham, Matthew; Twitchen, Daniel; Lukin, Mikhail

    2016-05-01

    Nitrogen-vacancy (NV) centers in diamond have emerged as a versatile atom-like system, finding diverse applications in metrology and quantum information science, but interaction between the NV center's electronic spin and its nuclear spin environment represent a major source of decoherence. We use optical techniques to monitor and control the nuclear bath surrounding an NV center. Specifically, we create an optical Λ-system using the | +/- 1 > components of the NV center's spin-triplet ground state. When the Zeeman splitting between the two states is equal to the two-photon detuning between the lasers, population is trapped in the resulting dark state. Measuring the rate at which the NV center escapes from the dark state therefore gives information on how spin bath dynamics change the effective magnetic field experienced by the NV center. By monitoring statistics of the emitted photons, we plan to probe non-equilibrium dynamics of the bath.

  8. Probing the thiol-gold planar interface by spin polarized tunneling

    SciTech Connect

    Zhang, Xiaohang; McGill, Stephen A.; Xiong, Peng; Wang, Xiaolei; Zhao, Jianhua

    2014-04-14

    Reports of induced magnetism at thiol-gold interface have generated considerable recent interest. In these studies, the sample magnetization was generally measured by superconducting quantum interference device magnetometry which has limitation in determining surface and interface magnetism. In this work, we have fabricated planar tunnel junctions incorporating a thiol-gold interface. An observed room temperature humidity effect together with low temperature inelastic electron tunneling spectroscopy confirmed the existence of a thiol-gold interface in the organic-inorganic hybrid heterostructure. Spin polarized tunneling measurements were performed to probe the spin polarization at the thiol-gold interface; however, the obtained spin polarized tunneling spectra indicate no measurable spin polarization at the thiol-gold interface.

  9. Possible spin frustration in Nd2Ti2O7 probed by muon spin relaxation.

    PubMed

    Guo, Hanjie; Xing, Hui; Tong, Jun; Tao, Qian; Watanabe, Isao; Xu, Zhu-an

    2014-10-29

    Muon spin relaxation on Nd2Ti2O7 (NTO) and NdLaTi2O7 (NLTO) compounds are presented. The time spectra for both compounds are as expected for the paramagnetic state at high temperatures, but deviate from the exponential function below around 100 K. Firstly, the muon spin relaxation rate increases with decreasing temperature and then levels off below around 10 K, which is reminiscent of the frustrated systems. An enhancement of the relaxation rate by a longitudinal field in the paramagnetic state is observed for NTO and eliminated by a magnetic dilution for the NLTO sample. This suggests that the spectral density is modified by a magnetic dilution and thus indicates that the spins behave cooperatively rather than individually. The zero-field measurement at 0.3 K indicates that the magnetic ground state for NTO is ferromagnetic.

  10. Detection of nanoscale electron spin resonance spectra demonstrated using nitrogen-vacancy centre probes in diamond

    PubMed Central

    Hall, L. T.; Kehayias, P.; Simpson, D. A.; Jarmola, A.; Stacey, A.; Budker, D.; Hollenberg, L. C. L.

    2016-01-01

    Electron spin resonance (ESR) describes a suite of techniques for characterizing electronic systems with applications in physics, chemistry, and biology. However, the requirement for large electron spin ensembles in conventional ESR techniques limits their spatial resolution. Here we present a method for measuring ESR spectra of nanoscale electronic environments by measuring the longitudinal relaxation time of a single-spin probe as it is systematically tuned into resonance with the target electronic system. As a proof of concept, we extracted the spectral distribution for the P1 electronic spin bath in diamond by using an ensemble of nitrogen-vacancy centres, and demonstrated excellent agreement with theoretical expectations. As the response of each nitrogen-vacancy spin in this experiment is dominated by a single P1 spin at a mean distance of 2.7 nm, the application of this technique to the single nitrogen-vacancy case will enable nanoscale ESR spectroscopy of atomic and molecular spin systems. PMID:26728001

  11. Interaction of polyene antibiotics with sterols in phosphatidylcholine bilayer membranes as studied by spin probes.

    PubMed

    Ohki, K; Nozawa, Y; Ohnishi, S I

    1979-06-13

    Interaction of filipin and amphotericin B with sterols in phosphatidylcholine membranes has been studied using various spin probes; epiandrosterone, cholestanone, phosphatidylcholine with 12-nitroxide or 5-nitroxide stearate attached to 2 position and also with tempocholine at the head group. Filipin caused increase in the fluidity of cholesterol-containing phosphatidylcholine membranes near the center, while it rather decreased the fluidity near the polar surface. On the other hand, amphotericin B did not apparently affect the fluidity. In the electron spin resonance spectrum of steriod spin probes in the antibiotic-containing membranes, both bound and free signals were observed and the association constant was calculated from the siganal intensity. In the binding of steriods with filipin, both 3 and 17 positions were involved, while the 17 positions was less involved in the binding with amphotericin B. Phase change in the host membrane markedly affected the interaction of filipin with epiandrosterone probe. The bound fraction jumped from 0.4 to 0.8 on going to the crystalline state and increased further with decrease in temperature. The overall splitting of the bound signal also increased on lowering the temperature below phase transition. This change was attributed to aggregate formation of filipin-steriod complexes in the crystalline state. On the other hand, effect of phase transition was much smaller on the interaction of amphotericin B with the steriod probe.

  12. NMR probing of spin and charge order near odd-integer filling in the second Landau level

    NASA Astrophysics Data System (ADS)

    Rhone, T. D.; Tiemann, L.; Muraki, K.

    2015-07-01

    Studies of spin degrees of freedom near odd-integer filling ν =3 in the second Landau level have engendered conflicting accounts of the spin properties in this regime. Using resistively detected NMR as a probe of local spin density, we explore the nature of the ground state in the quantum Hall regime near ν =3 . Our Knight shift measurements reveal anomalies in NMR spectral line shapes near ν =3 , which demonstrate the presence of solid phases formed from charged quasiparticles, with maximal spin polarization (i.e., no additional spin flips) at each ν . The long nuclear spin relaxation times demonstrate the absence of Skyrmions, or spin textures, in this phase. On the basis of these observations, we attempt to reconcile conflicting reports on the quasiparticle properties and spin wave excitations at ν ˜3 , which may engender new paradigms for the understanding of spin excitations in a collinear ferromagnet with broken translational symmetry.

  13. The use of simulation in the EPR spin probe technique for detection of irradiated seeds.

    PubMed

    Sünnetçioğlu, M M; Dadaylı, D

    2000-10-02

    An electron paramagnetic resonance (EPR) spin probe study of irradiated wheat seeds was performed depending on irradiation dose. The structural changes in the membrane integrity were followed using aqueous solutions of 4-hydroxy-TEMPO (TANOL) spin probe and a line broadening material. In the studies dry seed embryos were kept in these solutions for 150 min. The spectra were recorded at various times of air drying process. The simulation of these spectra indicated a decrease in the water content of the embryos depending on the increasing irradiation dose. This indicates the increase in the permeability of the membranes as a result of the radiation damage. From the decay curves it is possible to determine about irradiation dose, however, this approach is not very successful at close irradiation doses.

  14. Study of coal tar pitch microstructure by using spin probe technique

    SciTech Connect

    Shklyaev, A.A.; Ugay, M.Y.

    1994-12-31

    One of the copper porphyrin complexes has been adopted as a spin probe in order to provide insight into the nature of paramagnetic species of coal tar pitch. It was found that there are three kinds of nonequivalent radical centers displaying a different sensitivity to the spin probes. The majority of radical centers in original coal tar pitch cannot be detected in E.S.R. spectra due to considerable broadening of its lines. These invisible centers give rise to sudden broadening of E.S.R. signals of complex dissolved in the pitch heated over 400 C. The questions regarding the nature of radical states and the reason of abrupt high temperature broadening of pitch signals are discussed.

  15. Triplet excitons as sensitive spin probes for structure analysis of extended defects in microcrystalline silicon

    NASA Astrophysics Data System (ADS)

    Meier, Christoph; Teutloff, Christian; Behrends, Jan; Bittl, Robert; Astakhov, Oleksandr; Lips, Klaus

    2016-07-01

    Electrically detected magnetic resonance (EDMR) spectroscopy is employed to study the influence of triplet excitons on the photocurrent in state-of-the-art microcrystalline silicon thin-film solar cells. These triplet excitons are used as sensitive spin probes for the investigation of their electronic and nuclear environment in this mixed-phase material. According to low-temperature EDMR results obtained from solar cells with different spins in conduction band tail states nearby, and take part in a spin-dependent recombination process. Our study shows that extended defects such as grain boundaries or stacking faults in the crystalline part of the material act as charge carrier traps that can influence the material conductivity.

  16. Molecular dynamics in rod-like liquid crystals probed by muon spin resonance spectroscopy.

    PubMed

    McKenzie, Iain; Scheuermann, Robert; Sedlak, Kamil; Stoykov, Alexey

    2011-08-04

    Muoniated spin probes were produced by the addition of muonium (Mu) to two rod-like liquid crystals: N-(4-methoxybenzylidene)-4'-n-butylaniline (MBBA) and cholesteryl nonanoate (CN). Avoided level crossing muon spin resonance spectroscopy was used to characterize the muoniated spin probes and to probe dynamics at the molecular level. In MBBA Mu adds predominantly to the carbon of the bridging imine group and the muon and methylene proton hyperfine coupling constants (hfccs) of the resulting radical shift in the nematic phase due to the dipolar hyperfine coupling, the ordering of the molecules along the applied magnetic field and fluctuations about the local director. The amplitude of these fluctuations in in the nematic phase of MBBA is determined from the temperature dependence of the methylene proton hfcc. Mu adds to the double bond of the steroidal ring system of CN and the temperature dependence of the Δ(1) line width provides information about the amplitude of the fluctuations about the local director in the chiral nematic phase and the slow isotropic reorientation in the isotropic phase.

  17. Fatty Acid Desaturase Mutants of Yeast: Growth Requirements and Electron Spin Resonance Spin-Label Distribution

    PubMed Central

    Wisnieski, Bernadine J.; Kiyomoto, Richard K.

    1972-01-01

    Two respiratory-sufficient and one respiratory-deficient (nuclear petite) strains of yeast Δ9-desaturase mutants were analyzed to determine which fatty acids would serve as replacements for the naturally occurring fatty acids, 16:1 Δ9cis and 18:1 Δ9cis. The requirement can be satisfied by several fatty acids differing in double-bond position, steric configuration, chain length, and degree of unsaturation. The features common to growth-supporting fatty acids are presented and the effects of varying the carbon source and temperature are considered. In addition, we illustrate several pitfalls encountered in membrane studies which exploit lipid-requiring organisms. Since the membrane fatty acid composition of these mutants can be modified readily, electron spin resonance spectroscopy is used to compare membranes of mutant strains enriched for different fatty acids. The lipid distribution pattern of the most commonly employed electron spin resonance spin-label, 12-nitroxide stearate, was ascertained and compared to that of 18:1 Δ9cis. PMID:4333377

  18. Wet spinning of solid polyamic acid fibers

    NASA Technical Reports Server (NTRS)

    Dorogy, William E., Jr. (Inventor); St.clair, Anne K. (Inventor)

    1991-01-01

    The invention is a process for the production of solid aromatic polyamic acid and polyimide fibers from a wet gel or coagulation bath wet gel using N,N-dimethylacetamide (DMAc) solutions of the polyamic acid derived from aromatic dianhydrides such as 3,3',4,4' benzophenonetetra carboxylic dianhydride (BTDA) and aromatic diamines such as 4,4'-oxydianiline (4,4'-ODA). By utilizing the relationship among coagulation medium and concentration, resin inherent viscosity, resin percent solids, filament diameter, and fiber void content, it is possible to make improved polyamic acid fibers. Solid polyimide fibers, obtained by the thermal cyclization of the polyamic acid precursor, have increased tensile properties compared to fibers containing macropores from the same resin system.

  19. Interaction of poly(ethylene oxide) with the sodium dodecyl sulfate micelle interface studied with nitroxide spin probes

    SciTech Connect

    Kang, Y.S.; Kevan, L. )

    1994-08-04

    Electron spin resonance (ESR) line widths of 5-, 7-, 12-, and 16-doxylstearic acid (x-DSA) and tempo nitroxides versus the concentration of poly(ethylene oxide) (PEO) in sodium dodecyl sulfate (SDS) micelles show different trends. The ESR line widths of 5-, 7-, and 16-DSA increase with increasing concentration of PEO, which is interpreted as due to increasing viscosity in the environment of the nitroxide spin probe. The tempo and 12-DSA line widths were independent of the concentration of PEO. The line width showed the highest value for 5-DSA and the lowest value of tempo. The line width of x-DSA decreases from 5-DSA to a minimum value for 12-DSA and then increases somewhat for 16-DSA. This is interpreted as bending of the alkyl chain to provide different locations for the nitroxide moiety relative to the micelle interface. The relative distances of the nitroxide moiety of [chi]-DSA from deuterated water at the SDS micelle interface was measured by deuterium electron spin echo modulation. The distances increased from 5-DSA to 12-DSA and then decreased for 16-DSA. The interpretation of the DSR line width trend is supported by the deuterium modulation depth trend. 28 refs., 5 figs., 2 tabs.

  20. Extended pump-probe Faraday rotation spectroscopy of the submicrosecond electron spin dynamics in n -type GaAs

    NASA Astrophysics Data System (ADS)

    Belykh, V. V.; Evers, E.; Yakovlev, D. R.; Fobbe, F.; Greilich, A.; Bayer, M.

    2016-12-01

    We develop an extended pump-probe Faraday rotation technique to study submicrosecond electron spin dynamics with picosecond time resolution in a wide range of magnetic fields. The electron spin dephasing time T2* and the longitudinal spin relaxation time T1, both approaching 250 ns in weak fields, are measured thereby in n -type bulk GaAs. By tailoring the pump pulse train through increasing the contained number of pulses, the buildup of resonant spin amplification is demonstrated for the electron spin polarization. The spin precession amplitude in high magnetic fields applied in the Voigt geometry shows a nonmonotonic dynamics deviating strongly from a monoexponential decay and revealing slow beatings. The beatings indicate a two spin component behavior with a g -factor difference of Δ g ˜4 ×10-4 , much smaller than the Δ g expected for free and donor-bound electrons. This g -factor variation indicates efficient, but incomplete spin exchange averaging.

  1. Antiferromagnetic Spin Coupling between Rare Earth Adatoms and Iron Islands Probed by Spin-Polarized Tunneling

    PubMed Central

    Coffey, David; Diez-Ferrer, José Luis; Serrate, David; Ciria, Miguel; Fuente, César de la; Arnaudas, José Ignacio

    2015-01-01

    High-density magnetic storage or quantum computing could be achieved using small magnets with large magnetic anisotropy, a requirement that rare-earth iron alloys fulfill in bulk. This compelling property demands a thorough investigation of the magnetism in low dimensional rare-earth iron structures. Here, we report on the magnetic coupling between 4f single atoms and a 3d magnetic nanoisland. Thulium and lutetium adatoms deposited on iron monolayer islands pseudomorphically grown on W(110) have been investigated at low temperature with scanning tunneling microscopy and spectroscopy. The spin-polarized current indicates that both kind of adatoms have in-plane magnetic moments, which couple antiferromagnetically with their underlying iron islands. Our first-principles calculations explain the observed behavior, predicting an antiparallel coupling of the induced 5d electrons magnetic moment of the lanthanides with the 3d magnetic moment of iron, as well as their in-plane orientation, and pointing to a non-contribution of 4f electrons to the spin-polarized tunneling processes in rare earths. PMID:26333417

  2. Pneumatic switched angle spinning NMR probe with capacitively coupled double saddle coil.

    PubMed

    Litvak, Ilya M; Espinosa, Catalina A; Shapiro, Rebecca A; Oldham, Andrew N; Duong, Vincent V; Martin, Rachel W

    2010-10-01

    Switched angle spinning (SAS) experiments can be used for generating isotropic-anisotropic correlations in oriented samples in a single experiment. In order for these methods to become widespread, specialized hardware is required. Here we describe the electronic and mechanical design and performance of a double-resonance SAS probe. Unlike many previous SAS probe implementations, the focus here is on systems where the dipolar couplings are partially averaged by molecular motion. This probe has a moving double saddle coil capacitively coupled to the stationary circuit. Angle switching is accomplished by a steam engine-type pneumatic mechanism. The speed and stability of the switching hardware for SAS experiments are demonstrated using spectra of model compounds.

  3. Pneumatic switched angle spinning NMR probe with capacitively coupled double saddle coil

    NASA Astrophysics Data System (ADS)

    Litvak, Ilya M.; Espinosa, Catalina A.; Shapiro, Rebecca A.; Oldham, Andrew N.; Duong, Vincent V.; Martin, Rachel W.

    2010-10-01

    Switched angle spinning (SAS) experiments can be used for generating isotropic-anisotropic correlations in oriented samples in a single experiment. In order for these methods to become widespread, specialized hardware is required. Here we describe the electronic and mechanical design and performance of a double-resonance SAS probe. Unlike many previous SAS probe implementations, the focus here is on systems where the dipolar couplings are partially averaged by molecular motion. This probe has a moving double saddle coil capacitively coupled to the stationary circuit. Angle switching is accomplished by a steam engine-type pneumatic mechanism. The speed and stability of the switching hardware for SAS experiments are demonstrated using spectra of model compounds.

  4. The Utilization of Spin Polarized Photoelectron Spectroscopy as a Probe of Electron Correlation with an Ultimate Goal of Pu

    SciTech Connect

    Tobin, J G; Yu, S W; Chung, B W; Morton, S A; Komesu, T; Waddill, G D

    2008-02-07

    We are developing the technique of spin-polarized photoelectron spectroscopy as a probe of electron correlation with the ultimate goal of resolving the Pu electronic structure controversy. Over the last several years, we have demonstrated the utility of spin polarized photoelectron spectroscopy for determining the fine details of the electronic structure in complex systems such as those shown in this report.

  5. The Utilization of Spin Polarized Photoelectron Spectroscopy as a Probe of Electron Correlation with an Ultimate Goal of Pu

    SciTech Connect

    Tobin, James; Yu, Sung; Chung, Brandon; Morton, Simon; Komesu, Takashi; Waddill, George

    2008-02-11

    We are developing the technique of spin-polarized photoelectron spectroscopy as a probe of electron correlation with the ultimate goal of resolving the Pu electronic structure controversy. Over the last several years, we have demonstrated the utility of spin polarized photoelectron spectroscopy for determining the fine details of the electronic structure in complex systems such as those shown in the paper.

  6. Probing iron spin state by optical absorption in laser-heated diamond anvil cell

    NASA Astrophysics Data System (ADS)

    Lobanov, S.; Goncharov, A. F.; Holtgrewe, N.; Lin, J. F.

    2015-12-01

    Pressure-induced spin-pairing transitions in iron-bearing minerals have been in the focus of geophysical studies1. Modern consensus is that iron spin state in the lower mantle is a complex function of crystal structure, composition, pressure, and temperature. Discontinuities in physical properties of lower mantle minerals have been revealed over the spin transition pressure range, but at room temperature. In this work, we have used a supercontinuum laser source and an intensified CCD camera to probe optical properties of siderite, FeCO3, and post-perovskite, Mg0.9Fe0.1SiO3, across the spin transition in laser-heated diamond anvil cell. Synchronously gating the CCD with the supercontinuum pulses (Fig. 1A) allowed diminishing thermal background to ~8.3*10-4. Utilizing the experimental setup we infer the spin state of ferrous iron in siderite at high pressure and temperature conditions (Fig. 1B). Similar behavior is observed for low spin ferric iron in post-perovskite at 130 GPa indicating that all iron in post-perovskite is high spin at lower mantle conditions. Also, our experimental setup holds promise for measuring radiative thermal conductivity of mantle minerals at relevant mantle conditions. Figure 1. (A) Timing of the optical absorption measurements at high temperature. (B) High temperature siderite absorption spectra at 45 GPa. Before heating and quenched after 1300 K spectra are shown in light and dark blue, respectively. Green and red curves are absorption spectra at 1200 K and 1300 K, respectively. Spectra shown in black represent room temperature absorption data on HS (43 GPa) and LS (45.5 GPa) siderite after Lobanov et al., 2015, shown for comparison.

  7. Localized excitation of magnetostatic surface spin waves in yttrium iron garnet by shorted coaxial probe detected via spin pumping and rectification effect

    SciTech Connect

    Soh, Wee Tee Ong, C. K.; Peng, Bin

    2015-04-21

    We demonstrate the localized excitation and dc electrical detection of magnetostatic surface spin waves (MSSWs) in yttrium iron garnet (YIG) by a shorted coaxial probe. Thin films of NiFe and Pt are patterned at different regions onto a common bulk YIG substrate. A shorted coaxial probe is used to excite spin precession locally near various patterned regions. The dc voltages across the corresponding regions are recorded. For excitation of the Pt regions, the dc voltage spectra are dominated by the spin pumping of MSSWs from YIG, where various modes can be clearly distinguished. For the NiFe region, it is also found that spin pumping from MSSWs generated in YIG dominated the spectra, indicating that the spin pumped currents are dissipated into charge currents via the inverse Spin Hall effect (ISHE) in NiFe. For all regions, dc signals from YIG MSSWs are observed to be much stronger than the ferromagnetic resonance (FMR) uniform mode, likely due to the nature of the microwave excitation. The results indicate the potential of this probe for microwave imaging via dc detection of spin dynamics in continuous and patterned films.

  8. Spin-labeled psoralen probes for the study of DNA dynamics

    SciTech Connect

    Spielmann, H.P.; Chi, D.Y.; Hunt, N.G.

    1995-11-14

    Six nitroxide spin-labeled psoralen derivatives have been synthesized and evaluated as probes for structural and dynamic studies. Sequence specific photoaddition of these derivatives to DNA oligonucleotides resulted in site-specifically cross-linked and spin-labeled oligomers. Comparison of the general line shape features of the observed electron paramagnetic resonance (EPR) spectra of several duplexes ranging in size from 8 to 46 base pairs with simulated EPR spectra indicate that the nitroxide spin-labeled probe reports the global tumbling motion of the oligomers. While there is no apparent large amplitude motion of the psoralen other than the overall tumbling of DNA on the time scales investigated, there are no indications of bending and other residual motions. The (A)BC excinuclease DNA repair system detects structural or dynamic features of the DNA that distinguish between damaged and undamaged DNA and are independent of the intrinsic structure of the lesion. NMR studies have shown that psoralen-cross-linked DNA has altered backbone dynamics and conformational populations in the immediate vicinity of the adduct. We suggested that the signal for recognition of a lesion to be repaired is in the sugar-phosphate backbone and not in the damaged base(s). 71 refs., 11 figs., 1 tab.

  9. Advanced slow-magic angle spinning probe for magnetic resonance imaging and spectroscopy

    DOEpatents

    Wind, Robert A.; Hu, Jian Zhi; Minard, Kevin R.; Rommereim, Donald N.

    2006-01-24

    The present invention relates to a probe and processes useful for magnetic resonance imaging and spectroscopy instruments. More particularly, the invention relates to a MR probe and processes for obtaining resolution enhancements of fluid objects, including live specimens, using an ultra-slow (magic angle) spinning (MAS) of the specimen combined with a modified phase-corrected magic angle turning (PHORMAT) pulse sequence. Proton NMR spectra were measured of the torso and the top part of the belly of a female BALBc mouse in a 2T field, while spinning the animal at a speed of 1.5 Hz. Results show that even in this relatively low field with PHORMAT, an isotropic spectrum is obtained with line widths that are a factor 4.6 smaller than those obtained in a stationary mouse. Resolution of 1H NMR metabolite spectra are thus significantly enhanced. Results indicate that PHORMAT has the potential to significantly increase the utility of 1H NMR spectroscopy for in vivo biochemical, biomedical and/or medical applications involving large-sized biological objects such as mice, rats and even humans within a hospital setting. For small-sized objects, including biological objects, such as excised tissues, organs, live bacterial cells, and biofilms, use of PASS at a spinning rate of 30 Hz and above is preferred.

  10. Hyperfine interaction, spin polarization, and spin delocalization as probes of donor-bridge-acceptor interactions in exchange-coupled biradicals.

    PubMed

    Kirk, Martin L; Shultz, David A; Habel-Rodriguez, Diana; Schmidt, Robert D; Sullivan, Ubie

    2010-11-18

    Computations and EPR spectroscopy are used to probe the spin distribution of donor-bridge-acceptor (D-B-A) biradical complexes: Tp(Cum,Me)Zn(SQ-NN) (1), Tp(Cum,Me)Zn(SQ-1,4-Ph-NN) (2), Tp(Cum,Me)Zn(SQ-2,5-TP-NN) (3), and Tp(Cum,Me)Zn(SQ-2,5-Xyl-NN) (4) (SQ = orthosemiquinone and NN = nitronylnitroxide). These complexes are ground-state analogs of the charge-separated excited states formed in photoinduced electron transfer reactions. The intraligand magnetic exchange interaction (J) in these complexes is mediated by the bridges and has been found to stabilize the triplet ground states of 1 and 2. Detailed spectroscopic and bonding calculations have been used to elucidate the role of the bridge fragment (B) and its conformation relative to donor (SQ) and acceptor (NN) on spin density distributions. The computed results correlate well with experimental nitrogen hyperfine coupling constants.

  11. Probing ultrafast spin dynamics through a magnon resonance in the antiferromagnetic multiferroic HoMnO3

    DOE PAGES

    Bowlan, P.; Trugman, S. A.; Bowlan, J.; ...

    2016-09-26

    Here, we demonstrate an approach for directly tracking antiferromagnetic (AFM) spin dynamics by measuring ultrafast changes in a magnon resonance. We also test this idea on the multiferroic HoMnO 3 by optically photoexciting electrons, after which changes in the spin order are probed with a THz pulse tuned to a magnon resonance. This reveals a photoinduced change in the magnon line shape that builds up over 5–12 picoseconds, which we show to be the spin-lattice thermalization time, indicating that electrons heat the spins via phonons. We compare our results to previous studies of spin-lattice thermalization in ferromagnetic manganites, giving insightmore » into fundamental differences between the two systems. Finally, our work sheds light on the microscopic mechanism governing spin-phonon interactions in AFMs and demonstrates a powerful approach for directly monitoring ultrafast spin dynamics.« less

  12. Designer nucleic acids to probe and program the cell.

    PubMed

    Krishnan, Yamuna; Bathe, Mark

    2012-12-01

    Recent advances in nucleic acid sequencing, structural, and computational technologies have resulted in dramatic progress in our understanding of nucleic acid structure and function in the cell. This knowledge, together with the predictable base-pairing of nucleic acids and powerful synthesis and expression capabilities now offers the unique ability to program nucleic acids to form precise 3D architectures with diverse applications in synthetic and cell biology. The unique modularity of structural motifs that include aptamers, DNAzymes, and ribozymes, together with their well-defined construction rules, enables the synthesis of functional higher-order nucleic acid complexes from these subcomponents. As we illustrate here, these highly programmable, smart complexes are increasingly enabling researchers to probe and program the cell in a sophisticated manner that moves well beyond the use of nucleic acids for conventional genetic manipulation alone.

  13. Nanoscale magnetic field mapping with a single spin scanning probe magnetometer

    SciTech Connect

    Rondin, L.; Tetienne, J.-P.; Spinicelli, P.; Roch, J.-F.; Jacques, V.; Dal Savio, C.; Karrai, K.; Dantelle, G.; Thiaville, A.; Rohart, S.

    2012-04-09

    We demonstrate quantitative magnetic field mapping with nanoscale resolution, by applying a lock-in technique on the electron spin resonance frequency of a single nitrogen-vacancy defect placed at the apex of an atomic force microscope tip. In addition, we report an all-optical magnetic imaging technique which is sensitive to large off-axis magnetic fields, thus extending the operation range of diamond-based magnetometry. Both techniques are illustrated by using a magnetic hard disk as a test sample. Owing to the non-perturbing and quantitative nature of the magnetic probe, this work should open up numerous perspectives in nanomagnetism and spintronics.

  14. Probing the flat band of optically trapped spin-orbital-coupled Bose gases using Bragg spectroscopy

    NASA Astrophysics Data System (ADS)

    Li, Wu; Chen, Lei; Chen, Zhu; Hu, Ying; Zhang, Zhidong; Liang, Zhaoxin

    2015-02-01

    Motivated by recent efforts in creating flat bands in ultracold atomic systems, we investigate how to probe a flat band in an optically trapped spin-orbital-coupled Bose-Einstein condensate using Bragg spectroscopy. We find that the excitation spectrum and the dynamic structure factor of the condensate are dramatically altered when the band structure exhibits various levels of flatness. In particular, when the band exhibits perfect flatness around the band minima corresponding to a near-infinite effective mass, a quadratic dispersion emerges in the low-energy excitation spectrum; in sharp contrast, for the opposite case when an ordinary band is present, the familiar linear dispersion arises. Such linear-to-quadratic crossover in the low-energy spectrum presents a striking manifestation of the transition of an ordinary band into a flat band, thereby allowing a direct probe of the flat band by using Bragg spectroscopy.

  15. Probing the dynamics of high-viscosity entangled polymers under shear using Neutron Spin Echo spectroscopy

    NASA Astrophysics Data System (ADS)

    Kawecki, M.; Gutfreund, P.; Adlmann, F. A.; Lindholm, E.; Longeville, S.; Lapp, A.; Wolff, M.

    2016-09-01

    Neutron Spin Echo spectroscopy provides unique insight into molecular and submolecular dynamics as well as intra- and inter-molecular interactions in soft matter. These dynamics may change drastically under shear flow. In particular in polymer physics a stress plateau is observed, which might be explained by an entanglement-disentanglement transition. However, such a transition is difficult to identify directly by experiments. Neutron Spin Echo has been proven to provide information about entanglement length and degree by probing the local dynamics of the polymer chains. Combining shear experiments and neutron spin echo is challenging since, first the beam polarisation has to be preserved during scattering and second, Doppler scattered neutrons may cause inelastic scattering. In this paper we present a new shear device adapted for these needs. We demonstrate that a high beam polarisation can be preserved and present first data on an entangled polymer solution under shear. To complement the experiments on the dynamics we present novel SANS data revealing shear- induced conformational changes in highly entangled polymers.

  16. Effects of oxygen on EPR spectra of nitroxide spin-label probes of model membranes

    NASA Astrophysics Data System (ADS)

    Popp, Carol A.; Hyde, James S.

    The use of a methylpentene polymer, TPX, for construction of sample containers that allow easy equilibration of electron paramagnetic resonance samples with nitrogen is described. The effects of oxygen-dependent shortening of the electron spin relaxation times of nitroxide spin labels were studied in dispersions of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylchohne (DPPC). First-harmonic, in-phase, absorption spectra of deoxygenated samples of 2-(14-carboxytetradecyl)-2-ethyl-4,4-dimethyl-3-oxazolidinyloxyl (16SASL) in DMPC display decreased linewidths and increased peak-to-peak heigths and resolution of 13C splittings. Continuous-wave (cw) saturation studies of 16SASL/DMPC and both lipid- and aqueous-phase components of 2,2,6,6-tetramethyl-piperidinooxyl (Tempo) partitioned into DPPC show that the rf field at which the signal intensity is maximized decreases when aerated samples are equilibrated with nitrogen. Second-harmonic, out-of-phase, absorption (saturation transfer) spectra of deoxygenated samples of 16SASUDMPC at -22°C and 2-(3-carboxypropyl)-4,4-dimethyl-2-tridecyl-3-oxazolidinyloxyl (5SASL) in DPPC at 35°C display increased signal intensity and lineshape changes. Electron-electron double resonance (ELDOR) spectra display much greater ELDOR reduction in signal intensity when a deoxygenated sample of 16SASL/DMPC is used. Our results indicate that the routine use of deoxygenated samples in biologically relevant studies using spin-label probes should be considered.

  17. Parametric Harmonic Generation as a Probe of Unconstrained Spin Magnetization Precession in the Shallow Barrier Limit.

    PubMed

    Capua, Amir; Rettner, Charles; Parkin, Stuart S P

    2016-01-29

    We study the parametric excitation of high orders of magnetization precession in ultrathin films having perpendicular magnetic anisotropy. We observe that for a given driving field amplitude the harmonic generation can be increased by lowering the barrier with the application of an in-plane magnetic field in the manner of the Smit-Beljers effect. In this effect, the magnetic stiffness is reduced not by lowering the magnitude of the magnetic field upon which the spins precess, but rather by effectively releasing the field's "anchoring" point. This results in a shallow energy barrier where the electrons' spin is locally unconstrained. While the observation is unveiled in the form of nonlinear high harmonic generation, we believe that the physics whereby the barrier is suppressed by an external magnetic field may apply to other phenomena associated with ultrathin films. In these cases, such unconstrained motion may serve as a sensitive probe of the torques associated with proximate spin currents. Moreover, our approach may be used as a model system for the study of phase transitions in the field of nonlinear dynamics.

  18. Diffusion studies on permeable nitroxyl spin probe through lipid bilayer membrane

    SciTech Connect

    Benial, A. Milton Franklin; Meenakumari, V.; Ichikawa, Kazuhiro; Yamada, Ken-ichi; Utsumi, Hideo; Hyodo, Fuminori; Jawahar, A.

    2014-04-24

    Electron spin resonance (ESR) studies were carried out for 2mM {sup 14}N labeled deutrated permeable 3- methoxycarbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl (MC-PROXYL) in pure water, 1 mM, 2 mM, 3 mM and 4 mM concentration of MC-PROXYL in 300 mM concentration of liposomal solution by using a L-band ESR spectrometer. The ESR parameters such as linewidth, hyperfine coupling constant, g-factor, partition parameter and permeability were reported. The partition parameter and permeability values indicate the maximum spin distribution in the lipid phase at 2 mM concentration. This study illustrates that ESR can be used to differentiate between the intra and extra-membrane water by loading the liposome vesicles with a lipid-permeable nitroxyl spin probe. From the ESR results, the radical concentration was optimized as 2 mM in liposomal solution for ESR phantom studies and experiments.

  19. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.

    PubMed

    Tangprasertchai, Narin S; Zhang, Xiaojun; Ding, Yuan; Tham, Kenneth; Rohs, Remo; Haworth, Ian S; Qin, Peter Z

    2015-01-01

    The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve "correct" all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements.

  20. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids

    PubMed Central

    Tangprasertchai, Narin S.; Zhang, Xiaojun; Ding, Yuan; Tham, Kenneth; Rohs, Remo; Haworth, Ian S.; Qin, Peter Z.

    2015-01-01

    The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve “correct” all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements. PMID:26477260

  1. Spin-exchange relaxation-free magnetometer with nearly parallel pump and probe beams

    SciTech Connect

    Karaulanov, Todor; Savukov, Igor; Kim, Young Jin

    2016-03-22

    We constructed a spin-exchange relaxation-free (SERF) magnetometer with a small angle between the pump and probe beams facilitating a multi-channel design with a flat pancake cell. This configuration provides almost complete overlap of the beams in the cell, and prevents the pump beam from entering the probe detection channel. By coupling the lasers in multi-mode fibers, without an optical isolator or field modulation, we demonstrate a sensitivity of 10 fT$/\\sqrt{\\text{Hz}}$ for frequencies between 10 Hz and 100 Hz. In addition to the experimental study of sensitivity, we present a theoretical analysis of SERF magnetometer response to magnetic fields for small-angle and parallel-beam configurations, and show that at optimal DC offset fields the magnetometer response is comparable to that in the orthogonal-beam configuration. Based on the analysis, we also derive fundamental and probe-limited sensitivities for the arbitrary non-orthogonal geometry. The expected practical and fundamental sensitivities are of the same order as those in the orthogonal geometry. As a result, we anticipate that our design will be useful for magnetoencephalography (MEG) and magnetocardiography (MCG) applications.

  2. Cryogenic sample exchange NMR probe for magic angle spinning dynamic nuclear polarization

    PubMed Central

    Barnes, Alexander B.; Mak-Jurkauskas, Melody L.; Matsuki, Yoh; Bajaj, Vikram S.; van der Wel, Patrick C. A.; DeRocher, Ronald; Bryant, Jeffrey; Sirigiri, Jagadishwar R.; Temkin, Richard J.; Lugtenburg, Johan; Herzfeld, Judith; Griffin, Robert G.

    2009-01-01

    We describe a cryogenic sample exchange system that dramatically improves the efficiency of magic angle spinning (MAS) dynamic nuclear polarization (DNP) experiments by reducing the time required to change samples and by improving long-term instrument stability. Changing samples in conventional cryogenic MAS DNP/NMR experiments involves warming the probe to room temperature, detaching all cryogenic, RF, and microwave connections, removing the probe from the magnet, replacing the sample, and reversing all the previous steps, with the entire cycle requiring a few hours. The sample exchange system described here — which relies on an eject pipe attached to the front of the MAS stator and a vacuum jacketed dewar with a bellowed hole — circumvents these procedures. To demonstrate the excellent sensitivity, resolution, and stability achieved with this quadruple resonance sample exchange probe, we have performed high precision distance measurements on the active site of the membrane protein bacteriorhodopsin. We also include a spectrum of the tripeptide N-f-MLF-OH at 100 K which shows 30 Hz linewidths. PMID:19356957

  3. Cryogenic sample exchange NMR probe for magic angle spinning dynamic nuclear polarization.

    PubMed

    Barnes, Alexander B; Mak-Jurkauskas, Melody L; Matsuki, Yoh; Bajaj, Vikram S; van der Wel, Patrick C A; Derocher, Ronald; Bryant, Jeffrey; Sirigiri, Jagadishwar R; Temkin, Richard J; Lugtenburg, Johan; Herzfeld, Judith; Griffin, Robert G

    2009-06-01

    We describe a cryogenic sample exchange system that dramatically improves the efficiency of magic angle spinning (MAS) dynamic nuclear polarization (DNP) experiments by reducing the time required to change samples and by improving long-term instrument stability. Changing samples in conventional cryogenic MAS DNP/NMR experiments involves warming the probe to room temperature, detaching all cryogenic, RF, and microwave connections, removing the probe from the magnet, replacing the sample, and reversing all the previous steps, with the entire cycle requiring a few hours. The sample exchange system described here-which relies on an eject pipe attached to the front of the MAS stator and a vacuum jacketed dewar with a bellowed hole-circumvents these procedures. To demonstrate the excellent sensitivity, resolution, and stability achieved with this quadruple resonance sample exchange probe, we have performed high precision distance measurements on the active site of the membrane protein bacteriorhodopsin. We also include a spectrum of the tripeptide N-f-MLF-OH at 100K which shows 30 Hz linewidths.

  4. Spin-exchange relaxation-free magnetometer with nearly parallel pump and probe beams

    DOE PAGES

    Karaulanov, Todor; Savukov, Igor; Kim, Young Jin

    2016-03-22

    We constructed a spin-exchange relaxation-free (SERF) magnetometer with a small angle between the pump and probe beams facilitating a multi-channel design with a flat pancake cell. This configuration provides almost complete overlap of the beams in the cell, and prevents the pump beam from entering the probe detection channel. By coupling the lasers in multi-mode fibers, without an optical isolator or field modulation, we demonstrate a sensitivity of 10 fTmore » $$/\\sqrt{\\text{Hz}}$$ for frequencies between 10 Hz and 100 Hz. In addition to the experimental study of sensitivity, we present a theoretical analysis of SERF magnetometer response to magnetic fields for small-angle and parallel-beam configurations, and show that at optimal DC offset fields the magnetometer response is comparable to that in the orthogonal-beam configuration. Based on the analysis, we also derive fundamental and probe-limited sensitivities for the arbitrary non-orthogonal geometry. The expected practical and fundamental sensitivities are of the same order as those in the orthogonal geometry. As a result, we anticipate that our design will be useful for magnetoencephalography (MEG) and magnetocardiography (MCG) applications.« less

  5. Spin reorientation transition in Fe/CeH2 multilayers probed by soft X-ray resonant magnetic scattering

    NASA Astrophysics Data System (ADS)

    Dürr, H. A.; Münzenberg, M.; Felsch, W.; Dhesi, S. S.

    The magnetic domain configurations of Fe 3d spins in Fe/CeH2 multilayers were measured by soft X-ray resonant magnetic scattering. The interface region could be probed by setting up X-ray standing waves due to the multilayer periodicity. By resolving first- and second-order magnetic scattering contributions, we show that the latter probe directly the magneto-crystalline anisotropy which is dominated by the Fe interface layers causing a spin reorientation transition when the temperature is lowered.

  6. Selective Probing of Hidden Spin-Polarized States in Inversion-Symmetric Bulk MoS2

    NASA Astrophysics Data System (ADS)

    Razzoli, E.; Jaouen, T.; Mottas, M.-L.; Hildebrand, B.; Monney, G.; Pisoni, A.; Muff, S.; Fanciulli, M.; Plumb, N. C.; Rogalev, V. A.; Strocov, V. N.; Mesot, J.; Shi, M.; Dil, J. H.; Beck, H.; Aebi, P.

    2017-02-01

    Spin- and angle-resolved photoemission spectroscopy is used to reveal that a large spin polarization is observable in the bulk centrosymmetric transition metal dichalcogenide MoS2 . It is found that the measured spin polarization can be reversed by changing the handedness of incident circularly polarized light. Calculations based on a three-step model of photoemission show that the valley and layer-locked spin-polarized electronic states can be selectively addressed by circularly polarized light, therefore providing a novel route to probe these hidden spin-polarized states in inversion-symmetric systems as predicted by Zhang et al. [Nat. Phys. 10, 387 (2014)., 10.1038/nphys2933].

  7. Intrinsic spin and momentum relaxation in organic single-crystalline semiconductors probed by ESR and Hall measurements

    NASA Astrophysics Data System (ADS)

    Tsurumi, Junto; Häusermann, Roger; Watanabe, Shun; Mitsui, Chikahiko; Okamoto, Toshihiro; Matsui, Hiroyuki; Takeya, Jun

    Spin and charge momentum relaxation mechanism has been argued among organic semiconductors with various methods, devices, and materials. However, little is known in organic single-crystalline semiconductors because it has been hard to obtain an ideal organic crystal with an excellent crystallinity and controllability required for accurate measurements. By using more than 1-inch sized single crystals which are fabricated via contentious edge-casting method developed by our group, we have successfully demonstrated a simultaneous determination of spin and momentum relaxation time for gate-induced charges of 3,11-didecyldinaphtho[2,3- d:2',3'- d']benzo[1,2- b:4,5- b']dithiophene, by combining electron spin resonance (ESR) and Hall effect measurements. The obtained temperature dependences of spin and momentum relaxation times are in good agreement in terms of power law with a factor of approximately -2. It is concluded that Elliott-Yafet spin relaxation mechanism can be dominant at room temperature regime (200 - 300 K). Probing characteristic time scales such as spin-lattice, spin-spin, and momentum relaxation times, demonstrated in the present work, would be a powerful tool to elucidate fundamental spin and charge transport mechanisms. We acknowledge the New Energy and Industrial Technology Developing Organization (NEDO) for financial support.

  8. Nitrogen nuclear spin flips in nitroxide spin probes of different sizes in glassy o-terphenyl: Possible relation with α- and β-relaxations

    NASA Astrophysics Data System (ADS)

    Isaev, N. P.; Dzuba, S. A.

    2011-09-01

    The pulsed electron-electron double resonance (ELDOR) technique was employed to study nitroxide spin probes of three different sizes dissolved in glassy o-terphenyl. A microwave pulse applied to the central hyperfine structure (hfs) component of the nitroxide electron paramagnetic resonance spectrum was followed by two echo-detecting pulses of different microwave frequency to probe the magnetization transfer (MT) to the low-field hfs component. The MT between hfs components is readily related to flips in the nitrogen nuclear spin, which in turn are induced by molecular motion. The MT on the time scale of tens of microseconds was observed over a wide temperature range, including temperatures near and well below the glass transition. For a bulky nitroxide, it was found that MT rates approach dielectric α (primary) relaxation frequencies reported for o-terphenyl in the literature. For small nitroxides, MT rates were found to match the frequencies of dielectric β (secondary) Johari-Goldstein relaxation. The most probable motional mechanism inducing the nitrogen nuclear spin flips is large-angle angular jumps, between some orientations of unequal occupation probabilities. The pulsed ELDOR of nitroxide spin probes may provide additional insight into the nature of Johari-Goldstein relaxation in glassy media and may serve as a tool for studying this relaxation in substances consisting of non-rigid molecules (such as branched polymers) and in heterogeneous and non-polar systems (such as a core of biological membranes).

  9. Scanned probe imaging of nanoscale magnetism at cryogenic temperatures with a single-spin quantum sensor

    NASA Astrophysics Data System (ADS)

    Pelliccione, Matthew; Jenkins, Alec; Ovartchaiyapong, Preeti; Reetz, Christopher; Emmanuelidu, Eve; Ni, Ni; Bleszynski Jayich, Ania

    The nitrogen vacancy (NV) defect in diamond has emerged as a promising candidate for high resolution magnetic imaging based on its atomic size and quantum-limited sensing capabilities afforded by long spin coherence times. Although the NV center has been successfully implemented as a nanoscale scanning magnetic probe at room temperature, it has remained an outstanding challenge to extend this capability to cryogenic temperatures, where many solid-state systems exhibit non-trivial magnetic order. In this talk, we present NV magnetic imaging at T = 6 K, first benchmarking the technique with a magnetic hard disk sample, then utilizing the technique to image vortices in the iron pnictide superconductor BaFe2(As0.7P0.3)2 with Tc = 30 K. In addition, we discuss other candidate solid-state systems that can benefit from the high spatial resolution and field sensitivity of the scanning NV magnetometer.

  10. GDR as a Probe of the Collective Motion in Nuclei at High Spins, Temperatures or Isospins

    SciTech Connect

    Maj, Adam

    2008-11-11

    The gamma-decay of the Giant Dipole Resonance (GDR), the high-frequency collective vibration of protons against neutrons, has been proven to be a basic probe for the shapes of hot nuclei, especially to study the effective shape evolution caused by the collective rotation of a nucleus. In this context an interesting question arises: what is the nuclear shape at extreme values of spin or temperatures, close to the limit impose by another collective motion--fission, and how evolves the giant dipole collective vibrations as a function of isospin. Short overview of the results from the experiments aimed to answer these questions are presented and possible perspectives of these type of studies for exotic nuclei to be obtained with the novel gamma-calorimeter PARIS and soon available intense radioactive beams are discussed.

  11. Li diffusion in LixCoO2 probed by muon-spin spectroscopy.

    PubMed

    Sugiyama, Jun; Mukai, Kazuhiko; Ikedo, Yutaka; Nozaki, Hiroshi; Månsson, Martin; Watanabe, Isao

    2009-10-02

    The diffusion coefficient of Li+ ions (D(Li)) in the battery material LixCoO2 has been investigated by muon-spin relaxation (mu+SR). Based on experiments in zero and weak longitudinal fields at temperatures up to 400 K, we determined the fluctuation rate (nu) of the fields on the muons due to their interaction with the nuclear moments. Combined with susceptibility data and electrostatic potential calculations, clear Li+ ion diffusion was detected above approximately 150 K. The D(Li) estimated from nu was in very good agreement with predictions from first-principles calculations, and we present the mu+SR technique as an optimal probe to detect D(Li) for materials containing magnetic ions.

  12. Li Diffusion in LixCoO2 Probed by Muon-Spin Spectroscopy

    NASA Astrophysics Data System (ADS)

    Sugiyama, Jun; Mukai, Kazuhiko; Ikedo, Yutaka; Nozaki, Hiroshi; Månsson, Martin; Watanabe, Isao

    2009-10-01

    The diffusion coefficient of Li+ ions (DLi) in the battery material LixCoO2 has been investigated by muon-spin relaxation (μ+SR). Based on experiments in zero and weak longitudinal fields at temperatures up to 400 K, we determined the fluctuation rate (ν) of the fields on the muons due to their interaction with the nuclear moments. Combined with susceptibility data and electrostatic potential calculations, clear Li+ ion diffusion was detected above ˜150K. The DLi estimated from ν was in very good agreement with predictions from first-principles calculations, and we present the μ+SR technique as an optimal probe to detect DLi for materials containing magnetic ions.

  13. 57 Fe Mössbauer probe of spin crossover thin films on a bio-membrane

    NASA Astrophysics Data System (ADS)

    Naik, Anil D.; Garcia, Yann

    2012-03-01

    An illustrious complex [Fe(ptz)6](BF4)2 (ptz = 1-propyl-tetrazole) ( 1) which was produced in the form of submicron crystals and thin film on Allium cepa membrane was probed by 57Fe Mossbauer spectroscopy in order to follow its intrinsic spin crossover. In addition to a weak signal that corresponds to neat SCO compound significant amount of other iron compounds are found that could have morphed from 1 due to specific host-guest interaction on the lipid-bilayer of bio-membrane. Further complimentary information about biogenic role of membrane, was obtained from variable temperature Mossbauer spectroscopy on a ~5% enriched [57Fe(H2O)6](BF4)2 salt on this membrane.

  14. Probing spin-orbit-interaction-induced electron dynamics in the carbon atom by multiphoton ionization

    NASA Astrophysics Data System (ADS)

    Rey, H. F.; van der Hart, H. W.

    2014-09-01

    We use R-matrix theory with time dependence (RMT) to investigate multiphoton ionization of ground-state atomic carbon with initial orbital magnetic quantum number ML=0 and ML=1 at a laser wavelength of 390 nm and peak intensity of 1014W/cm2. Significant differences in ionization yield and ejected-electron momentum distribution are observed between the two values for ML. We use our theoretical results to model how the spin-orbit interaction affects electron emission along the laser polarization axis. Under the assumption that an initial C atom is prepared at zero time delay with ML=0, the dynamics with respect to time delay of an ionizing probe pulse modeled by using RMT theory is found to be in good agreement with available experimental data.

  15. Probing Spin and Spin-Orbit Coupling effects in Narrow-gap Semiconductor Nano-structures by THz Magneto-photoresponse Spectroscopy and Magneto-transport Measurements

    NASA Astrophysics Data System (ADS)

    Pakmehr, Mehdi

    Using the spin degree of freedom in a emergent field Known as Spintronics has motivated scientist in different disciplines including physicist within last 10 years. Due to different interaction mechanisms which affects the physical behavior of spin (eg its state and transport properties) within solid medium (Semiconductors in our case), one needs to distinguish these mechanisms and their importance for making any practical spin based devices. For example the idea of making spin based transistors with electrons being transported within InGaAs and their spin state is being controlled by Rashba type field has been around for around 25 years but injection of spin polarized currents from a source into the channel has not been solved yet. Spin orbit coupling (SOC) is one of the mechanisms which changes the spin state of electrons and avoid the existence of pure spin state as a favorable one from device point of view. SOC could have a different origin depending on material type or structure of device. One method of measuring and quantifying this mechanisms within semiconductor nanostructures is through measuring the parameters known as Lande g-factor. This parameters turns out to be a promising one to probe different effects on electronic band structure including quantum confinement, strain, electric filed, etc. We probe a combination of these effects (SOC, Strain, band mixing, etc) by measuring different g-factor tensor components of narrow gap Zinc blend semiconductor nanostructures which we hope finally serve to the purpose of making reliable spin based devices* (Spintronics). To reach this goal we have developed and implemented THz magneto-Photoresponse spectroscopy in conjunction with magneto-transport measurements at cryogenic temperatures. The samples include InAs and HgTe based Quantum wells as well as InAs based quantum point contact. Our findings clarify the situation where the combination of SOC, Strain, quantum confinements as well as many body electron effect

  16. Isoindoline nitroxide-labeled porphyrins as potential fluorescence-suppressed spin probes.

    PubMed

    Liu, F; Zou, T J; Tan, Z L; Chen, S; Wu, Z H; Yan, G P; Zhang, Q; Liang, S C; Yang, J

    2017-02-07

    A series of isoindoline nitroxide-labeled porphyrins were synthesized by the reaction of 5-phenyldipyrromethane and 5-(4'-carboethoxy-methyleneoxyphenyl)dipyrromethane with 5-formyl-1,1,3,3-tetramethylisoindolin-2-yloxyl (FTMIO) using the Lindsey method. The corresponding water-soluble spin-labeled porphyrins were also prepared. Subsequently, these compounds were characterized and their in vitro properties were evaluated. The electrochemical assay demonstrated that these isoindoline nitroxide-labeled porphyrins had similar electrochemical and redox properties to 5-carboxy-1,1,3,3-tetramethylisoindolin-2-yloxyl (CTMIO). The electron paramagnetic resonance test showed that these porphyrins exhibited hyperfine splittings and characteristic spectra of CTMIO with typical nitroxide g-values and nitrogen isotropic hyperfine coupling constants. The in vitro cytotoxicity assay indicated that these porphyrins possessed low cytotoxicity to human renal tubular epithelial 293T cells (normal cells) and human hepatoma HepG2 cells (tumor cells). Fluorescence spectroscopy revealed that free base isoindoline nitroxide-labeled porphyrins exhibited fluorescence suppression characteristic of nitroxide-fluorophore systems. In vitro fluorescene imaging demonstrated that the reduced isoindoline nitroxide-labeled porphyrins eliminated fluorescence suppression and displayed strong red fluorescence imaging in HepG2 cells. Thus these isoindoline nitroxide-labeled porphyrins may be considered potentially as biological spin probes for fluorescence imaging and EPR spectroscopy.

  17. Computer selection of oligonucleotide probes from amino acid sequences for use in gene library screening.

    PubMed

    Yang, J H; Ye, J H; Wallace, D C

    1984-01-11

    We present a computer program, FINPROBE, which utilizes known amino acid sequence data to deduce minimum redundancy oligonucleotide probes for use in screening cDNA or genomic libraries or in primer extension. The user enters the amino acid sequence of interest, the desired probe length, the number of probes sought, and the constraints on oligonucleotide synthesis. The computer generates a table of possible probes listed in increasing order of redundancy and provides the location of each probe in the protein and mRNA coding sequence. Activation of a next function provides the amino acid and mRNA sequences of each probe of interest as well as the complementary sequence and the minimum dissociation temperature of the probe. A final routine prints out the amino acid sequence of the protein in parallel with the mRNA sequence listing all possible codons for each amino acid.

  18. In situ magnetic compensation for potassium spin-exchange relaxation-free magnetometer considering probe beam pumping effect

    SciTech Connect

    Fang, Jiancheng; Wang, Tao Quan, Wei; Yuan, Heng; Li, Yang; Zhang, Hong; Zou, Sheng

    2014-06-15

    A novel method to compensate the residual magnetic field for an atomic magnetometer consisting of two perpendicular beams of polarizations was demonstrated in this paper. The method can realize magnetic compensation in the case where the pumping rate of the probe beam cannot be ignored. In the experiment, the probe beam is always linearly polarized, whereas, the probe beam contains a residual circular component due to the imperfection of the polarizer, which leads to the pumping effect of the probe beam. A simulation of the probe beam's optical rotation and pumping rate was demonstrated. At the optimized points, the wavelength of the probe beam was optimized to achieve the largest optical rotation. Although, there is a small circular component in the linearly polarized probe beam, the pumping rate of the probe beam was non-negligible at the optimized wavelength which if ignored would lead to inaccuracies in the magnetic field compensation. Therefore, the dynamic equation of spin evolution was solved by considering the pumping effect of the probe beam. Based on the quasi-static solution, a novel magnetic compensation method was proposed, which contains two main steps: (1) the non-pumping compensation and (2) the sequence compensation with a very specific sequence. After these two main steps, a three-axis in situ magnetic compensation was achieved. The compensation method was suitable to design closed-loop spin-exchange relaxation-free magnetometer. By a combination of the magnetic compensation and the optimization, the magnetic field sensitivity was approximately 4 fT/Hz{sup 1/2}, which was mainly dominated by the noise of the magnetic shield.

  19. In situ magnetic compensation for potassium spin-exchange relaxation-free magnetometer considering probe beam pumping effect.

    PubMed

    Fang, Jiancheng; Wang, Tao; Quan, Wei; Yuan, Heng; Zhang, Hong; Li, Yang; Zou, Sheng

    2014-06-01

    A novel method to compensate the residual magnetic field for an atomic magnetometer consisting of two perpendicular beams of polarizations was demonstrated in this paper. The method can realize magnetic compensation in the case where the pumping rate of the probe beam cannot be ignored. In the experiment, the probe beam is always linearly polarized, whereas, the probe beam contains a residual circular component due to the imperfection of the polarizer, which leads to the pumping effect of the probe beam. A simulation of the probe beam's optical rotation and pumping rate was demonstrated. At the optimized points, the wavelength of the probe beam was optimized to achieve the largest optical rotation. Although, there is a small circular component in the linearly polarized probe beam, the pumping rate of the probe beam was non-negligible at the optimized wavelength which if ignored would lead to inaccuracies in the magnetic field compensation. Therefore, the dynamic equation of spin evolution was solved by considering the pumping effect of the probe beam. Based on the quasi-static solution, a novel magnetic compensation method was proposed, which contains two main steps: (1) the non-pumping compensation and (2) the sequence compensation with a very specific sequence. After these two main steps, a three-axis in situ magnetic compensation was achieved. The compensation method was suitable to design closed-loop spin-exchange relaxation-free magnetometer. By a combination of the magnetic compensation and the optimization, the magnetic field sensitivity was approximately 4 fT/Hz(1/2), which was mainly dominated by the noise of the magnetic shield.

  20. Probing lipid peroxidation by using linoleic acid and benzophenone.

    PubMed

    Andreu, Inmaculada; Neshchadin, Dmytro; Rico, Enrique; Griesser, Markus; Samadi, Abdelouahid; Morera, Isabel M; Gescheidt, Georg; Miranda, Miguel A

    2011-08-29

    A thorough mechanistic study has been performed on the reaction between benzophenone (BZP) and a series of 1,4-dienes, including 1,4-cyclohexadiene (CHD), 1,4-dihydro-2-methylbenzoic acid (MBA), 1,4-dihydro-1,2-dimethylbenzoic acid (DMBA) and linoleic acid (LA). A combination of steady-state photolysis, laser flash photolysis (LFP), and photochemically induced dynamic nuclear polarization (photo-CIDNP) have been used. Irradiation of BZP and CHD led to a cross-coupled sensitizer-diene product, together with 6, 7, and 8. With MBA and DMBA as hydrogen donors, photoproducts arising from cross-coupling of sensitizer and diene radicals were found; compound 7 was also obtained, but 6 and o-toluic acid were only isolated in the irradiation of BZP with MBA. Triplet lifetimes were determined in the absence and in the presence of several diene concentrations. All three model compounds showed similar reactivity (k(q) ≈10(8)  M(-1)  s(-1)) towards triplet excited BZP. Partly reversible hydrogen abstraction of the allylic hydrogen atoms of CHD, MBA, and DMBA was also detected by photo-CIDNP on different timescales. Polarizations of the diamagnetic products were in full agreement with the results derived from LFP. Finally, LA also underwent partly reversible hydrogen abstraction during photoreaction with BZP. Subsequent hydrogen transfer between primary radicals led to conjugated derivatives of LA. The unpaired electron spin population in linoleyl radical (LA(.)) was predominantly found on H(1-5) protons. To date, LA-related radicals were only reported upon hydrogen transfer from highly substituted model compounds by steady-state EPR spectroscopy. Herein, we have experimentally established the formation of LA(.) and shown that it converts into two dominating conjugated isomers on the millisecond timescale. Such processes are at the basis of alterations of membrane structures caused by oxidative stress.

  1. Method for producing labeled single-stranded nucleic acid probes

    DOEpatents

    Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

    1999-10-19

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  2. Spin current and inverse spin Hall effect in ferromagnetic metals probed by Y{sub 3}Fe{sub 5}O{sub 12}-based spin pumping

    SciTech Connect

    Wang, Hailong; Du, Chunhui; Chris Hammel, P. Yang, Fengyuan

    2014-05-19

    Using ferromagnetic (FM) resonance spin pumping, we observe injection of spin currents from Y{sub 3}Fe{sub 5}O{sub 12} (YIG) films to FM metals, including Ni{sub 81}Fe{sub 19} (Py), Fe, Co, and Ni, and detection of spin currents by inverse spin Hall effect (ISHE) in the FM metals. We obtain a high effective spin mixing conductance of 6.3 × 10{sup 18} m{sup −2} in a YIG/Cu/Py trilayer and a spin Hall angle of 0.020 for Py. The spin pumping signals in Fe, Co, and Ni confirm the mechanism of ISHE in FMs is the inverse process of the anomalous Hall effect.

  3. Electronic spin polarization and the spin-dependent bandstructure in GaAs probed by optically pumped NMR

    SciTech Connect

    Crooker, Scott A; Ramaswamy, Kannan; Mui, Stacy; Hayes, Sophia E; Pan, Xingyuan; Sanders, Gary D; Stanton, Christopher J

    2008-01-01

    High resolution optically pumped NMR (OPNMR) experiments are used to resolve fine features in the spin-dependent electronic structure of the valence bands in semi-insulating GaAs. By theoretically calculating oscillations in the OPNMR signal intensity with respect to the excitation energy, we have mapped out the conduction band electronic spin polarization under optical pumping. Comparison with a theoretical analysis of the oscillatory experimental features allows the extraction of semiconductor energy band parameters.

  4. Probing the Specificity Determinants of Amino Acid Recognition by Arginase

    SciTech Connect

    Shishova, E.; Di Costanzo, L; Emig, F; Ash, D; Christianson, D

    2009-01-01

    Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site-directed mutagenesis, enzyme kinetics, and X-ray crystallography to probe the molecular recognition of the amino acid moiety (i.e., the ?-amino and ?-carboxylate groups) of substrate l-arginine and inhibitors in the active site of arginase I. Specifically, we focus on (1) a water-mediated hydrogen bond between the substrate ?-carboxylate and T135, (2) a direct hydrogen bond between the substrate ?-carboxylate and N130, and (3) a direct charged hydrogen bond between the substrate ?-amino group and D183. Amino acid substitutions for T135, N130, and D183 generally compromise substrate affinity as reflected by increased KM values but have less pronounced effects on catalytic function as reflected by minimal variations of kcat. As with substrate KM values, inhibitor Kd values increase for binding to enzyme mutants and suggest that the relative contribution of intermolecular interactions to amino acid affinity in the arginase active site is water-mediated hydrogen bond < direct hydrogen bond < direct charged hydrogen bond. Structural comparisons of arginase with the related binuclear manganese metalloenzymes agmatinase and proclavaminic acid amidinohydrolase suggest that the evolution of substrate recognition in the arginase fold occurs by mutation of residues contained in specificity loops flanking the mouth of the active site (especially loops 4 and 5), thereby allowing diverse guanidinium substrates to be accommodated for catalysis.

  5. Intermediate scattering function for macromolecules in solutions probed by neutron spin echo

    NASA Astrophysics Data System (ADS)

    Liu, Yun

    2017-02-01

    The neutron-spin-echo method (NSE) is a powerful technique for studying internal dynamics of macromolecules in solutions because it can simultaneously probe length and time scales comparable to intramolecular density fluctuations of macromolecules. Recently, there has been increased, strong interest in studying protein internal motions using NSE. The coherent intermediate scattering function (ISF) measured by NSE depends on internal, rotational, and translational motions of macromolecules in solutions. It is thus critical, but highly nontrivial, to separate the internal motion from other motions in order to properly understand protein internal dynamics. Even though many experiments are performed at relatively high concentrations, current theories of calculating the ISF of concentrated protein solutions are either inaccurate or flawed by incorrect assumptions for realistic protein systems with anisotropic shapes. Here, a theoretical framework is developed to establish the quantitative relationship of different motions included in the ISF. This theory based on the dynamic decoupling approximation is applicable to a wide range of protein concentrations, including dilute cases. It is also, in general, useful for studying many other types of macromolecule systems studied by NSE.

  6. Characterization of molecular mobility in seed tissues: an electron paramagnetic resonance spin probe study.

    PubMed

    Buitink, J; Hemminga, M A; Hoekstra, F A

    1999-06-01

    The relationship between molecular mobility (tauR) of the polar spin probe 3-carboxy-proxyl and water content and temperature was established in pea axes by electron paramagnetic resonance (EPR) and saturation transfer EPR. At room temperature, tauR increased during drying from 10(-11) s at 2.0 g water/g dry weight to 10(-4) s in the dry state. At water contents below 0.07 g water/g dry weight, tauR remained constant upon further drying. At the glass transition temperature, tauR was constant at approximately 10(-4) s for all water contents studied. Above Tg, isomobility lines were found that were approximately parallel to the Tg curve. The temperature dependence of tauR at all water contents studied followed Arrhenius behavior, with a break at Tg. Above Tg the activation energy for rotational motion was approximately 25 kJ/mol compared to 10 kJ/mol below Tg. The temperature dependence of tauR could also be described by the WLF equation, using constants deviating considerably from the universal constants. The temperature effect on tauR above Tg was much smaller in pea axes, as found previously for sugar and polymer glasses. Thus, although glasses are present in seeds, the melting of the glass by raising the temperature will cause only a moderate increase in molecular mobility in the cytoplasm as compared to a huge increase in amorphous sugars.

  7. Order and dynamics inside H-PDLC nanodroplets: an ESR spin probe study.

    PubMed

    Bacchiocchi, Corrado; Miglioli, Isabella; Arcioni, Alberto; Vecchi, Ilaria; Rai, Kashma; Fontecchio, Adam; Zannoni, Claudio

    2009-04-23

    We have performed a detailed study of the order and dynamics of the commercially available BL038 liquid crystal (LC) inside nanosized (50-300 nm) droplets of a reflection-mode holographic-polymer dispersed liquid crystal (H-PDLC) device where LC nanodroplet layers and polymer layers are alternately arranged, forming a diffraction grating. We have determined the configuration of the LC local director and derived a model of the nanodroplet organization inside the layers. To achieve this, we have taken advantage of the high sensitivity of the ESR spin probe technique to study a series of temperatures ranging from the nematic to the isotropic phase of the LC. Using also additional information on the nanodroplet size and shape distribution provided by SEM images of the H-PDLC cross section, the observed director configuration has been modeled as a bidimensional distribution of elongated nanodroplets whose long axis is, on the average, parallel to the layers and whose internal director configuration is a uniaxial quasi-monodomain aligned along the nanodroplet long axis. Interestingly, at room temperature the molecules tend to keep their average orientation even when the layers are perpendicular to the magnetic field, suggesting that the molecular organization is dictated mainly by the confinement. This result might explain, at least in part, (i) the need for switching voltages significantly higher and (ii) the observed faster turn-off times in H-PDLCs compared to standard PDLC devices.

  8. DC and AC Electric Field Measurements by Spin-Plane Double Probes Onboard MMS

    NASA Astrophysics Data System (ADS)

    Lindqvist, P. A.; Marklund, G. T.; Khotyaintsev, Y. V.; Ergun, R. E.; Goodrich, K.; Torbert, R. B.; Argall, M. R.; Nakamura, R.

    2015-12-01

    The four spacecraft of the NASA Magnetospheric Multiscale mission (MMS) were launched on 12 March 2015 into a 1.2 x 12 Re equatorial orbit to study energy conversion processes in Earth's magnetosphere. After a 5-month commissioning period the first scientific phase starts on 1 September as the orbit enters the dusk magnetopause region. The Spin-plane Double Probe electric field instrument (SDP), part of the electric and magnetic fields instrument suite FIELDS, measures the electric field in the range 0.3 - 500 mV/m with a continuous time resolution up to 8192 samples/s. The instrument features adjustable bias currents and guard voltages to optimize the measurement performance. SDP also measures the spacecraft potential, which can be controlled by the Active Spacecraft Potential Control (ASPOC) ion emitter, and under certain conditions can be used to determine plasma density. We present observations of DC and AC electric fields in different plasma regions covered by MMS since launch including the night side flow braking region, reconnection regions at the dusk and dayside magnetopause, and in the magnetosheath. We compare the electric field measurements by SDP to other, independent determinations of the electric field, in particular by the Electron Drift Instrument (EDI), in order to assess the accuracy of the electric field measurement under different plasma conditions. We also study the influence of the currents emitted by ASPOC and EDI on the SDP measurements.

  9. Characterization of molecular mobility in seed tissues: an electron paramagnetic resonance spin probe study.

    PubMed Central

    Buitink, J; Hemminga, M A; Hoekstra, F A

    1999-01-01

    The relationship between molecular mobility (tauR) of the polar spin probe 3-carboxy-proxyl and water content and temperature was established in pea axes by electron paramagnetic resonance (EPR) and saturation transfer EPR. At room temperature, tauR increased during drying from 10(-11) s at 2.0 g water/g dry weight to 10(-4) s in the dry state. At water contents below 0.07 g water/g dry weight, tauR remained constant upon further drying. At the glass transition temperature, tauR was constant at approximately 10(-4) s for all water contents studied. Above Tg, isomobility lines were found that were approximately parallel to the Tg curve. The temperature dependence of tauR at all water contents studied followed Arrhenius behavior, with a break at Tg. Above Tg the activation energy for rotational motion was approximately 25 kJ/mol compared to 10 kJ/mol below Tg. The temperature dependence of tauR could also be described by the WLF equation, using constants deviating considerably from the universal constants. The temperature effect on tauR above Tg was much smaller in pea axes, as found previously for sugar and polymer glasses. Thus, although glasses are present in seeds, the melting of the glass by raising the temperature will cause only a moderate increase in molecular mobility in the cytoplasm as compared to a huge increase in amorphous sugars. PMID:10354457

  10. Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

    DOEpatents

    Ramsey, J. Michael; Foote, Robert S.

    2002-01-01

    A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

  11. Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

    DOEpatents

    Ramsey, J. Michael; Foote, Robert S.

    2003-12-09

    A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

  12. Determination of the 14N quadrupole coupling constant of nitroxide spin probes by W-band ELDOR-detected NMR.

    PubMed

    Florent, Marc; Kaminker, Ilia; Nagarajan, Vijayasarathi; Goldfarb, Daniella

    2011-06-01

    Nitroxide spin probe electron paramagnetic resonance (EPR) has proven to be a very successful method to probe local polarity and solvent hydrogen bonding properties at the molecular level. The g(xx) and the (14)N hyperfine A(zz) principal values are the EPR parameters of the nitroxide spin probe that are sensitive to these properties and are therefore monitored experimentally. Recently, the (14)N quadrupole interaction of nitroxides has been shown to be also highly sensitive to polarity and H-bonding (A. Savitsky et al., J. Phys. Chem. B 112 (2008) 9079). High-field electron spin echo envelope modulation (ESEEM) was used successfully to determine the P(xx) and P(yy) principal components of the (14)N quadrupole tensor. The P(zz) value was calculated from the traceless character of the quadrupole tensor. We introduce here high-field (W-band, 95 GHz, 3.5 T) electron-electron double resonance (ELDOR)-detected NMR as a method to obtain the (14)N P(zz) value directly, together with A(zz). This is complemented by W-band hyperfine sublevel correlation (HYSCORE) measurements carried out along the g(xx) direction to determine the principal P(xx) and P(yy) components. Through measurements of TEMPOL dissolved in solvents of different polarities, we show that A(zz) increases, while |P(zz)| decreases with polarity, as predicted by Savitsky et al.

  13. Determination of the 14N quadrupole coupling constant of nitroxide spin probes by W-band ELDOR-detected NMR

    NASA Astrophysics Data System (ADS)

    Florent, Marc; Kaminker, Ilia; Nagarajan, Vijayasarathi; Goldfarb, Daniella

    2011-06-01

    Nitroxide spin probe electron paramagnetic resonance (EPR) has proven to be a very successful method to probe local polarity and solvent hydrogen bonding properties at the molecular level. The g xx and the 14N hyperfine A zz principal values are the EPR parameters of the nitroxide spin probe that are sensitive to these properties and are therefore monitored experimentally. Recently, the 14N quadrupole interaction of nitroxides has been shown to be also highly sensitive to polarity and H-bonding (A. Savitsky et al., J. Phys. Chem. B 112 (2008) 9079). High-field electron spin echo envelope modulation (ESEEM) was used successfully to determine the P xx and P yy principal components of the 14N quadrupole tensor. The P zz value was calculated from the traceless character of the quadrupole tensor. We introduce here high-field (W-band, 95 GHz, 3.5 T) electron-electron double resonance (ELDOR)-detected NMR as a method to obtain the 14N P zz value directly, together with A zz. This is complemented by W-band hyperfine sublevel correlation (HYSCORE) measurements carried out along the g xx direction to determine the principal P xx and P yy components. Through measurements of TEMPOL dissolved in solvents of different polarities, we show that A zz increases, while | P zz| decreases with polarity, as predicted by Savitsky et al.

  14. Probing spin ordering in iron-platinum based antiferromagnetic films using neutron diffraction

    NASA Astrophysics Data System (ADS)

    Mani, Prakash

    The antiferromagnetic properties of chemically ordered and epitaxial films of FexPt100-x grown on MgO(111) & MgO(100) and Fe50Pt50- xRhx grown on MgO(100) have been studied with neutron diffraction. Epitaxial films of FexPt 100-x (x = 25, 30) have two kinds of antiferromagnetic ordering. The Neel temperature of spin wave vector QA = (1/2 1/2 0) is T N = 160 K and QB = (1/2 0 0) is TN = 100 K, respectively. Neutron diffraction is used to determine the phase diagram of the antiferromagnetic ordering as a function of composition and temperature. The nature of antiferromagnetic ordering was found to be strongly related to the lattice strain present in the system. Lattice-matched antiferromagnetic/ferromagnetic films offer an ideal layered system to study exchange bias. The loop shifts in FePt3(AF)/CoPt 3(F) multilayers are correlated with rocking curve peak widths, and it has been shown that films with a narrower full-width-half-maximum have a smaller exchange bias. Neutron reflectivity is also applied to CoPt 3/FePt3 multilayers in order to probe layer-specific magnetizations owing to the significant difference in neutron scattering length density between Fe and Co. Fe50Pt50-xRh x (x˜10) exhibits a temperature dependent antiferromagnetic-ferromagnetic-paramagnetic triple point near 400 K. The temperature and composition dependent spin structure of Fe50Pt 50-xRhx alloy films grown on MgO(100) have been determined for the first time with neutron diffraction. Three types of antiferromagnetic orderings were observed: (0 0 1/2), (1/2 1/2 1/2), and (1/2 1/2 3/2). Future studies have been planned to explore a magnetic field induced antiferromagnetic to ferromagnetic transition in Fe50Pt50-xRh x alloy films.

  15. Method for replicating an array of nucleic acid probes

    DOEpatents

    Cantor, C.R.; Przetakiewicz, M.; Smith, C.L.; Sano, T.

    1998-08-18

    The invention relates to the replication of probe arrays and methods for replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5{prime}- and/or 3{prime}-overhangs. 16 figs.

  16. Method for replicating an array of nucleic acid probes

    DOEpatents

    Cantor, Charles R.; Przetakiewicz, Marek; Smith, Cassandra L.; Sano, Takeshi

    1998-01-01

    The invention relates to the replication of probe arrays and methods for replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5'- and/or 3'-overhangs.

  17. Development of a magic-angle spinning nuclear magnetic resonance probe with a cryogenic detection system for sensitivity enhancement.

    PubMed

    Mizuno, Takashi; Hioka, Katsuya; Fujioka, Koji; Takegoshi, K

    2008-04-01

    A novel nuclear magnetic resonance (NMR) probe for high-resolution solid-state NMR has been developed. In this probe, temperature of the detection coil is kept at cryogenic temperature (approximately 12 K) for sensitivity enhancement, which is achieved not only by suppression of thermal noise but also by increment of a Q factor of the coil. A marked feature of this probe is that a sample rotating at magic angle is thermally isolated from the cryogenic system in order to realize high-resolution solid-state NMR measurement at various sample temperatures. We call this system as cryocoil magic-angle spinning (cryocoil MAS). (1)H MAS NMR with the coil temperature of approximately 20 K was successfully observed for solid adamantane rotating at room temperature, and signal-to-noise increment due to this cryocoil approach was confirmed.

  18. Sensitive determination of nucleic acids using organic nanoparticle fluorescence probes

    NASA Astrophysics Data System (ADS)

    Zhou, Yunyou; Bian, Guirong; Wang, Leyu; Dong, Ling; Wang, Lun; Kan, Jian

    2005-06-01

    This paper describes the preparation of organic nanoparticles by reprecipitation method under sonication and vigorous stirring. Transmission electron microscopy (TEM) was used to characterize the size and size distribution of the luminescent nanoparticles. Their average diameter was about 25 nm with a size variation of ±18%. The fluorescence decay lifetime of the nanoparticles also was determined on a self-equipped fluorospectrometer with laser light source. The lifetime (˜0.09 μs) of nanoparticles is about three times long as that of the monomer. The nanoparticles were in abundant of hydrophilic groups, which increased their miscibility in aqueous solution. These organic nanoparticles have high photochemical stability, excellent resistance to chemical degradation and photodegradation, and a good fluorescence quantum yield (25%). The fluorescence can be efficiently quenched by nucleic acids. Based on the fluorescence quenching of nanoparticles, a fluorescence quenching method was developed for determination of microamounts of nucleic acids by using the nanoparticles as a new fluorescent probe. Under optimal conditions, maximum fluorescence quenching is produced, with maximum excitation and emission wavelengths of 345 and 402 nm, respectively. Under optimal conditions, the calibration graphs are linear over the range 0.4-19.0 μg ml -1 for calf thymus DNA (ct-DNA) and 0.3-19.0 μg ml -1 for fish sperm DNA (fs-DNA). The corresponding detection limits are 0.25 μg ml -1 for ct-DNA and 0.17 μg ml -1 for fs-DNA. The relative standard deviation of six replicate measurements is 1.3-2.1%. The method is simple, rapid and sensitive with wide linear range. The recovery and relative standard deviation are very satisfactory.

  19. Coherent ultrafast spin-dynamics probed in three dimensional topological insulators

    PubMed Central

    Boschini, F.; Mansurova, M.; Mussler, G.; Kampmeier, J.; Grützmacher, D.; Braun, L.; Katmis, F.; Moodera, J. S.; Dallera, C.; Carpene, E.; Franz, C.; Czerner, M.; Heiliger, C.; Kampfrath, T.; Münzenberg, M.

    2015-01-01

    Topological insulators are candidates to open up a novel route in spin based electronics. Different to traditional ferromagnetic materials, where the carrier spin-polarization and magnetization are based on the exchange interaction, the spin properties in topological insulators are based on the coupling of spin- and orbit interaction connected to its momentum. Specific ways to control the spin-polarization with light have been demonstrated: the energy momentum landscape of the Dirac cone provides spin-momentum locking of the charge current and its spin. We investigate a spin-related signal present only during the laser excitation studying real and imaginary part of the complex Kerr angle by disentangling spin and lattice contributions. This coherent signal is only present at the time of the pump-pulses’ light field and can be described in terms of a Raman coherence time. The Raman transition involves states at the bottom edge of the conduction band. We demonstrate a coherent femtosecond control of spin-polarization for electronic states at around the Dirac cone. PMID:26510509

  20. Probing the Influence of Thermal Spin Torque on Magnetic Tunnel Junction Switching

    NASA Astrophysics Data System (ADS)

    Phung, Timothy; Pushp, Aakash; Rettner, Charles; Hughes, Brian; Yang, See-Hun; Parkin, Stuart

    2013-03-01

    It has been established in the past few years that heat flow within a ferromagnet can induce a spin current and an associated voltage. This so called Spin Seebeck effect, initially reported in ferromagnetic metals, has also been observed in magnetic semiconductors, magnetic insulators as well as in strongly spin orbit coupled systems. An open question has been whether heat induced spin currents can be used in switching a magnetic tunnel junction (MTJ) via thermal spin torque (TST). In order to answer this question, we investigate the MTJ switching with TST induced by sharp temperature gradients on the order of 1-10 K/nm. We will describe our experimental setup and present data that show the various roles that temperature plays on the saturation magnetization of the material and on the induced spin currents that influence MTJ switching.

  1. A Nucleic Acid Probe and Method for the Detection of Shigella and Enteroinvasive E. coli Bacteria.

    DTIC Science & Technology

    This invention relates to nucleic acid probes and a method for the rapid detection of Shigella and enteroinvasive Escherichia coli, the causative agents of bacterial dysentery, by use of a nucleic acid hybridization probe, equivalent to a plasmid DNA region encoding one of 4 specific invasion-associated, peptides of all strains of Shigella and enterinvasive E . coli , in a nucleic acid hybridization reaction with a clinical specimen containing dysentery bacteria.

  2. Permeability studies of redox-sensitive nitroxyl spin probes in corn oil using an L-band ESR spectrometer

    NASA Astrophysics Data System (ADS)

    Jebaraj, D. David; Utsumi, Hideo; Asath, R. Mohamed; Benial, A. Milton Franklin

    2016-05-01

    Electron spin resonance (ESR) studies were carried out for 2mM 14N labeled 2H enriched 3-methoxycarbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl (MC-PROXYL) and 3-carboxy-2,2,5,5,-tetramethyl-1-pyrrolidinyloxy (carboxy-PROXYL) in pure water and various concentrations of corn oil. The ESR parameters, such as the line width, hyperfine coupling constant, g-factor, rotational correlation time, partition parameter and permeability were reported for the samples. The line width broadening was observed for both nitroxyl radicals in corn oil solutions. The partition parameter for permeable MC-PROXYL in corn oil increases with increasing concentration of corn oil, which reveals that the nitroxyl spin probe permeates into the oil phase. From the results, the corn oil concentration was optimized as 50 % for phantom studies. The rotational correlation time also increases with increasing concentration of corn oil. The permeable and impermeable nature of nitroxyl spin probes was demonstrated. These results will be useful for the development of ESR/OMR imaging modalities in in vivo and in vitro studies.

  3. Probing multiferroicity and spin-spin interactions via angular dependent dielectric measurements on Y-doped HoMnO3 in high magnetic fields

    NASA Astrophysics Data System (ADS)

    Vasic, R.; Zhou, H. D.; Brooks, J. S.; Wiebe, C. R.

    2007-05-01

    Dielectric measurements are used to characterize magnetic phase transitions in the doped ferroelectric oxides Ho1-xYxMnO3 (x=0.4). The focus of this experiment is on the effects of the magnetic field direction on the reentrant T-B-θ phase diagram below the Néel temperature. The Ho sublattice plays a major role in all magnetic phase transitions for Y doping (x =0.4), consistent with previous results (x=0,0.6,0.8). Two successive Mn spin rotations in the ab plane in the antiferromagnetic state are driven by the interaction with the Ho subsystem, although the Ho ordering peak in data is not pronounced. The dielectric response is a very sensitive probe for fine analysis of all aspects of spin-spin interactions in diluted Ho1-xYxMnO3. The magnetic field anisotropy study is an important step towards the understanding of magnetic and electric phase competition in the diluted 4f system by the nonmagnetic yttrium (Y) ion.

  4. Probing ultrafast spin dynamics through a magnon resonance in the antiferromagnetic multiferroic HoMnO3

    SciTech Connect

    Bowlan, P.; Trugman, S. A.; Bowlan, J.; Zhu, J. -X.; Hur, N. J.; Taylor, A. J.; Yarotski, D. A.; Prasankumar, R. P.

    2016-09-26

    Here, we demonstrate an approach for directly tracking antiferromagnetic (AFM) spin dynamics by measuring ultrafast changes in a magnon resonance. We also test this idea on the multiferroic HoMnO 3 by optically photoexciting electrons, after which changes in the spin order are probed with a THz pulse tuned to a magnon resonance. This reveals a photoinduced change in the magnon line shape that builds up over 5–12 picoseconds, which we show to be the spin-lattice thermalization time, indicating that electrons heat the spins via phonons. We compare our results to previous studies of spin-lattice thermalization in ferromagnetic manganites, giving insight into fundamental differences between the two systems. Finally, our work sheds light on the microscopic mechanism governing spin-phonon interactions in AFMs and demonstrates a powerful approach for directly monitoring ultrafast spin dynamics.

  5. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes

    PubMed Central

    Junager, Nina P. L.; Kongsted, Jacob; Astakhova, Kira

    2016-01-01

    Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells. PMID:27472344

  6. Probing the Spin-Polarized Electronic Band Structure in Monolayer Transition Metal Dichalcogenides by Optical Spectroscopy.

    PubMed

    Wang, Zefang; Zhao, Liang; Mak, Kin Fai; Shan, Jie

    2017-02-08

    We study the electronic band structure in the K/K' valleys of the Brillouin zone of monolayer WSe2 and MoSe2 by optical reflection and photoluminescence spectroscopy on dual-gated field-effect devices. Our experiment reveals the distinct spin polarization in the conduction bands of these compounds by a systematic study of the doping dependence of the A and B excitonic resonances. Electrons in the highest-energy valence band and the lowest-energy conduction band have antiparallel spins in monolayer WSe2 and parallel spins in monolayer MoSe2. The spin splitting is determined to be hundreds of meV for the valence bands and tens of meV for the conduction bands, which are in good agreement with first-principles calculations. These values also suggest that both n- and p-type WSe2 and MoSe2 can be relevant for spin- and valley-based applications.

  7. Probing the Spin-Polarized Electronic Band Structure in Monolayer Transition Metal Dichalcogenides by Optical Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wang, Zefang; Zhao, Liang; Mak, Kin Fai; Shan, Jie

    2017-02-01

    We study the electronic band structure in the K/K' valleys of the Brillouin zone of monolayer WSe2 and MoSe2 by optical reflection and photoluminescence spectroscopy on dual-gated field-effect devices. Our experiment reveals the distinct spin polarization in the conduction bands of these compounds by a systematic study of the doping dependence of the A and B excitonic resonances. Electrons in the highest-energy valence band and the lowest-energy conduction band have antiparallel spins in monolayer WSe2, and parallel spins in monolayer MoSe2. The spin splitting is determined to be hundreds of meV for the valence bands and tens of meV for the conduction bands, which are in good agreement with first principles calculations. These values also suggest that both n- and p-type WSe2 and MoSe2 can be relevant for spin- and valley-based applications

  8. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1997-04-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided. 7 figs.

  9. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    1997-01-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided.

  10. Actin-binding cleft closure in myosin II probed by site-directed spin labeling and pulsed EPR.

    PubMed

    Klein, Jennifer C; Burr, Adam R; Svensson, Bengt; Kennedy, Daniel J; Allingham, John; Titus, Margaret A; Rayment, Ivan; Thomas, David D

    2008-09-02

    We present a structurally dynamic model for nucleotide- and actin-induced closure of the actin-binding cleft of myosin, based on site-directed spin labeling and electron paramagnetic resonance (EPR) in Dictyostelium myosin II. The actin-binding cleft is a solvent-filled cavity that extends to the nucleotide-binding pocket and has been predicted to close upon strong actin binding. Single-cysteine labeling sites were engineered to probe mobility and accessibility within the cleft. Addition of ADP and vanadate, which traps the posthydrolysis biochemical state, influenced probe mobility and accessibility slightly, whereas actin binding caused more dramatic changes in accessibility, consistent with cleft closure. We engineered five pairs of cysteine labeling sites to straddle the cleft, each pair having one label on the upper 50-kDa domain and one on the lower 50-kDa domain. Distances between spin-labeled sites were determined from the resulting spin-spin interactions, as measured by continuous wave EPR for distances of 0.7-2 nm or pulsed EPR (double electron-electron resonance) for distances of 1.7-6 nm. Because of the high distance resolution of EPR, at least two distinct structural states of the cleft were resolved. Each of the biochemical states tested (prehydrolysis, posthydrolysis, and rigor), reflects a mixture of these structural states, indicating that the coupling between biochemical and structural states is not rigid. The resulting model is much more dynamic than previously envisioned, with both open and closed conformations of the cleft interconverting, even in the rigor actomyosin complex.

  11. Fluorescence probe for the convenient and sensitive detection of ascorbic acid

    PubMed Central

    Matsuoka, Yuta; Yamato, Mayumi; Yamada, Ken-ichi

    2016-01-01

    Ascorbic acid is an important antioxidant that plays an essential role in the biosynthesis of numerous bioactive substances. The detection of ascorbic acid has traditionally been achieved using high-performance liquid chromatography and absorption spectrophotometry assays. However, the development of fluorescence probes for this purpose is highly desired because they provide a much more convenient and highly sensitive technique for the detection of this material. OFF-ON-type fluorescent probes have been developed for the detection of non-fluorescent compounds. Photo-induced electron transfer and fluorescence resonance energy transfer are the two main fluorescence quenching mechanisms for the detection of ascorbic acid, and several fluorescence probes have been reported based on redox-responsive metals and quantum dots. Profluorescent nitroxide compounds have also been developed as non-metal organic fluorescence probes for ascorbic acid. These nitroxide systems have a stable unpaired electron and can therefore react with ascorbic acid and a strong fluorescence quencher. Furthermore, recent synthetic advances have allowed for the synthesis of α-substituted nitroxides with varying levels of reactivity towards ascorbic acid. In this review, we have discussed the design strategies used for the preparation of fluorescent probes for ascorbic acid, with particular emphasis on profluorescent nitroxides, which are unique radical-based redox-active fluorescent probes. PMID:26798193

  12. Interactive fluorophore and quencher pairs for labeling fluorescent nucleic acid hybridization probes.

    PubMed

    Marras, Salvatore A E

    2008-03-01

    The use of fluorescent nucleic acid hybridization probes that generate a fluorescence signal only when they bind to their target enables real-time monitoring of nucleic acid amplification assays. Real-time nucleic acid amplification assays markedly improves the ability to obtain qualitative and quantitative results. Furthermore, these assays can be carried out in sealed tubes, eliminating carryover contamination. Fluorescent nucleic acid hybridization probes are available in a wide range of different fluorophore and quencher pairs. Multiple hybridization probes, each designed for the detection of a different nucleic acid sequence and each labeled with a differently colored fluorophore, can be added to the same nucleic acid amplification reaction, enabling the development of high-throughput multiplex assays. In order to develop robust, highly sensitive and specific real-time nucleic acid amplification assays it is important to carefully select the fluorophore and quencher labels of hybridization probes. Selection criteria are based on the type of hybridization probe used in the assay, the number of targets to be detected, and the type of apparatus available to perform the assay. This article provides an overview of different aspects of choosing appropriate labels for the different types of fluorescent hybridization probes used with different types of spectrofluorometric thermal cyclers currently available.

  13. Proximity induced room temperature ferromagnetism in graphene probed with spin currents

    NASA Astrophysics Data System (ADS)

    Leutenantsmeyer, Johannes Christian; Kaverzin, Alexey A.; Wojtaszek, Magdalena; van Wees, Bart J.

    2017-03-01

    We present a direct measurement of the exchange interaction in room temperature ferromagnetic graphene. We study the spin transport in exfoliated graphene on an yttrium-iron-garnet substrate where the observed spin precession clearly indicates the presence and strength of an exchange field that is an unambiguous evidence of induced ferromagnetism. We describe the results with a modified Bloch diffusion equation and extract an average exchange field of the order of 0.2 T. Further, we demonstrate that a proximity induced 2D ferromagnet can efficiently modulate a spin current by controlling the direction of the exchange field. These findings can create a building block for magnetic-gate tuneable spin transport in one-atom-thick spintronic devices.

  14. Diradicals acting through diamagnetic phenylene vinylene bridges: Raman spectroscopy as a probe to characterize spin delocalization.

    PubMed

    González, Sandra Rodríguez; Nieto-Ortega, Belén; González Cano, Rafael C; Lloveras, Vega; Novoa, Juan J; Mota, Fernando; Vidal-Gancedo, José; Rovira, Concepció; Veciana, Jaume; del Corro, Elena; Taravillo, Mercedes; Baonza, Valentín G; López Navarrete, Juan T; Casado, Juan

    2014-04-28

    We present a complete Raman spectroscopic study in two structurally well-defined diradical species of different lengths incorporating oligo p-phenylene vinylene bridges between two polychlorinated triphenylmethyl radical units, a disposition that allows sizeable conjugation between the two radicals through and with the bridge. The spectroscopic data are interpreted and supported by quantum chemical calculations. We focus the attention on the Raman frequency changes, interpretable in terms of: (i) bridge length (conjugation length); (ii) bridge conformational structure; and (iii) electronic coupling between the terminal radical units with the bridge and through the bridge, which could delineate through-bond spin polarization, or spin delocalization. These items are addressed by using the "oligomer approach" in conjunction with pressure and temperature dependent Raman spectroscopic data. In summary, we have attempted to translate the well-known strategy to study the electron (charge) structure of π-conjugated molecules by Raman spectroscopy to the case of electron (spin) interactions via the spin delocalization mechanism.

  15. Probing the Nuclear Spin-Lattice Relaxation Time at the Nanoscale

    NASA Astrophysics Data System (ADS)

    Wagenaar, J. J. T.; den Haan, A. M. J.; de Voogd, J. M.; Bossoni, L.; de Jong, T. A.; de Wit, M.; Bastiaans, K. M.; Thoen, D. J.; Endo, A.; Klapwijk, T. M.; Zaanen, J.; Oosterkamp, T. H.

    2016-07-01

    Nuclear spin-lattice relaxation times are measured on copper using magnetic-resonance force microscopy performed at temperatures down to 42 mK. The low temperature is verified by comparison with the Korringa relation. Measuring spin-lattice relaxation times locally at very low temperatures opens up the possibility to measure the magnetic properties of inhomogeneous electron systems realized in oxide interfaces, topological insulators, and other strongly correlated electron systems such as high-Tc superconductors.

  16. Long-Lived Hole Spin/Valley Polarization Probed by Kerr Rotation in Monolayer WSe2.

    PubMed

    Song, Xinlin; Xie, Saien; Kang, Kibum; Park, Jiwoong; Sih, Vanessa

    2016-08-10

    Time-resolved Kerr rotation and photoluminescence measurements are performed on MOCVD-grown monolayer tungsten diselenide (WSe2). We observe a surprisingly long-lived Kerr rotation signal (∼80 ns) at 10 K, which is attributed to spin/valley polarization of the resident holes. This polarization is robust to transverse magnetic field (up to 0.3 T). Wavelength-dependent measurements reveal that only excitation near the free exciton energy generates this long-lived spin/valley polarization.

  17. Probe kit for identifying a base in a nucleic acid

    DOEpatents

    Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

    2001-01-01

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  18. Detection and isolation of nucleic acid sequences using a bifunctional hybridization probe

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    2000-01-01

    A method for detecting and isolating a target sequence in a sample of nucleic acids is provided using a bifunctional hybridization probe capable of hybridizing to the target sequence that includes a detectable marker and a first complexing agent capable of forming a binding pair with a second complexing agent. A kit is also provided for detecting a target sequence in a sample of nucleic acids using a bifunctional hybridization probe according to this method.

  19. Fluorescent macrocyclic probes with pendant functional groups as markers of acidic organelles within live cells.

    PubMed

    Wadhavane, Prashant D; Izquierdo, M Ángeles; Lutters, Dennis; Burguete, M Isabel; Marín, María J; Russell, David A; Galindo, Francisco; Luis, Santiago V

    2014-02-07

    A new family of acidity sensitive fluorescent macrocycles has been synthesized and fully characterized. Their photophysical properties including emission quantum yield and fluorescence lifetime have been determined. The acid-base properties of the new molecules can be tuned by the incorporation of pendant functional groups. The nature of such functional groups (carboxylic acid or ester) influences dramatically the pKa of the probes, two compounds of which exhibit low values. Preliminary intracellular studies using confocal microscopy together with emission spectra of the probes from the cellular environment have shown that the synthesized fluorescent macrocycles mark the acidic organelles of RAW 264.7 macrophage cells.

  20. Application of locked nucleic acid-based probes in fluorescence in situ hybridization.

    PubMed

    Fontenete, Sílvia; Carvalho, Daniel; Guimarães, Nuno; Madureira, Pedro; Figueiredo, Céu; Wengel, Jesper; Azevedo, Nuno Filipe

    2016-07-01

    Fluorescence in situ hybridization (FISH) employing nucleic acid mimics as probes is becoming an emerging molecular tool in the microbiology area for the detection and visualization of microorganisms. However, the impact that locked nucleic acid (LNA) and 2'-O-methyl (2'-OMe) RNA modifications have on the probe that is targeting microorganisms is unknown. In this study, the melting and hybridization efficiency properties of 18 different probes in regards to their use in FISH for the detection of the 16S rRNA of Helicobacter pylori were compared. For the same sequence and target, probe length and the type of nucleic acid mimics used as mixmers in LNA-based probes strongly influence the efficiency of detection. LNA probes with 10 to 15 mers showed the highest efficiency. Additionally, the combination of 2'-OMe RNA with LNA allowed an increase on the fluorescence intensities of the probes. Overall, these results have significant implications for the design and applications of LNA probes for the detection of microorganisms.

  1. Terahertz probes of magnetic field induced spin reorientation in YFeO{sub 3} single crystal

    SciTech Connect

    Lin, Xian; Jiang, Junjie; Ma, Guohong; Jin, Zuanming; Wang, Dongyang; Tian, Zhen; Han, Jiaguang; Cheng, Zhenxiang

    2015-03-02

    Using the terahertz time-domain spectroscopy, we demonstrate the spin reorientation of a canted antiferromagnetic YFeO{sub 3} single crystal, by evaluating the temperature and magnetic field dependence of resonant frequency and amplitude for the quasi-ferromagnetic (FM) and quasi-antiferromagnetic modes (AFM), a deeper insight into the dynamics of spin reorientation in rare-earth orthoferrites is established. Due to the absence of 4f-electrons in Y ion, the spin reorientation of Fe sublattices can only be induced by the applied magnetic field, rather than temperature. In agreement with the theoretical predication, the frequency of FM mode decreases with magnetic field. In addition, an obvious step of spin reorientation phase transition occurs with a relatively large applied magnetic field of 4 T. By comparison with the family members of RFeO{sub 3} (R = Y{sup 3+} or rare-earth ions), our results suggest that the chosen of R would tailor the dynamical rotation properties of Fe ions, leading to the designable spin switching in the orthoferrite antiferromagnetic systems.

  2. Spin-wave thermal population as temperature probe in magnetic tunnel junctions

    NASA Astrophysics Data System (ADS)

    Le Goff, A.; Nikitin, V.; Devolder, T.

    2016-07-01

    We study whether a direct measurement of the absolute temperature of a Magnetic Tunnel Junction (MTJ) can be performed using the high frequency electrical noise that it delivers under a finite voltage bias. Our method includes quasi-static hysteresis loop measurements of the MTJ, together with the field-dependence of its spin wave noise spectra. We rely on an analytical modeling of the spectra by assuming independent fluctuations of the different sub-systems of the tunnel junction that are described as macrospin fluctuators. We illustrate our method on perpendicularly magnetized MgO-based MTJs patterned in 50 × 100 nm2 nanopillars. We apply hard axis (in-plane) fields to let the magnetic thermal fluctuations yield finite conductance fluctuations of the MTJ. Instead of the free layer fluctuations that are observed to be affected by both spin-torque and temperature, we use the magnetization fluctuations of the sole reference layers. Their much stronger anisotropy and their much heavier damping render them essentially immune to spin-torque. We illustrate our method by determining current-induced heating of the perpendicularly magnetized tunnel junction at voltages similar to those used in spin-torque memory applications. The absolute temperature can be deduced with a precision of ±60 K, and we can exclude any substantial heating at the spin-torque switching voltage.

  3. Probing the population of the spin-orbit split levels in the actinide 5f states.

    PubMed

    Moore, K T; van der Laan, G; Tobin, J G; Chung, B W; Wall, M A; Schwartz, A J

    2006-03-01

    Spin-orbit interaction in the 5f states is believed to strongly influence exotic behaviors observed in actinide metals and compounds. Understanding these interactions and how they relate to the actinide series is of considerable importance. To address this issue, the branching ratio of the white-line peaks of the N4,5 edge for the light actinide metals, alpha-Th, alpha-U, and alpha-Pu were recorded using electron energy-loss spectroscopy (EELS) in a transmission electron microscope (TEM) and synchrotron-radiation-based X-ray absorption spectroscopy (XAS). Using the spin-orbit sum rule and the branching ratios from both experimental spectra and many-electron atomic spectral calculations, accurate values of the spin-orbit interaction, and thus the relative occupation of the j = 5/2 and 7/2 levels, are determined for the actinide 5f states. Results show that the spin-orbit sum rule works very well with both EELS and XAS spectra, needing little or no correction. This is important, since the high spatial resolution of a TEM can be used to overcome the problems of single-crystal growth often encountered with actinide metals, allowing acquisition of EELS spectra, and subsequent spin-orbit analysis, from nm-sized regions. The relative occupation numbers obtained by our method have been compared with recent theoretical results and they show a good agreement in their trend.

  4. Collective Nature of Spin Excitations in Superconducting Cuprates Probed by Resonant Inelastic X-Ray Scattering

    NASA Astrophysics Data System (ADS)

    Minola, M.; Dellea, G.; Gretarsson, H.; Peng, Y. Y.; Lu, Y.; Porras, J.; Loew, T.; Yakhou, F.; Brookes, N. B.; Huang, Y. B.; Pelliciari, J.; Schmitt, T.; Ghiringhelli, G.; Keimer, B.; Braicovich, L.; Le Tacon, M.

    2015-05-01

    We used resonant inelastic x-ray scattering (RIXS) with and without analysis of the scattered photon polarization, to study dispersive spin excitations in the high temperature superconductor YBa2Cu3O6 +x over a wide range of doping levels (0.1 ≤x ≤1 ). The excitation profiles were carefully monitored as the incident photon energy was detuned from the resonant condition, and the spin excitation energy was found to be independent of detuning for all x . These findings demonstrate that the largest fraction of the spin-flip RIXS profiles in doped cuprates arises from magnetic collective modes, rather than from incoherent particle-hole excitations as recently suggested theoretically [Benjamin et al. Phys. Rev. Lett. 112, 247002 (2014)]. Implications for the theoretical description of the electron system in the cuprates are discussed.

  5. Transient gain-versus-absorption laser probing of spin-orbit states, kinetics and dynamics

    NASA Technical Reports Server (NTRS)

    Smedley, John E.; Hess, Wayne P.; Haugen, Harold K.; Leone, Stephen R.

    1986-01-01

    The spin-orbit populations of excited (2P1/2) and ground (2P3/2) state Br atoms at 2714 nm and I atoms at 1315 nm are examined using a tunable F-center laser and a diode laser. The transient laser gain-versus-absorption measurements are utilized to estimate quantum yields of the spin-orbit states in the photodissociation of Br- and I-containing compounds; the continuum yields for Br2 are investigated in terms of temperature. The collisional release, Doppler velocity effects, and differing reactivity of the spin-orbit excited and ground state atoms are studied. It is noted that the transient gain versus absorption technique is applicable to the analysis of kinetic phenomena due to its high sensitivity and excellent time resolution.

  6. Measurement of the proton $A_1$ and $A_2$ spin asymmetries. Probing Color Forces

    SciTech Connect

    Armstrong, Whitney

    2015-05-01

    The Spin Asymmetries of the Nucleon Experiment (SANE) measured the proton spin structure function $g_2$ in a range of Bjorken x, 0.3 < x < 0.8, where extraction of the twist-3 matrix element $d_2^p$ (an integral of $g_2$ weighted by $x^2$) is most sensitive. The data was taken from $Q^2$ equal to 2.5 $GeV^2$ up to 6.5 $GeV^2$. In this polarized electron scattering off a polarized hydrogen target experiment, two double spin asymmetries, A∥ and A⊥ were measured using the BETA (Big Electron Telescope Array) Detector. BETA consisted of a scintillator hodoscope, gas Cerenkov counter, lucite hodoscope and a large lead glass electromagnetic calorimeter. With a unique open geometry, a threshold gas Cerenkov detector allowed BETA to cleanly identify electrons for this inclusive experiment. A measurement of $d_2^p$ is compared to lattice QCD calculations.

  7. Methods of staining target chromosomal DNA employing high complexity nucleic acid probes

    DOEpatents

    Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Ol'li-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

    2006-10-03

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

  8. Genetic Incorporation of the Unnatural Amino Acid p-Acetyl Phenylalanine into Proteins for Site-Directed Spin Labeling

    PubMed Central

    Evans, Eric G.B.; Millhauser, Glenn L.

    2016-01-01

    Site-directed spin labeling (SDSL) is a powerful tool for the characterization of protein structure and dynamics; however, its application in many systems is hampered by the reliance on unique and benign cysteine substitutions for the site-specific attachment of the spin label. An elegant solution to this problem involves the use of genetically encoded unnatural amino acids (UAAs) containing reactive functional groups that are chemically orthogonal to those of the 20 amino acids found naturally in proteins. These unique functional groups can then be selectively reacted with an appropriately functionalized spin probe. In this chapter, we detail the genetic incorporation of the ketone-bearing amino acid p-acetyl phenylalanine (pAcPhe) into recombinant proteins expressed in E. coli. Incorporation of pAcPhe is followed by chemoselective reaction of the ketone side chain with a hydroxylamine-functionalized nitroxide to afford the spin-labeled side chain “K1,” and we present two protocols for successful K1 labeling of proteins bearing site-specific pAcPhe. We outline the basic requirements for pAcPhe incorporation and labeling, with an emphasis on practical aspects that must be considered by the researcher if high yields of UAA incorporation and efficient labeling reactions are to be achieved. To this end, we highlight recent advances that have led to increased yields of pAcPhe incorporation, and discuss the use of aniline-based catalysts allowing for facile conjugation of the hydroxylamine spin label under mild reaction conditions. To illustrate the utility of K1 labeling in proteins where traditional cysteine-based SDSL methods are problematic, we site-specifically K1 label the cellular prion protein at two positions in the C-terminal domain and determine the interspin distance using double electron–electron resonance EPR. Recent advances in UAA incorporation and ketone-based bioconjugation, in combination with the commercial availability of all requisite

  9. Freezing of Molecular Motions Probed by Cryogenic Magic Angle Spinning NMR.

    PubMed

    Concistrè, Maria; Carignani, Elisa; Borsacchi, Silvia; Johannessen, Ole G; Mennucci, Benedetta; Yang, Yifeng; Geppi, Marco; Levitt, Malcolm H

    2014-02-06

    Cryogenic magic angle spinning makes it possible to obtain the NMR spectra of solids at temperatures low enough to freeze out most molecular motions. We have applied cryogenic magic angle spinning NMR to a crystalline small-molecule solid (ibuprofen sodium salt), which displays a variety of molecular dynamics. Magic angle (13)C NMR spectra are shown for a wide range of temperatures, including in the cryogenic regime down to 20 K. The hydrophobic and hydrophilic regions of the molecular structure display different behavior in the cryogenic regime, with the hydrophilic region remaining well-structured, while the hydrophobic region exhibits a broad frozen conformational distribution.

  10. Time-resolved detection probe for homogeneous nucleic acid analyses in one-step format.

    PubMed

    Laitala, Ville; Ylikoski, Alice; Raussi, Hanna-Mari; Ollikka, Pia; Hemmilä, Ilkka

    2007-02-01

    We report here an extension of homogeneous assays based on fluorescence intensity and lifetime measuring on DNA hybridization. A novel decay probe that allows simple one-step nucleic acid detection with subnanomolar sensitivity, and is suitable for closed-tube applications, is introduced. The decay probe uses fluorescence resonance energy transfer (FRET) between a europium chelate donor and an organic fluorophore acceptor. The substantial change in the acceptor emission decay time on hybridization with the target sequence allows the direct separation of the hybridized and unhybridized probe populations in a time-resolved measurement. No additional sample manipulation or self-hybridization of the probes is required. The wavelength and decay time of a decay probe can be adjusted according to the selection of probe length and acceptor fluorophore, thereby making the probes applicable to multiplexed assays. Here we demonstrate the decay probe principle and decay probe-based, one-step, dual DNA assay using celiac disease-related target oligonucleotides (single-nucleotide polymorphisms [SNPs]) as model analytes. Decay probes showed specific response for their complementary DNA target and allowed good signal deconvolution based on simultaneous optical and temporal filtering. This technique potentially could be used to further increase the number of simultaneously detected DNA targets in a simple one-step homogeneous assay.

  11. Diradicals acting through diamagnetic phenylene vinylene bridges: Raman spectroscopy as a probe to characterize spin delocalization

    SciTech Connect

    González, Sandra Rodríguez; Nieto-Ortega, Belén; González Cano, Rafael C.; López Navarrete, Juan T. E-mail: teodomiro@uma.es Casado, Juan E-mail: teodomiro@uma.es; Novoa, Juan J.; Mota, Fernando; Corro, Elena del; Taravillo, Mercedes; Baonza, Valentín G.

    2014-04-28

    We present a complete Raman spectroscopic study in two structurally well-defined diradical species of different lengths incorporating oligo p-phenylene vinylene bridges between two polychlorinated triphenylmethyl radical units, a disposition that allows sizeable conjugation between the two radicals through and with the bridge. The spectroscopic data are interpreted and supported by quantum chemical calculations. We focus the attention on the Raman frequency changes, interpretable in terms of: (i) bridge length (conjugation length); (ii) bridge conformational structure; and (iii) electronic coupling between the terminal radical units with the bridge and through the bridge, which could delineate through-bond spin polarization, or spin delocalization. These items are addressed by using the “oligomer approach” in conjunction with pressure and temperature dependent Raman spectroscopic data. In summary, we have attempted to translate the well-known strategy to study the electron (charge) structure of π−conjugated molecules by Raman spectroscopy to the case of electron (spin) interactions via the spin delocalization mechanism.

  12. Spin-polarized photoelectron diffraction: A new probe of short-range magnetic order (invited) (abstract)

    NASA Astrophysics Data System (ADS)

    Fadley, C. S.; Sinkovic, B.; Hermsmeier, B. D.; Osterwalder, J.

    1988-04-01

    It has recently been pointed out theoretically and subsequently observed experimentally that core-level multiplet splittings can be used to yield a spin-polarized form of photoelectron diffraction (SPPD). This internally referenced source of electrons that are highly polarized with both orientations of spin thus eliminates the need for an external spin detector, permits studying both ferromagnetic and antiferromagnetic specimens, and can, in principle, detect short-range magnetic or for temperatures above the Curie or Néel temperature. In the first measurements of this type on the antiferromagnet KMnF3, an abrupt loss of short-range order at a transition temperature considerably above the bulk Néel temperature of the material was observed. More recent theoretical diffraction calculations have pointed out several ways in which SPPD should permit deriving unique information on short-range spin-order structures at and near the surfaces of magnetic materials. New experimental results have also been obtained for the antiferromagnet MnO. This paper will discuss these new developments, will review the advantages and disadvantages of SPPD, and also will consider some interesting future directions of investigation.

  13. Membrane-Sugar Interactions Probed by Pulsed Electron Paramagnetic Resonance of Spin Labels.

    PubMed

    Konov, Konstantin B; Leonov, Dmitry V; Isaev, Nikolay P; Fedotov, Kirill Yu; Voronkova, Violeta K; Dzuba, Sergei A

    2015-08-13

    Sugars can stabilize biological systems under extreme desiccation and freezing conditions. Hypothetical molecular mechanisms suggest that the stabilization effect may be determined either by specific interactions of sugars with biological molecules or by the influence of sugars on the solvating shell of the biomolecule. To explore membrane-sugar interactions, we applied electron spin echo envelope modulation (ESEEM) spectroscopy, a pulsed version of electron paramagnetic resonance (EPR), to phospholipid bilayers with spin-labeled lipids added and solvated by aqueous deuterated sucrose and trehalose solutions. The phospholipids were 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). The spin-labeled lipids were 1,2-dipalmitoyl-sn-glycero-3-phospho(TEMPO)choline (T-PCSL), with spin-label TEMPO at the lipid polar headgroup. The deuterium ESEEM amplitude was calibrated using known concentrations of glassy deuterated sugar solvents. The data obtained indicated that the sugar concentration near the membrane surface obeyed a simple Langmuir model of monolayer adsorption, which assumes direct sugar-molecule bonding to the bilayer surface.

  14. Terbium fluorescence as a sensitive, inexpensive probe for UV-induced damage in nucleic acids.

    PubMed

    El-Yazbi, Amira F; Loppnow, Glen R

    2013-07-05

    Much effort has been focused on developing methods for detecting damaged nucleic acids. However, almost all of the proposed methods consist of multi-step procedures, are limited, require expensive instruments, or suffer from a high level of interferences. In this paper, we present a novel simple, inexpensive, mix-and-read assay that is generally applicable to nucleic acid damage and uses the enhanced luminescence due to energy transfer from nucleic acids to terbium(III) (Tb(3+)). Single-stranded oligonucleotides greatly enhance the Tb(3+) emission, but duplex DNA does not. With the use of a DNA hairpin probe complementary to the oligonucleotide of interest, the Tb(3+)/hairpin probe is applied to detect ultraviolet (UV)-induced DNA damage. The hairpin probe hybridizes only with the undamaged DNA. However, the damaged DNA remains single-stranded and enhances the intrinsic fluorescence of Tb(3+), producing a detectable signal directly proportional to the amount of DNA damage. This allows the Tb(3+)/hairpin probe to be used for sensitive quantification of UV-induced DNA damage. The Tb(3+)/hairpin probe showed superior selectivity to DNA damage compared to conventional molecular beacons probes (MBs) and its sensitivity is more than 2.5 times higher than MBs with a limit of detection of 4.36±1.2 nM. In addition, this probe is easier to synthesize and more than eight times cheaper than MBs, which makes its use recommended for high-throughput, quantitative analysis of DNA damage.

  15. A novel acidic pH fluorescent probe based on a benzothiazole derivative.

    PubMed

    Ma, Qiujuan; Li, Xian; Feng, Suxiang; Liang, Beibei; Zhou, Tiqiang; Xu, Min; Ma, Zhuoyi

    2017-04-15

    A novel acidic pH fluorescent probe 1 based on a benzothiazole derivative has been designed, synthesized and developed. The linear response range covers the acidic pH range from 3.44 to 6.46, which is valuable for pH researches in acidic environment. The evaluated pKa value of the probe 1 is 4.23. The fluorescence enhancement of the studied probe 1 with an increase in hydrogen ions concentration is based on the hindering of enhanced photo-induced electron transfer (PET) process. Moreover, the pH sensor possesses a highly selective response to H(+) in the presence of metal ions, anions and other bioactive small molecules which would be interfere with its fluorescent pH response. Furthermore, the probe 1 responds to acidic pH with short response time that was less than 1min. The probe 1 has been successfully applied to confocal fluorescence imaging in live HeLa cells and can selectively stain lysosomes. All of such good properties prove it can be used to monitoring pH fluctuations in acidic environment with high sensitivity, pH dependence and short response time.

  16. A novel acidic pH fluorescent probe based on a benzothiazole derivative

    NASA Astrophysics Data System (ADS)

    Ma, Qiujuan; Li, Xian; Feng, Suxiang; Liang, Beibei; Zhou, Tiqiang; Xu, Min; Ma, Zhuoyi

    2017-04-01

    A novel acidic pH fluorescent probe 1 based on a benzothiazole derivative has been designed, synthesized and developed. The linear response range covers the acidic pH range from 3.44 to 6.46, which is valuable for pH researches in acidic environment. The evaluated pKa value of the probe 1 is 4.23. The fluorescence enhancement of the studied probe 1 with an increase in hydrogen ions concentration is based on the hindering of enhanced photo-induced electron transfer (PET) process. Moreover, the pH sensor possesses a highly selective response to H+ in the presence of metal ions, anions and other bioactive small molecules which would be interfere with its fluorescent pH response. Furthermore, the probe 1 responds to acidic pH with short response time that was less than 1 min. The probe 1 has been successfully applied to confocal fluorescence imaging in live HeLa cells and can selectively stain lysosomes. All of such good properties prove it can be used to monitoring pH fluctuations in acidic environment with high sensitivity, pH dependence and short response time.

  17. Probing Spin Frustration in High-symmetry Magnetic Nanomolecules by Inelastic Neutron Scattering

    SciTech Connect

    Garlea, Vasile O; Nagler, Stephen E; Zarestky, Jerel L; Stassis, C.; Vaknin, D.; Kogerler, P.; McMorrow, D. F.; Niedermayer, C.; Tennant, D. A.; Lake, B.; Qiu, Y.; Exler, M.; Schnack, J.; Luban, M.

    2006-01-01

    Low temperature inelastic neutron scattering studies have been performed to characterize the low energy magnetic excitation spectrum of the magnetic nanomolecule {l_brace}Mo{sub 72}Fe{sub 30}{r_brace}. This unique highly symmetric cluster features spin frustration and is one of the largest discrete magnetic molecules studied to date by inelastic neutron scattering. The 30 s=5/2 Fe{sup III} ions, embedded in a spherical polyoxomolybdate molecule, occupy the vertices of an icosidodecahedron and are coupled via nearest-neighbor antiferromagnetic interactions. The overall energy scale of the excitation and the gross features of the temperature dependence of the observed neutron scattering are explained by a quantum model of the frustrated spin cluster. However, no satisfactory theoretical explanation is yet available for the observed magnetic field dependence.

  18. Theoretical probing of inelastic spin-excitations in adatoms on surfaces

    NASA Astrophysics Data System (ADS)

    Lounis, Samir; Schweflinghaus, Benedikt; Dias, Manuel dos Santos; Bouhassoune, Mohammed; Muniz, Roberto B.; Costa, Antonio T.

    2014-12-01

    We review our recent work on the simulation, description and prediction of spin-excitations in adatoms and dimers deposited on metallic surfaces. This work done together with Douglas L. Mills, is an extension of his seminal contribution (with Pascal Lederer) published 50 years ago on the spin-dynamics of transition metal impurities embedded in transition metal hosts [Lederer et al. (1967)]. The main predictions of his model were verified experimentally with state of the art inelastic scanning tunneling spectroscopy on adatoms. Our formalism, presented in this review, is based on time-dependent density functional theory, combined with the Korringa-Kohn-Rostoker Green function method. Comparison to experiments is shown and discussed in detail. Our scheme enables the description and prediction of the main characteristics of these excitations, i.e. their resonance frequency, their lifetime and their behavior upon application of external perturbations such as a magnetic field.

  19. Negative spin polarization of Mn2VGa probed by tunnel magnetoresistance.

    PubMed

    Klewe, Christoph; Meinert, Markus; Schmalhorst, Jan; Reiss, Günter

    2013-02-20

    The ferrimagnetic Heusler compound Mn(2)VGa is predicted to have a pseudogap in the majority spin channel, which should lead to a negative tunnel magnetoresistance (TMR). We synthesized epitaxial Mn(2)VGa thin films on MgO(001) substrates by dc and rf magnetron co-sputtering, resulting in nearly stoichiometric films. XRD analysis revealed a mostly B2 ordered structure for the films deposited at substrate temperatures of 350, 450, and 550 °C. Magnetic tunnel junctions with MgO barriers and CoFe counter-electrodes were fabricated. After post-annealing at up to T(a) = 425 °C negative TMR was obtained around zero bias, providing evidence for inverted spin polarization. The band structures of both electrodes were computed within the coherent potential approximation and used to calculate the TMR(V) characteristics, which were in good agreement with our experimental findings.

  20. Solvent additive effects on small molecule crystallization in bulk heterojunction solar cells probed during spin casting.

    PubMed

    Perez, Louis A; Chou, Kang Wei; Love, John A; van der Poll, Thomas S; Smilgies, Detlef-M; Nguyen, Thuc-Quyen; Kramer, Edward J; Amassian, Aram; Bazan, Guillermo C

    2013-11-26

    Solvent additive processing can lead to drastic improvements in the power conversion efficiency (PCE) in solution processable small molecule (SPSM) bulk heterojunction solar cells. In situ grazing incidence wide-angle X-ray scattering is used to investigate the kinetics of crystallite formation during and shortly after spin casting. The additive is shown to have a complex effect on structural evolution invoking polymorphism and enhanced crystalline quality of the donor SPSM.

  1. Nonlinear susceptibilities as a probe to unambiguously distinguish between canonical and cluster spin glasses

    NASA Astrophysics Data System (ADS)

    Bitla, Yugandhar; Kaul, S. N.; Fernández Barquín, L.

    2012-09-01

    Treating the randomly Fe-substituted optimally hole-doped manganite La0.7Pb0.3(Mn1-yFey)O3 (y=0.2,0.3) as a test case, we demonstrate that a combined investigation of both odd and even harmonics of the ac magnetic response permits an unambiguous distinction between the canonical and cluster spin glasses. As expected for a spin glass (SG), the nonlinear ac magnetic susceptibilities χ3(T,ω) and χ5(T,ω) (odd harmonics) diverge at the SG freezing temperature Tg=80.00(3) K [Tg=56.25(5) K] in the static limit and, like the imaginary part of the linear susceptibility, follow dynamic scaling with the critical exponents β=0.56(3) [β=0.63(3)], γ=1.80(5) [γ=2.0(1)], and zν=10.1(1) [zν=8.0(5)] in the sample with composition y=0.2 (y=0.3). The nonlinear susceptibility χNL, which has contributions from both χ3 and χ5, satisfies static scaling with the same choice of Tg, β, and γ. Irrespective of the Fe concentration, the values of the critical exponents γ, ν, and η are in much better agreement with those theoretically predicted for a three-dimensional (d=3) Heisenberg chiral SG than for a d=3 Ising SG. The true thermodynamic nature of the “zero-field” spin-glass transition is preserved even in finite magnetic fields. Unlike odd harmonics, even harmonics χ2(T,ω) and χ4(T,ω) make it evident that, apart from the macroscopic length scale of the spin-glass order in the static limit, there exists a length scale that corresponds to the short-range ferromagnetic order.

  2. Probing the antiferromagnetic long-range order with Glauber spin states

    NASA Technical Reports Server (NTRS)

    Cabrera, Guillermo G.

    1994-01-01

    It is well known that the ground state of low-dimensional antiferromagnets deviates from Neel states due to strong quantum fluctuations. Even in the presence of long-range order, those fluctuations produce a substantial reduction of the magnetic moment from its saturation value. Numerical simulations in anisotropic antiferromagnetic chains suggest that quantum fluctuations over Neel order appear in the form of localized reversal of pairs of neighboring spins. In this paper, we propose a coherent state representation for the ground state to describe the above situation. In the one-dimensional case, our wave function corresponds to a two-mode Glauber state, when the Neel state is used as a reference, while the boson fields are associated to coherent flip of spin pairs. The coherence manifests itself through the antiferromagnetic long-range order that survives the action of quantum fluctuations. The present representation is different from the standard zero-point spin wave state, and is asymptotically exact in the limit of strong anisotropy. The fermionic version of the theory, obtained through the Jordan-Wigner transformation, is also investigated.

  3. Development of Peptide Nucleic Acid Probes for Detection of the HER2 Oncogene

    PubMed Central

    Song, Young K.; Evangelista, Jennifer; Aschenbach, Konrad; Johansson, Peter; Wen, Xinyu; Chen, Qingrong; Lee, Albert; Hempel, Heidi; Gheeya, Jinesh S.; Getty, Stephanie; Gomez, Romel; Khan, Javed

    2013-01-01

    Peptide nucleic acids (PNAs) have gained much interest as molecular recognition tools in biology, medicine and chemistry. This is due to high hybridization efficiency to complimentary oligonucleotides and stability of the duplexes with RNA or DNA. We have synthesized 15/16-mer PNA probes to detect the HER2 mRNA. The performance of these probes to detect the HER2 target was evaluated by fluorescence imaging and fluorescence bead assays. The PNA probes have sufficiently discriminated between the wild type HER2 target and the mutant target with single base mismatches. Furthermore, the probes exhibited excellent linear concentration dependence between 0.4 to 400 fmol for the target gene. The results demonstrate potential application of PNAs as diagnostic probes with high specificity for quantitative measurements of amplifications or over-expressions of oncogenes. PMID:23593123

  4. Depolarization in reentrant spin glasses: a comparison between neutron and muon probes

    NASA Astrophysics Data System (ADS)

    Mirebeau, I.; Hennion, M.; Gingras, M. J. P.; Keren, A.; Kojima, K.; Larkin, M.; Luke, G. M.; Nachumi, B.; Wu, W. D.; Uemura, Y. J.; Campbell, I. A.; Morris, G. D.

    1997-04-01

    In the amorphous ( Fe1-x Mn_x)75 P16 B_6 Al_3 alloys, muon and neutron depolarization data, combined with the results of small angle neutron scattering, magnetization and Mössbauer spectroscopy, probe the existence of three distinct magnetic transitions at TC, TK and TF (TF < K < C).

  5. On the mutual relationships between spin probe mobility, free volume and relaxation dynamics in organic glass-formers: Glycerol

    NASA Astrophysics Data System (ADS)

    Bartoš, J.; Švajdlenková, H.

    2017-02-01

    The rotation dynamics of the spin probe TEMPO in glycerol from ESR is compared with the ortho-positronium (o-Ps) annihilation from PALS and interpreted using the relaxation dynamics from BDS. Rotation time scale within the slow motion regime exhibits two Arrhenius regions with the characteristic ESR temperature, TX1τ, close to the characteristic PALS temperature, Tb1L, which is related to the secondary β process above Tg. Next, a slow to fast motion regime transition at the characteristic ESR temperature, Tcτ, close to the characteristic PALS temperature, Tb2L, followed by non-Arrhenius fast motion regime region is fully coupled with the primary α process.

  6. Quantum electronics. Probing Johnson noise and ballistic transport in normal metals with a single-spin qubit.

    PubMed

    Kolkowitz, S; Safira, A; High, A A; Devlin, R C; Choi, S; Unterreithmeier, Q P; Patterson, D; Zibrov, A S; Manucharyan, V E; Park, H; Lukin, M D

    2015-03-06

    Thermally induced electrical currents, known as Johnson noise, cause fluctuating electric and magnetic fields in proximity to a conductor. These fluctuations are intrinsically related to the conductivity of the metal. We use single-spin qubits associated with nitrogen-vacancy centers in diamond to probe Johnson noise in the vicinity of conductive silver films. Measurements of polycrystalline silver films over a range of distances (20 to 200 nanometers) and temperatures (10 to 300 kelvin) are consistent with the classically expected behavior of the magnetic fluctuations. However, we find that Johnson noise is markedly suppressed next to single-crystal films, indicative of a substantial deviation from Ohm's law at length scales below the electron mean free path. Our results are consistent with a generalized model that accounts for the ballistic motion of electrons in the metal, indicating that under the appropriate conditions, nearby electrodes may be used for controlling nanoscale optoelectronic, atomic, and solid-state quantum systems.

  7. A Hyperpolarizable 1H Magnetic Resonance Probe for Signal Detection 15 Minutes after Spin Polarization Storage

    PubMed Central

    Roy, Soumya S.; Norcott, Philip; Rayner, Peter J.; Green, Gary G. R.

    2016-01-01

    Abstract Nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) are two extremely important techniques with applications ranging from molecular structure determination to human imaging. However, in many cases the applicability of NMR and MRI are limited by inherently poor sensitivity and insufficient nuclear spin lifetime. Here we demonstrate a cost‐efficient and fast technique that tackles both issues simultaneously. We use the signal amplification by reversible exchange (SABRE) technique to hyperpolarize the target 1H nuclei and store this polarization in long‐lived singlet (LLS) form after suitable radiofrequency (rf) pulses. Compared to the normal scenario, we achieve three orders of signal enhancement and one order of lifetime extension, leading to 1H NMR signal detection 15 minutes after the creation of the detected states. The creation of such hyperpolarized long‐lived polarization reflects an important step forward in the pipeline to see such agents used as clinical probes of disease. PMID:27862799

  8. Probing linker design in citric acid-ciprofloxacin conjugates.

    PubMed

    Milner, Stephen J; Snelling, Anna M; Kerr, Kevin G; Abd-El-Aziz, Ahmad; Thomas, Gavin H; Hubbard, Roderick E; Routledge, Anne; Duhme-Klair, Anne-Kathrin

    2014-08-15

    A series of structurally related citric acid-ciprofloxacin conjugates was synthesised to investigate the influence of the linker between citric acid and ciprofloxacin on antibacterial activities. Minimum inhibitory concentrations (MICs) were determined against a panel of reference strains and clinical isolates of bacteria associated with infection in humans and correlated with the DNA gyrase inhibitory activity. The observed trend was rationalised by computational modelling.

  9. Domain wall spin structures in mesoscopic Fe rings probed by high resolution SEMPA

    NASA Astrophysics Data System (ADS)

    Krautscheid, Pascal; Reeve, Robert M.; Lauf, Maike; Krüger, Benjamin; Kläui, Mathias

    2016-10-01

    We present a combined theoretical and experimental study of the energetic stability and accessibility of different domain wall spin configurations in mesoscopic magnetic iron rings. The evolution is investigated as a function of the width and thickness in a regime of relevance to devices, while Fe is chosen as a material due to its simple growth in combination with attractive magnetic properties including high saturation magnetization and low intrinsic anisotropy. Micromagnetic simulations are performed to predict the lowest energy states of the domain walls, which can be either the transverse or vortex wall spin structure, in good agreement with analytical models, with further simulations revealing the expected low temperature configurations observable on relaxation of the magnetic structure from saturation in an external field. In the latter case, following the domain wall nucleation process, transverse domain walls are found at larger widths and thicknesses than would be expected by just comparing the competing energy terms demonstrating the importance of metastability of the states. The simulations are compared to high spatial resolution experimental images of the magnetization using scanning electron microscopy with polarization analysis to provide a phase diagram of the various spin configurations. In addition to the vortex and simple symmetric transverse domain wall, a significant range of geometries are found to exhibit highly asymmetric transverse domain walls with properties distinct from the symmetric transverse wall. Simulations of the asymmetric walls reveal an evolution of the domain wall tilting angle with ring thickness which can be understood from the thickness dependencies of the contributing energy terms. Analysis of all the data reveals that in addition to the geometry, the influence of materials properties, defects and thermal activation all need to be taken into account in order to understand and reliably control the experimentally accessible

  10. Spin transport in intermediate-energy heavy-ion collisions as a probe of in-medium spin-orbit interactions

    NASA Astrophysics Data System (ADS)

    Xia, Yin; Xu, Jun; Li, Bao-An; Shen, Wen-Qing

    2016-11-01

    The spin up-down splitting of collective flows in intermediate-energy heavy-ion collisions as a result of the nuclear spin-orbit interaction is investigated within a spin- and isospin-dependent Boltzmann-Uehling-Uhlenbeck transport model SIBUU12. Using a Skyrme-type spin-orbit coupling quadratic in momentum, we found that the spin splittings of the directed flow and elliptic flow are largest in peripheral Au+Au collisions at beam energies of about 100-200 MeV/nucleon, and the effect is considerable even in smaller systems especially for nucleons with high transverse momenta. The collective flows of light clusters of different spin states are also investigated using an improved dynamical coalescence model with spin. Our study can be important in understanding the properties of in-medium nuclear spin-orbit interactions once the spin-dependent observables proposed in this work can be measured.

  11. Permeabilization of mycolic-acid-containing actinomycetes for in situ hybridization with fluorescently labelled oligonucleotide probes.

    PubMed

    Macnaughton, S J; O'Donnell, A G; Embley, T M

    1994-10-01

    The application of whole-cell hybridization using labelled oligonucleotide probes in microbial systematics and ecology is limited by difficulties in permeabilizing many Gram-positive organisms. In this investigation paraformaldehyde treatment, acid methanolysis and acid hydrolysis were evaluated as a means of permeabilizing mycolic-acid-containing actinomycetes prior to hybridization with a fluorescently labelled oligonucleotide probe designed to bind to a conserved sequence of bacterial 16S rRNA. Methods were evaluated on stationary-phase cultures of Gordona bronchialis, Mycobacterium fortuitum, Nocardia asteroides, N. brasiliensis, Rhodococcus equi, R. erythropolis, R. fascians, R. rhodochrous and Tsukamurella paurometabola, none of which could be probed following 4% (w/v) paraformaldehyde fixation. For comparison and to test the general applicability of mild acid pretreatments, Bacillus subtilis, Lactobacillus plantarum, Escherichia coli and Pseudomonas putida were also studied. The data showed that most of the mycolic-acid-containing organisms were successfully permeabilized by mild acid hydrolysis in 1 M HCl at 37 degrees C. Cells were treated for different lengths of time. In general, the mycolic-acid-containing organisms required between 30 and 50 min hydrolysis, whereas B. subtilis, E. coli and P. putida were rendered permeable in only 10 min. Interestingly, L. plantarum could not be permeabilized using acid hydrolysis even after 60 min exposure to 1 M HCl.

  12. Hemoglobin magnetism in aqueous solution probed by muon spin relaxation and future applications to brain research.

    PubMed

    Nagamine, Kanetada; Shimomura, Koichiro; Miyadera, Haruo; Kim, Yong-Jae; Scheicher, Ralph Hendrik; Das, Tara Prasad; Schultz, Jerome Samson

    2007-05-01

    A marked difference in spin relaxation behavior due to hemoglobin magnetism was found for positive muons (μ(+)) in deoxyhemoglobin in comparison with that observed in oxyhemoglobin in aqueous solution at room temperature under zero and external longitudinal magnetic fields upto 0.4 Tesla. At the same time, small but significant unique relaxation pattern was observed in nonmagnetic oxyhemoglobin. Combined with our previous measurements on hemoglobin in human blood, application of this type of measurement to the studies of the level of oxygenation in various regions of the human brain is suggested.

  13. Few-second-long correlation times in a quantum dot nuclear spin bath probed by frequency-comb nuclear magnetic resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Waeber, A. M.; Hopkinson, M.; Farrer, I.; Ritchie, D. A.; Nilsson, J.; Stevenson, R. M.; Bennett, A. J.; Shields, A. J.; Burkard, G.; Tartakovskii, A. I.; Skolnick, M. S.; Chekhovich, E. A.

    2016-07-01

    One of the key challenges in spectroscopy is the inhomogeneous broadening that masks the homogeneous spectral lineshape and the underlying coherent dynamics. Techniques such as four-wave mixing and spectral hole-burning are used in optical spectroscopy, and spin-echo in nuclear magnetic resonance (NMR). However, the high-power pulses used in spin-echo and other sequences often create spurious dynamics obscuring the subtle spin correlations important for quantum technologies. Here we develop NMR techniques to probe the correlation times of the fluctuations in a nuclear spin bath of individual quantum dots, using frequency-comb excitation, allowing for the homogeneous NMR lineshapes to be measured without high-power pulses. We find nuclear spin correlation times exceeding one second in self-assembled InGaAs quantum dots--four orders of magnitude longer than in strain-free III-V semiconductors. This observed freezing of the nuclear spin fluctuations suggests ways of designing quantum dot spin qubits with a well-understood, highly stable nuclear spin bath.

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

    PubMed

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

    2013-01-01

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

  15. Development of a polarized 31Mg+ beam as a spin-1/2 probe for BNMR

    NASA Astrophysics Data System (ADS)

    Levy, C. D. P.; Pearson, M. R.; Dehn, M. H.; Karner, V. L.; Kiefl, R. F.; Lassen, J.; Li, R.; MacFarlane, W. A.; McFadden, R. M. L.; Morris, G. D.; Stachura, M.; Teigelhöfer, A.; Voss, A.

    2016-12-01

    A 28 keV beam of 31Mg+ ions was extracted from a uranium carbide, proton-beam-irradiated target coupled to a laser ion source. The ion beam was nuclear-spin polarized by collinear optical pumping on the 2it {S}_{1/2}-2it {P}_{1/2} transition at 280 nm. The polarization was preserved by an extended 1 mT guide field as the beam was transported via electrostatic bends into a 2.5 T longitudinal magnetic field. There the beam was implanted into a single crystal MgO target and the beta decay asymmetry was measured. Both hyperfine ground states were optically pumped with a single frequency light source, using segmentation of the beam energy, which boosted the polarization by approximately 50 % compared to pumping a single ground state. The total decay asymmetry of 0.06 and beam intensity were sufficient to provide a useful spin-1/2 beam for future BNMR experiments. A variant of the method was used previously to optically pump the full Doppler-broadened absorption profile of a beam of 11Be+ with a single-frequency light source.

  16. Unconventional superconductivity in Y5Rh6Sn18 probed by muon spin relaxation.

    PubMed

    Bhattacharyya, Amitava; Adroja, Devashibhai; Kase, Naoki; Hillier, Adrian; Akimitsu, Jun; Strydom, Andre

    2015-08-19

    Conventional superconductors are robust diamagnets that expel magnetic fields through the Meissner effect. It would therefore be unexpected if a superconducting ground state would support spontaneous magnetics fields. Such broken time-reversal symmetry states have been suggested for the high-temperature superconductors, but their identification remains experimentally controversial. We present magnetization, heat capacity, zero field and transverse field muon spin relaxation experiments on the recently discovered caged type superconductor Y5Rh6Sn18 ( TC= 3.0 K). The electronic heat capacity of Y5Rh6Sn18 shows a T(3) dependence below Tc indicating an anisotropic superconducting gap with a point node. This result is in sharp contrast to that observed in the isostructural Lu5Rh6Sn18 which is a strong coupling s-wave superconductor. The temperature dependence of the deduced superfluid in density Y5Rh6Sn18 is consistent with a BCS s-wave gap function, while the zero-field muon spin relaxation measurements strongly evidences unconventional superconductivity through a spontaneous appearance of an internal magnetic field below the superconducting transition temperature, signifying that the superconducting state is categorized by the broken time-reversal symmetry.

  17. Tethered phytic acid as a probe for measuring phytase activity.

    PubMed

    Berry, Duane F; Berry, David A

    2005-06-15

    A novel approach for measuring phytase activity is presented. We have developed a new chromophoric substrate analog of phytic acid, 5-O-[6-(benzoylamino)hexyl]-d-myo-inositol-1,2,3,4,6-pentakisphosphate that permits direct measurement of the phosphate ester bond-cleavage reaction using HPLC. This compound, along with its dephosphorylated T-phosphatidylinositol intermediates, are quantified using reversed phase chromatography with UV detection.

  18. Probing fatty acid metabolism in bacteria, cyanobacteria, green microalgae and diatoms with natural and unnatural fatty acids.

    PubMed

    Beld, Joris; Abbriano, Raffaela; Finzel, Kara; Hildebrand, Mark; Burkart, Michael D

    2016-04-01

    In both eukaryotes and prokaryotes, fatty acid synthases are responsible for the biosynthesis of fatty acids in an iterative process, extending the fatty acid by two carbon units every cycle. Thus, odd numbered fatty acids are rarely found in nature. We tested whether representatives of diverse microbial phyla have the ability to incorporate odd-chain fatty acids as substrates for their fatty acid synthases and their downstream enzymes. We fed various odd and short chain fatty acids to the bacterium Escherichia coli, cyanobacterium Synechocystis sp. PCC 6803, green microalga Chlamydomonas reinhardtii and diatom Thalassiosira pseudonana. Major differences were observed, specifically in the ability among species to incorporate and elongate short chain fatty acids. We demonstrate that E. coli, C. reinhardtii, and T. pseudonana can produce longer fatty acid products from short chain precursors (C3 and C5), while Synechocystis sp. PCC 6803 lacks this ability. However, Synechocystis can incorporate and elongate longer chain fatty acids due to acyl-acyl carrier protein synthetase (AasS) activity, and knockout of this protein eliminates the ability to incorporate these fatty acids. In addition, expression of a characterized AasS from Vibrio harveyii confers a similar capability to E. coli. The ability to desaturate exogenously added fatty acids was only observed in Synechocystis and C. reinhardtii. We further probed fatty acid metabolism of these organisms by feeding desaturase inhibitors to test the specificity of long-chain fatty acid desaturases. In particular, supplementation with thia fatty acids can alter fatty acid profiles based on the location of the sulfur in the chain. We show that coupling sensitive gas chromatography mass spectrometry to supplementation of unnatural fatty acids can reveal major differences between fatty acid metabolism in various organisms. Often unnatural fatty acids have antibacterial or even therapeutic properties. Feeding of short

  19. Measurements of d2n and A1n : Probing the neutron spin structure

    NASA Astrophysics Data System (ADS)

    Flay, D.; Posik, M.; Parno, D. S.; Allada, K.; Armstrong, W. R.; Averett, T.; Benmokhtar, F.; Bertozzi, W.; Camsonne, A.; Canan, M.; Cates, G. D.; Chen, C.; Chen, J.-P.; Choi, S.; Chudakov, E.; Cusanno, F.; Dalton, M. M.; Deconinck, W.; de Jager, C. W.; Deng, X.; Deur, A.; Dutta, C.; Fassi, L. El; Franklin, G. B.; Friend, M.; Gao, H.; Garibaldi, F.; Gilad, S.; Gilman, R.; Glamazdin, O.; Golge, S.; Gomez, J.; Guo, L.; Hansen, O.; Higinbotham, D. W.; Holmstrom, T.; Huang, J.; Hyde, C.; Ibrahim, H. F.; Jiang, X.; Jin, G.; Katich, J.; Kelleher, A.; Kolarkar, A.; Korsch, W.; Kumbartzki, G.; LeRose, J. J.; Lindgren, R.; Liyanage, N.; Long, E.; Lukhanin, A.; Mamyan, V.; McNulty, D.; Meziani, Z.-E.; Michaels, R.; Mihovilovič, M.; Moffit, B.; Muangma, N.; Nanda, S.; Narayan, A.; Nelyubin, V.; Norum, B.; Nuruzzaman, Oh, Y.; Peng, J. C.; Qian, X.; Qiang, Y.; Rakhman, A.; Ransome, R. D.; Riordan, S.; Saha, A.; Sawatzky, B.; Shabestari, M. H.; Shahinyan, A.; Širca, S.; Solvignon, P.; Subedi, R.; Sulkosky, V.; Tobias, W. A.; Troth, W.; Wang, D.; Wang, Y.; Wojtsekhowski, B.; Yan, X.; Yao, H.; Ye, Y.; Ye, Z.; Yuan, L.; Zhan, X.; Zhang, Y.; Zhang, Y.-W.; Zhao, B.; Zheng, X.; Jefferson Lab Hall A Collaboration

    2016-09-01

    We report on the results of the E06-014 experiment performed at Jefferson Lab in Hall A, where a precision measurement of the twist-3 matrix element d2 of the neutron (d2n) was conducted. The quantity d2n represents the average color Lorentz force a struck quark experiences in a deep inelastic electron scattering event off a neutron due to its interaction with the hadronizing remnants. This color force was determined from a linear combination of the third moments of the 3He spin structure functions, g1 and g2, after nuclear corrections had been applied to these moments. The structure functions were obtained from a measurement of the unpolarized cross section and of double-spin asymmetries in the scattering of a longitudinally polarized electron beam from a transversely and a longitudinally polarized 3He target. The measurement kinematics included two average Q2 bins of 3.2 GeV2 and 4.3 GeV2 , and Bjorken-x 0.25 ≤x ≤0.90 covering the deep inelastic and resonance regions. We have found that d2n is small and negative for ⟨Q2⟩ =3.2 GeV2 , and even smaller for ⟨Q2⟩ =4.3 GeV2 , consistent with the results of a lattice QCD calculation. The twist-4 matrix element f2n was extracted by combining our measured d2n with the world data on the first moment in x of g1n, Γ1n. We found f2n to be roughly an order of magnitude larger than d2n. Utilizing the extracted d2n and f2n data, we separated the Lorentz color force into its electric and magnetic components, FEy ,n and FBy ,n, and found them to be equal and opposite in magnitude, in agreement with the predictions from an instanton model but not with those from QCD sum rules. Furthermore, using the measured double-spin asymmetries, we have extracted the virtual photon-nucleon asymmetry on the neutron A1n, the structure function ratio g1n/F1n, and the quark ratios (Δ u +Δ u ¯)/(u +u ¯) and (Δ d +Δ d ¯)/(d +d ¯). These results were found to be consistent with deep-inelastic scattering world data and with the

  20. A flash-photolysis electron spin resonance study of radicals formed from carboxylic acids; exchange effects in spin-polarized radicals

    NASA Astrophysics Data System (ADS)

    McLauchlan, K. A.; Ritchie, A. J. D.

    The time-integration spectroscopy (TIS) technique has been applied to the study of transient radicals created by flash photolysis of solutions of benzene-1,2,4,5-tetracarboxylic acid (pyromellitic acid), benzene-1,2,-dicarboxylic acid (phthalic acid) and benzene-1,4-dicarboxylic acid (terephthalic acid). In these systems electron transfer, proton transfer and rotational isomerism all affect the spin-polarized spectra observed. The exchange processes are analysed theoretically, in the case of proton exchange for the first time in the polarized situation, and it is shown that the two different exchange processes can be simply differentiated in the time-dependent TIS spectra.

  1. N-tert-butylmethanimine N-oxide is an efficient spin-trapping probe for EPR analysis of glutathione thiyl radical

    PubMed Central

    Scott, Melanie J.; Billiar, Timothy R.; Stoyanovsky, Detcho A.

    2016-01-01

    The electron spin resonance (EPR) spin-trapping technique allows detection of radical species with nanosecond half-lives. This technique is based on the high rates of addition of radicals to nitrones or nitroso compounds (spin traps; STs). The paramagnetic nitroxides (spin-adducts) formed as a result of reactions between STs and radical species are relatively stable compounds whose EPR spectra represent “structural fingerprints” of the parent radical species. Herein we report a novel protocol for the synthesis of N-tert-butylmethanimine N-oxide (EBN), which is the simplest nitrone containing an α-H and a tertiary α′-C atom. We present EPR spin-trapping proof that: (i) EBN is an efficient probe for the analysis of glutathione thiyl radical (GS•); (ii) β-cyclodextrins increase the kinetic stability of the spin-adduct EBN/•SG; and (iii) in aqueous solutions, EBN does not react with superoxide anion radical (O2−•) to form EBN/•OOH to any significant extent. The data presented complement previous studies within the context of synthetic accessibility to EBN and efficient spin-trapping analysis of GS•. PMID:27941944

  2. Bioavailability of xenobiotics in unsaturated soils – implications for nucleic acid based stable isotope probing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The use of stable isotopes to label phylogenetically informative biomolecules (phospholipid fatty acids, DNA, or RNA), typically referred to as stable isotope probing (SIP) has the potential of providing definitive evidence that a detected population is active in a specific process, if that process ...

  3. Effect of humidity on the supramolecular structure of cotton, studied by quantitative spin probing.

    PubMed

    Frantz, S; Hübner, G A; Wendland, O; Roduner, E; Mariani, C; Ottaviani, M F; Batchelor, S N

    2005-06-16

    content. At loadings above 10(-3) mol kg(-1), signals from radicals strongly interacting via spin exchange were observed, which are assigned to aggregated radicals; simulation of the spectra gave an activation energy of 13 kJ mol(-1) for the spin exchange process. These effects are rationalized on the basis of microdomains of different character within cotton, reflecting the variation in pore sizes (0.5-8 nm) and the relaxation behavior of the cellulose chains.

  4. Ultrafast high harmonics for probing the fastest spin and charge dynamics in magnetic materials

    NASA Astrophysics Data System (ADS)

    Grychtol, Patrick

    2015-03-01

    Ultrafast light based on the high-harmonic up-conversion of femtosecond laser pulses have been successfully employed to access resonantly enhanced magnetic contrast at the Mabsorption edges of the 3d ferromagnets Fe, Co and Ni in a table-top setup. Thus, it has been possible to study element-specific dynamics in magnetic materials at femtosecond time scales in a laboratory environment, providing a wealth of opportunities for a greater fundamental understanding of correlated phenomena in solid-state matter. However, these investigations have so far been limited to linear polarized harmonics, since most techniques by which circular soft x-rays can be generated are highly inefficient reducing the photon flux to a level unfit for scientific applications. Besides presenting key findings of our ultrafast studies on charge and spin dynamics, we introduce a simple setup which allows for the efficient generation of circular harmonics bright enough for XMCD experiments. Our work thus represents a critical advance that enables element-specific imaging and spectroscopy of multiple elements simultaneously in magnetic and other chiral media with very high spatial and temporal resolution on the tabletop. In collboration with Ronny Knut, Emrah Turgut, Dmitriy Zusin, Christian Gentry, Henry Kapteyn, Margaret Murnane, JILA, University of Colorado, Boulder; Justin Shaw, Hans Nembach, Tom Silva, Electromagnetics Division, NIST, Boulder, CO; and Ofer Kfir, Avner Fleischer, Oren Cohen, Extreme Nonlinear Optics Group, Solid State Institute, Technion, Israel.

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

    PubMed

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

    2006-07-06

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

  6. Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe

    PubMed Central

    Qin, Peter Z; Haworth, Ian S; Cai, Qi; Kusnetzow, Ana K; Grant, Gian Paola G; Price, Eric A; Sowa, Glenna Z; Popova, Anna; Herreros, Bruno; He, Honghang

    2008-01-01

    This protocol describes the procedures for measuring nanometer distances in nucleic acids using a nitroxide probe that can be attached to any nucleotide within a given sequence. Two nitroxides are attached to phosphorothioates that are chemically substituted at specific sites of DNA or RNA. Inter-nitroxide distances are measured using a four-pulse double electron–electron resonance technique, and the measured distances are correlated to the parent structures using a Web-accessible computer program. Four to five days are needed for sample labeling, purification and distance measurement. The procedures described herein provide a method for probing global structures and studying conformational changes of nucleic acids and protein/nucleic acid complexes. PMID:17947978

  7. Modeling aqueous ozone/UV process using oxalic acid as probe chemical.

    PubMed

    Garoma, Temesgen; Gurol, Mirat D

    2005-10-15

    A kinetic model that describes the removal of organic pollutants by an ozone/UV process is described. Oxalic acid, which reacts with a very low rate constant with ozone and relatively high rate constant with hydroxyl radical (OH*), was used as the probe chemical to model the process. The model was verified by experimental data on concentrations of oxalic acid and hydrogen peroxide (H202) under various experimental conditions, i.e., ozone gas dosage, UV light intensity, and varying oxalic acid concentrations.

  8. Imaging thermal conductivity with nanoscale resolution using a scanning spin probe

    SciTech Connect

    Laraoui, Abdelghani; Aycock-Rizzo, Halley; Gao, Yang; Lu, Xi; Riedo, Elisa; Meriles, Carlos A.

    2015-11-20

    The ability to probe nanoscale heat flow in a material is often limited by lack of spatial resolution. Here, we use a diamond-nanocrystal-hosted nitrogen-vacancy centre attached to the apex of a silicon thermal tip as a local temperature sensor. We apply an electrical current to heat up the tip and rely on the nitrogen vacancy to monitor the thermal changes the tip experiences as it is brought into contact with surfaces of varying thermal conductivity. By combining atomic force and confocal microscopy, we image phantom microstructures with nanoscale resolution, and attain excellent agreement between the thermal conductivity and topographic maps. The small mass and high thermal conductivity of the diamond host make the time response of our technique short, which we demonstrate by monitoring the tip temperature upon application of a heat pulse. Our approach promises multiple applications, from the investigation of phonon dynamics in nanostructures to the characterization of heterogeneous phase transitions and chemical reactions in various solid-state systems.

  9. Imaging thermal conductivity with nanoscale resolution using a scanning spin probe

    DOE PAGES

    Laraoui, Abdelghani; Aycock-Rizzo, Halley; Gao, Yang; ...

    2015-11-20

    The ability to probe nanoscale heat flow in a material is often limited by lack of spatial resolution. Here, we use a diamond-nanocrystal-hosted nitrogen-vacancy centre attached to the apex of a silicon thermal tip as a local temperature sensor. We apply an electrical current to heat up the tip and rely on the nitrogen vacancy to monitor the thermal changes the tip experiences as it is brought into contact with surfaces of varying thermal conductivity. By combining atomic force and confocal microscopy, we image phantom microstructures with nanoscale resolution, and attain excellent agreement between the thermal conductivity and topographic maps.more » The small mass and high thermal conductivity of the diamond host make the time response of our technique short, which we demonstrate by monitoring the tip temperature upon application of a heat pulse. Our approach promises multiple applications, from the investigation of phonon dynamics in nanostructures to the characterization of heterogeneous phase transitions and chemical reactions in various solid-state systems.« less

  10. Probing the Axis Alignment of an Ultracold Spin-polarized Rb2 Molecule

    NASA Astrophysics Data System (ADS)

    Deiß, Markus; Drews, Björn; Deissler, Benjamin; Hecker Denschlag, Johannes

    2014-12-01

    We present a novel method for probing the alignment of the molecular axis of an ultracold, nonpolar dimer. These results are obtained using diatomic 87Rb2 molecules in the vibrational ground state of the lowest triplet potential a3Σu+ trapped in a 3D optical lattice. We measure the molecular polarizabilities, which are directly linked to the alignment, along each of the x , y , and z directions of the lab coordinate system. By preparing the molecules in various, precisely defined rotational quantum states we can control the degree of alignment of the molecular axis with high precision over a large range. Furthermore, we derive the dynamical polarizabilities for a laser wavelength of 1064.5 nm parallel and orthogonal to the molecular axis of the dimer, α∥=(8.9 ±0.9 )×1 03 a .u . and α⊥=(0.9 ±0.4 )×1 03 a .u . , respectively. Our findings highlight that the depth of an optical lattice strongly depends on the rotational state of the molecule, which has to be considered in collision experiments. The present work paves the way for reaction studies between aligned molecules in the ultracold temperature regime.

  11. Imaging thermal conductivity with nanoscale resolution using a scanning spin probe

    PubMed Central

    Laraoui, Abdelghani; Aycock-Rizzo, Halley; Gao, Yang; Lu, Xi; Riedo, Elisa; Meriles, Carlos A.

    2015-01-01

    The ability to probe nanoscale heat flow in a material is often limited by lack of spatial resolution. Here, we use a diamond-nanocrystal-hosted nitrogen-vacancy centre attached to the apex of a silicon thermal tip as a local temperature sensor. We apply an electrical current to heat up the tip and rely on the nitrogen vacancy to monitor the thermal changes the tip experiences as it is brought into contact with surfaces of varying thermal conductivity. By combining atomic force and confocal microscopy, we image phantom microstructures with nanoscale resolution, and attain excellent agreement between the thermal conductivity and topographic maps. The small mass and high thermal conductivity of the diamond host make the time response of our technique short, which we demonstrate by monitoring the tip temperature upon application of a heat pulse. Our approach promises multiple applications, from the investigation of phonon dynamics in nanostructures to the characterization of heterogeneous phase transitions and chemical reactions in various solid-state systems. PMID:26584676

  12. Scanned probe imaging of nanoscale magnetism at cryogenic temperatures with a single-spin quantum sensor.

    PubMed

    Pelliccione, Matthew; Jenkins, Alec; Ovartchaiyapong, Preeti; Reetz, Christopher; Emmanouilidou, Eve; Ni, Ni; Bleszynski Jayich, Ania C

    2016-08-01

    High-spatial-resolution magnetic imaging has driven important developments in fields ranging from materials science to biology. However, to uncover finer details approaching the nanoscale with greater sensitivity requires the development of a radically new sensor technology. The nitrogen-vacancy (NV) defect in diamond has emerged as a promising candidate for such a sensor on the basis of its atomic size and quantum-limited sensing capabilities. It has remained an outstanding challenge to implement the NV centre as a nanoscale scanning magnetic probe at cryogenic temperatures, however, where many solid-state systems exhibit non-trivial magnetic order. Here, we present NV magnetic imaging down to 6 K with 3 μT Hz(-1/2) field sensitivity, and use the technique to image vortices in the iron pnictide superconductor BaFe2(As0.7P0.3)2 with critical temperature Tc = 30 K. The expansion of NV-based magnetic imaging to cryogenic temperatures will enable future studies of previously inaccessible nanoscale magnetism in condensed-matter systems.

  13. The magnetic particle in a box: Analytic and micromagnetic analysis of probe-localized spin wave modes

    NASA Astrophysics Data System (ADS)

    Adur, Rohan; Du, Chunhui; Manuilov, Sergei A.; Wang, Hailong; Yang, Fengyuan; Pelekhov, Denis V.; Hammel, P. Chris

    2015-05-01

    The dipole field from a probe magnet can be used to localize a discrete spectrum of standing spin wave modes in a continuous ferromagnetic thin film without lithographic modification to the film. Obtaining the resonance field for a localized mode is not trivial due to the effect of the confined and inhomogeneous magnetization precession. We compare the results of micromagnetic and analytic methods to find the resonance field of localized modes in a ferromagnetic thin film, and investigate the accuracy of these methods by comparing with a numerical minimization technique that assumes Bessel function modes with pinned boundary conditions. We find that the micromagnetic technique, while computationally more intensive, reveals that the true magnetization profiles of localized modes are similar to Bessel functions with gradually decaying dynamic magnetization at the mode edges. We also find that an analytic solution, which is simple to implement and computationally much faster than other methods, accurately describes the resonance field of localized modes when exchange fields are negligible, and demonstrating the accessibility of localized mode analysis.

  14. The magnetic particle in a box: Analytic and micromagnetic analysis of probe-localized spin wave modes

    SciTech Connect

    Adur, Rohan Du, Chunhui; Manuilov, Sergei A.; Wang, Hailong; Yang, Fengyuan; Pelekhov, Denis V.; Hammel, P. Chris

    2015-05-07

    The dipole field from a probe magnet can be used to localize a discrete spectrum of standing spin wave modes in a continuous ferromagnetic thin film without lithographic modification to the film. Obtaining the resonance field for a localized mode is not trivial due to the effect of the confined and inhomogeneous magnetization precession. We compare the results of micromagnetic and analytic methods to find the resonance field of localized modes in a ferromagnetic thin film, and investigate the accuracy of these methods by comparing with a numerical minimization technique that assumes Bessel function modes with pinned boundary conditions. We find that the micromagnetic technique, while computationally more intensive, reveals that the true magnetization profiles of localized modes are similar to Bessel functions with gradually decaying dynamic magnetization at the mode edges. We also find that an analytic solution, which is simple to implement and computationally much faster than other methods, accurately describes the resonance field of localized modes when exchange fields are negligible, and demonstrating the accessibility of localized mode analysis.

  15. Measurements of d2n and A1n: Probing the neutron spin structure

    DOE PAGES

    Flay, D.; Posik, M.; Parno, D. S.; ...

    2016-09-06

    We report on the results of the E06-014 experiment performed at Jefferson Lab in Hall A, where a precision measurement of the twist-3 matrix elementmore » $$d_2$$ of the neutron ($$d_{2}^{n}$$) was conducted. This quantity represents the average color Lorentz force a struck quark experiences in a deep inelastic electron scattering event off a neutron due to its interaction with the hadronizing remnants. This color force was determined from a linear combination of the third moments of the spin structure functions $$g_1$$ and $$g_2$$ on $$^{3}$$He after nuclear corrections had been applied to these moments. The kinematics included two average $$Q^{2}$$ bins of $3.2$ GeV$$^{2}$$ and $4.3$ GeV$$^{2}$$, and Bjorken-$x$ $$0.25 \\leq x \\leq 0.90$$ covering the DIS and resonance regions. We found $$d_2^n$$ to be small and negative for $ = 3.2$ GeV$$^{2}$$, and smaller for $ = 4.3$ GeV$$^{2}$$, consistent with a lattice QCD calculation. The twist-4 matrix element $$f_{2}^{n}$$ was extracted by combining our $$d_{2}^{n}$$ with the world data on $$\\Gamma_{1}^{n} = \\int_{0}^{1} g_{1}^{n} dx$$. We found $$f_{2}^{n}$$ to be roughly an order of magnitude larger than $$d_{2}^{n}$$. Utilizing the extracted $$d_{2}^{n}$$ and $$f_{2}^{n}$$ data, we separated the color force into its electric and magnetic components, $$F_{E}^{y,n}$$ and $$F_{B}^{y,n}$$, and found them to be equal and opposite in magnitude, in agreement with instanton model predictions but not with those from QCD sum rules. Additionally, we have extracted the neutron virtual photon-nucleon asymmetry $$A_{1}^{n}$$, the structure function ratio $$g_{1}^{n}/F_{1}^{n}$$, and the quark ratios $$(\\Delta u + \\Delta \\bar{u})/(u + \\bar{u})$$ and $$(\\Delta d + \\Delta \\bar{d})/(d + \\bar{d})$$. Lastly, these results were found to be consistent with DIS world data and with the prediction of the constituent quark model but at odds with those of perturbative QCD at large $x$.« less

  16. Development of specific fluorescent oligonucleotide probes for in situ identification of wine lactic acid bacteria.

    PubMed

    Blasco, Lucía; Ferrer, Sergi; Pardo, Isabel

    2003-08-08

    A rapid method for the identification of lactic acid bacteria (LAB) from wine has been developed. This method is based on fluorescence in situ hybridisation (FISH), using fluorescent oligonucleotide probes, homologous to 16S rDNA of those species of LAB commonly found in wines. The protocol for the specific detection of these bacteria was established through the hybridisation of 36 reference strains. The specificity of the probes was evaluated by using pure cultures. Probes were used to identify species in different wines, making it evident that direct identification and quantification from natural samples without culturing is also possible. The results show that FISH is a promising technique for the rapid identification of LAB, allowing positive identification in a few hours (4-16 h).

  17. Photo-Induced Spin-State Conversion in Solvated Transition Metal Complexes Probed via Time-Resolved Soft X-ray Spectroscopy

    SciTech Connect

    Huse, Nils; Kim, Tae Kyu; Jamula, Lindsey; McCusker, James K.; de Groot, Frank M. F.; Schoenlein, Robert W.

    2010-04-30

    Solution-phase photoinduced low-spin to high-spin conversion in the FeII polypyridyl complex [Fe(tren(py)3)]2+ (where tren(py)3 is tris(2-pyridylmethyliminoethyl)amine) has been studied via picosecond soft X-ray spectroscopy. Following 1A1 --> 1MLCT (metal-to-ligand charge transfer) excitation at 560 nm, changes in the iron L2- and L3-edges were observed concomitant with formation of the transient high-spin 5T2 state. Charge-transfer multiplet calculations coupled with data acquired on low-spin and high-spin model complexes revealed a reduction in ligand field splitting of 1 eV in the high-spin state relative to the singlet ground state. A significant reduction in orbital overlap between the central Fe-3d and the ligand N-2p orbitals was directly observed, consistent with the expected ca. 0.2 Angstrom increase in Fe-N bond length upon formation of the high-spin state. The overall occupancy of the Fe-3d orbitals remains constant upon spin crossover, suggesting that the reduction in sigma-donation is compensated by significant attenuation of pi-back-bonding in the metal-ligand interactions. These results demonstrate the feasibility and unique potential of time-resolved soft X-ray absorption spectroscopy to study ultrafast reactions in the liquid phase by directly probing the valence orbitals of first-row metals as well as lighter elements during the course of photochemical transformations.

  18. Docosahexaenoic acid conjugated near infrared flourescence probe for in vivo early tumor diagnosis

    NASA Astrophysics Data System (ADS)

    Li, Siwen; Cao, Jie; Qin, Jingyi; Zhang, Xin; Achilefu, Samuel; Qian, Zhiyu; Gu, Yueqing

    2013-02-01

    Docosahexaenoic acid(DHA) is an omega-3 C22 natural fatty acid with six cis double bonds and as a constituent of membranes used as a precursor for metabolic and biochemical path ways. In this manuscript,we describe the synthesis of near-infrared(NIR) flourescence ICG-Der-01 labeled DHA for in vitro and vivo tumor targeting.The structure of the probe was intensively characterized by UV and MS. The in vitro and vivo tumor targeting abilities of the DHA-based NIR probes were investigeted in MCF-7 cells and MCF-7 xenograft mice model differently by confocal microscopy and CCD camera. The cell cytotoxicity were tested in tumor cells MCF-7 .The results shows that the DHA-based NIR probes have high affinity with the tumor both in vitro and vivo.In addition ,we also found that the DHA-based NIR probes have the apparent cytotoxicity on MCF-7 cells .which demonstrated that DHA was conjugated with other antitumor drug could increase the abilities of antirumor efficacy .So DHA-ICG-Der-01 is a promising optical agent for diagnosis of tumors especially in their early stage.

  19. GFT projection NMR for efficient (1)H/ (13)C sugar spin system identification in nucleic acids.

    PubMed

    Atreya, Hanudatta S; Sathyamoorthy, Bharathwaj; Jaipuria, Garima; Beaumont, Victor; Varani, Gabriele; Szyperski, Thomas

    2012-12-01

    A newly implemented G-matrix Fourier transform (GFT) (4,3)D HC(C)CH experiment is presented in conjunction with (4,3)D HCCH to efficiently identify (1)H/(13)C sugar spin systems in (13)C labeled nucleic acids. This experiment enables rapid collection of highly resolved relay 4D HC(C)CH spectral information, that is, shift correlations of (13)C-(1)H groups separated by two carbon bonds. For RNA, (4,3)D HC(C)CH takes advantage of the comparably favorable 1'- and 3'-CH signal dispersion for complete spin system identification including 5'-CH. The (4,3)D HC(C)CH/HCCH based strategy is exemplified for the 30-nucleotide 3'-untranslated region of the pre-mRNA of human U1A protein.

  20. Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes.

    PubMed

    Wang, Yongxiang; Li, Jishan; Wang, Hao; Jin, Jianyu; Liu, Jinhua; Wang, Kemin; Tan, Weihong; Yang, Ronghua

    2010-08-01

    Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.

  1. Probing the formation and evolution of comets via nuclear spin temperatures of C_2H_6, CH_3OH, CH_4, NH_3, and H_2O

    NASA Astrophysics Data System (ADS)

    Villanueva, G.; Mumma, M.; Bonev, B.; DiSanti, M.; Paganini, L.; Magee-Sauer, K.; Gibb, E.

    2014-07-01

    Comets are true remnants of our primordial Solar System, and provide unique clues to its formation and evolution, including the delivery of organics and water to our planet. A key indicator stored in the molecular structure of the nuclear ices is the spin temperature (T_{spin}), derived from spin-isomeric ratios (R_{spin}, e.g., ortho/para). At the time when cometary ices formed, the prevailing temperature defined the relative abundance of the different spin-isomeric species, and herewith R_{spin} and T_{spin} are normally treated as ''remnant thermometers'' probing the formation environments of cometary molecules. Radiative and collisional transitions between the ortho and para states are strongly forbidden and herewith this indicator is preserved over time. Most of our knowledge of this indicator comes from the measurements of the ortho-para ratios in water and NH_2 (a proxy for ammonia), suggesting a common T_{spin} near 30 K. This information is based on a restricted sample of comets, and the measurements are particularly sensitive to the molecular modeling technique and adopted spectral database. Here, we present new methodologies for extracting spin temperatures from ethane (C_2H_6), methane (CH_4), and methanol (CH_3OH), and advanced new models for ortho/para water (H_2O) and ammonia (NH_3). Our H_2O analysis is based on the most complete fluorescence radiative-transfer model to date, which incorporates 1,200 million transitions including those originating from high-energy levels that are activated in comets via a non-resonant cascade. In a similar fashion, we developed non-resonant fluorescence models for NH_3 and HCN, and quantum-band models for the ν_7 band of C_2H_6 and ν_3 band of CH_3OH. All models respect spin-symmetry non-conversion radiative rules, and make use of a realistic solar spectrum for the computation of fluorescence pumps. We applied these new methods to derive spin-isomeric ratios for H_2O, CH_4, C_2H_6, CH_3OH, and NH_3 from three high

  2. Fast Magic-Angle Spinning Three-Dimensional NMR Experiment for Simultaneously Probing H-H and N-H Proximities in Solids.

    PubMed

    Reddy, G N Manjunatha; Malon, Michal; Marsh, Andrew; Nishiyama, Yusuke; Brown, Steven P

    2016-12-06

    A fast magic-angle spinning (MAS, 70 kHz) solid-state NMR experiment is presented that combines (1)H Double-Quantum (DQ) and (14)N-(1)H HMQC (Heteronuclear Multiple-Quantum Coherence) pulse-sequence elements, so as to simultaneously probe H-H and N-H proximities in molecular solids. The proposed experiment can be employed in both two-dimensional (2D) and three-dimensional (3D) versions: first, a 2D (14)N HMQC-filtered (1)H-DQ experiment provides specific DQ-SQ correlation peaks for proton pairs that are in close proximities to the nitrogen sites, thereby achieving spectral filtration. Second, a proton-detected three-dimensional (3D) (1)H(DQ)-(14)N(SQ)-(1)H(SQ) experiment correlates (1)H(DQ)-(1)H(SQ) chemical shifts with (14)N shifts such that longer range N···H-H correlations are observed between protons and nitrogen atoms with internuclear NH distances exceeding 3 Å. Both 2D and 3D versions of the proposed experiment are demonstrated for an amino acid hydrochloride salt, l-histidine·HCl·H2O, and a DNA nucleoside, guanosine·2H2O. In the latter case, the achieved spectral filtration ensures that DQ cross peaks are only observed for guanine NH and CH8 (1)H resonances and not ribose and water (1)H resonances, thus providing insight into the changes in the solid-state structure of this hydrate that occur over time; significant changes are observed in the NH and NH2(1)H chemical shifts as compared to the freshly recrystallized sample previously studied by Reddy et al., Cryst. Growth Des. 2015, 15, 5945.

  3. A Large Sample Volume Magic Angle Spinning Nuclear Magnetic Resonance Probe for In-Situ Investigations with Constant Flow of Reactants

    SciTech Connect

    Hu, Jian Z.; Sears, Jesse A.; Mehta, Hardeep S.; Ford, Joseph J.; Kwak, Ja Hun; Zhu, Kake; Wang, Yong; Liu, Jun; Hoyt, David W.; Peden, Charles HF

    2012-02-21

    A large-sample-volume constant-flow magic angle sample spinning (CF-MAS) NMR probe is reported for in-situ studies of the reaction dynamics, stable intermediates/transition states, and mechanisms of catalytic reactions. In our approach, the reactants are introduced into the catalyst bed using a fixed tube at one end of the MAS rotor while a second fixed tube, linked to a vacuum pump, is attached at the other end of the rotor. The pressure difference between both ends of the catalyst bed inside the sample cell space forces the reactants flowing through the catalyst bed, which improves the diffusion of the reactants and products. This design allows the use of a large sample volume for enhanced sensitivity and thus permitting in-situ 13C CF-MAS studies at natural abundance. As an example of application, we show that reactants, products and reaction transition states associated with the 2-butanol dehydration reaction over a mesoporous silicalite supported heteropoly acid catalyst (HPA/meso-silicalite-1) can all be detected in a single 13C CF-MAS NMR spectrum at natural abundance. Coke products can also be detected at natural 13C abundance and under the stopped flow condition. Furthermore, 1H CF-MAS NMR is used to identify the surface functional groups of HPA/meso-silicalite-1 under the condition of in-situ drying . We also show that the reaction dynamics of 2-butanol dehydration using HPA/meso-silicalite-1 as a catalyst can be explored using 1H CF-MAS NMR.

  4. Properties of the silica layer during the formation of MCM-41 studied by EPR of a silica-bound spin probe.

    PubMed

    Baute, Debbie; Frydman, Veronica; Zimmermann, Herbert; Kababya, Shifi; Goldfarb, Daniella

    2005-04-28

    The properties of the silica layer during the formation of the mesoporous material MCM-41 were investigated by electron paramagnetic resonance (EPR) experiments carried out on a specifically designed, organo(trialkoxy)silane spin probe, SL1SiEt. Minute amounts of the spin probe were co-condensed with the silica source, tetraethyl orthosilicate (TEOS), in the synthesis of MCM-41 with cetyltrimethylammonium bromide (CTAB) under basic conditions. The mobility and location of the spin probe were followed in the CTAB micellar solution before the reaction, in the reaction mixture and in the final ordered material. It was found that the EPR spectra of hydrolyzed SL1SiEt throughout the room temperature part of the reaction are characteristic of a fast tumbling species, indicating that the silica is highly fluid prior to drying. After filtering, a slow motion type spectrum was observed, showing that the spin-label experiences considerable motional hindrance. The liquidlike behavior could be restored upon stirring the material in water. When the reaction is performed with a hydrothermal stage, the spectrum of SL1SiEt in the final product is the same as that of the room temperature synthesized material, but the addition of water did not restore the high mobility, due to a higher degree of silica cross-linking. The location of SL1SiEt throughout the formation process was obtained from electron spin-echo envelope modulation (ESEEM) measurements on MCM-41 prepared with CTAB deuterated either at the N-methyl or the alpha position and in a reaction carried out in D2O. Comparing the deuterium modulation depth, k(2H), induced by CTAB-alpha-d2, CTAB-d9, or D2O in CTAB micellar solutions of a number of reference spin probes with those of SL1SiEt revealed that the hydrolyzed SL1SiEt is located near the polar heads of the surfactant in the absence of base and TEOS. This supports the postulation of charge matching at the interface as a driving force for the formation of the mesostructure

  5. The use of variable temperature and magic-angle sample spinning in studies of fulvic acids

    USGS Publications Warehouse

    Earl, W.L.; Wershaw, R. L.; Thorn, K.A.

    1987-01-01

    Intensity distortions and poor signal to noise in the cross-polarization magic-angle sample spinning NMR of fulvic acids were investigated and attributed to molecular mobility in these ostensibly "solid" materials. We have shown that inefficiencies in cross polarization can be overcome by lowering the sample temperature to about -60??C. These difficulties can be generalized to many other synthetic and natural products. The use of variable temperature and cross-polarization intensity as a function of contact time can yield valuable qualitative information which can aid in the characterization of many materials. ?? 1987.

  6. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

    DOEpatents

    Weier, Heinz-Ulrich G.; Gray, Joe W.

    1995-01-01

    A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers ard probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity.

  7. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

    DOEpatents

    Weier, H.U.G.; Gray, J.W.

    1995-06-27

    A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers and probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity. 18 figs.

  8. Efficacy of Nucleic Acid Probes for Detection of Poliovirus in Water Disinfected by Chlorine, Chlorine Dioxide, Ozone, and UV Radiation

    PubMed Central

    Moore, Norman J.; Margolin, Aaron B.

    1994-01-01

    MilliQ water was inoculated with poliovirus type 1 strain LSc-1 and was treated with disinfectants, including chlorine, chlorine dioxide, ozone, and UV light. No relationship between probes and plaque assays were seen, demonstrating that viral nucleic acids were not destroyed. These findings suggest that nucleic acid probes cannot distinguish between infectious and noninfectious viruses and cannot be used in the evaluation of treated waters. PMID:16349448

  9. (1) Majorana fermions in pinned vortices; (2) Manipulating and probing Majorana fermions using superconducting circuits; and (3) Controlling a nanowire spin-orbit qubit via electric-dipole spin resonance

    NASA Astrophysics Data System (ADS)

    Nori, Franco

    2014-03-01

    We study a heterostructure which consists of a topological insulator and a superconductor with a hole. This system supports a robust Majorana fermion state bound to the vortex core. We study the possibility of using scanning tunneling spectroscopy (i) to detect the Majorana fermion in this setup and (ii) to study excited states bound to the vortex core. The Majorana fermion manifests itself as an H-dependent zero-bias anomaly of the tunneling conductance. The excited states spectrum differs from the spectrum of a typical Abrikosov vortex, providing additional indirect confirmation of the Majorana state observation. We also study how to manipulate and probe Majorana fermions using super-conducting circuits. In we consider a semiconductor nanowire quantum dot with strong spin-orbit coupling (SOC), which can be used to achieve a spin-orbit qubit. In contrast to a spin qubit, the spin-orbit qubit can respond to an external ac electric field, i.e., electric-dipole spin resonance. We develop a theory that can apply in the strong SOC regime. We find that there is an optimal SOC strength ηopt = √ 2/2, where the Rabi frequency induced by the ac electric field becomes maximal. Also, we show that both the level spacing and the Rabi frequency of the spin-orbit qubit have periodic responses to the direction of the external static magnetic field. These responses can be used to determine the SOC in the nanowire. FN is partly supported by the RIKEN CEMS, iTHES Project, MURI Center for Dynamic Magneto-Optics, JSPS-RFBR Contract No. 12-02-92100, Grant-in-Aid for Scientific Research (S), MEXT Kakenhi on Quantum Cybernetics, and the JSPS via its FIRST program.

  10. Intrinsically Labeled Fluorescent Oligonucleotide Probes on Quantum Dots for Transduction of Nucleic Acid Hybridization.

    PubMed

    Shahmuradyan, Anna; Krull, Ulrich J

    2016-03-15

    Quantum dots (QDs) have been widely used in chemical and biosensing due to their unique photoelectrical properties and are well suited as donors in fluorescence resonance energy transfer (FRET). Selective hybridization interactions of oligonucleotides on QDs have been determined by FRET. Typically, the QD-FRET constructs have made use of labeled targets or have implemented labeled sandwich format assays to introduce dyes in proximity to the QDs for the FRET process. The intention of this new work is to explore a method to incorporate the acceptor dye into the probe molecule. Thiazole orange (TO) derivatives are fluorescent intercalating dyes that have been used for detection of double-stranded nucleic acids. One such dye system has been reported in which single-stranded oligonucleotide probes were doubly labeled with adjacent thiazole orange derivatives. In the absence of the fully complementary (FC) oligonucleotide target, the dyes form an H-aggregate, which results in quenching of fluorescence emission due to excitonic interactions between the dyes. The hybridization of the FC target to the probe provides for dissociation of the aggregate as the dyes intercalate into the double stranded duplex, resulting in increased fluorescence. This work reports investigation of the dependence of the ratiometric signal on the type of linkage used to conjugate the dyes to the probe, the location of the dye along the length of the probe, and the distance between adjacent dye molecules. The limit of detection for 34mer and 90mer targets was found to be identical and was 10 nM (2 pmol), similar to analogous QD-FRET using labeled oligonucleotide target. The detection system could discriminate a one base pair mismatch (1BPM) target and was functional without substantial compromise of the signal in 75% serum. The 1BPM was found to reduce background signal, indicating that the structure of the mismatch affected the environment of the intercalating dyes.

  11. Spin-lattice coupling in uranium dioxide probed by magnetostriction measurements at high magnetic fields (P08358-E001-PF)

    SciTech Connect

    Gofryk, K.; Jaime, M.

    2014-12-01

    Our preliminary magnetostriction measurements have already shown a strong interplay of lattice dynamic and magnetism in both antiferromagnetic and paramagnetic states, and give unambiguous evidence of strong spin- phonon coupling in uranium dioxide. Further studies are planned to address the puzzling behavior of UO2 in magnetic and paramagnetic states and details of the spin-phonon coupling.

  12. Site-directed spin labeling studies on nucleic acid structure and dynamics

    PubMed Central

    Sowa, Glenna Z.; Qin, Peter Z.

    2009-01-01

    Site-directed spin labeling (SDSL) uses electron paramagnetic resonance (EPR) spectroscopy to monitor the behavior of a stable nitroxide radical attached at specific locations within a macromolecule such as protein, DNA, or RNA. Parameters obtained from EPR measurements, such as internitroxide distances and descriptions of the rotational motion of a nitroxide, provide unique information on features near the labeling site. With recent advances in solid-phase synthesis of nucleic acids and developments in EPR methodologies, particularly pulsed EPR technologies, SDSL has been increasingly used to study the structure and dynamics of DNA and RNA at the level of the individual nucleotides. This chapter summarizes the current SDSL studies on nucleic acids, with discussions focusing on literature from the last decade. PMID:18929141

  13. The internal dynamics of mini c TAR DNA probed by electron paramagnetic resonance of nitroxide spin-labels at the lower stem, the loop, and the bulge.

    PubMed

    Sun, Yan; Zhang, Ziwei; Grigoryants, Vladimir M; Myers, William K; Liu, Fei; Earle, Keith A; Freed, Jack H; Scholes, Charles P

    2012-10-30

    Electron paramagnetic resonance (EPR) at 236.6 and 9.5 GHz probed the tumbling of nitroxide spin probes in the lower stem, in the upper loop, and near the bulge of mini c TAR DNA. High-frequency 236.6 GHz EPR, not previously applied to spin-labeled oligonucleotides, was notably sensitive to fast, anisotropic, hindered local rotational motion of the spin probe, occurring approximately about the NO nitroxide axis. Labels attached to the 2'-aminocytidine sugar in the mini c TAR DNA showed such anisotropic motion, which was faster in the lower stem, a region previously thought to be partially melted. More flexible labels attached to phosphorothioates at the end of the lower stem tumbled isotropically in mini c TAR DNA, mini TAR RNA, and ψ(3) RNA, but at 5 °C, the motion became more anisotropic for the labeled RNAs, implying more order within the RNA lower stems. As observed by 9.5 GHz EPR, the slowing of nanosecond motions of large segments of the oligonucleotide was enhanced by increasing the ratio of the nucleocapsid protein NCp7 to mini c TAR DNA from 0 to 2. The slowing was most significant at labels in the loop and near the bulge. At a 4:1 ratio of NCp7 to mini c TAR DNA, all labels reported tumbling times of >5 ns, indicating a condensation of NCp7 and TAR DNA. At the 4:1 ratio, pulse dipolar EPR spectroscopy of bilabels attached near the 3' and 5' termini showed evidence of an NCp7-induced increase in the 3'-5' end-to-end distance distribution and a partially melted stem.

  14. The Internal Dynamics of Mini c TAR DNA Probed by EPR of Nitroxide Spin Labels at the Lower Stem, the Loop, and the Bulge †

    PubMed Central

    Sun, Yan; Zhang, Ziwei; Grigoryants, Vladimir M.; Myers, William K.; Liu, Fei; Earle, Keith A.; Freed, Jack H.; Scholes, Charles P.

    2012-01-01

    Electron paramagnetic resonance (EPR) at 236.6 GHz and 9.5 GHz probed the tumbling of nitroxide spin probes in the lower stem, the upper loop, and near the bulge of mini c TAR DNA. High frequency 236.6 GHz EPR, not previously applied to spin labeled oligonucleotides, was notably sensitive to fast, anisotropic, hindered local rotational motion of the spin probe, occurring approximately about the NO nitroxide axis. Labels attached to the 2′-amino cytidine sugar in the mini c TAR DNA showed such anisotropic motion, which was faster in the lower stem, a region previously suggested to be partially melted. More flexible labels attached to phosphorothioates at the end of the lower stem tumbled isotropically in mini c TAR DNA, mini TAR RNA, and ψ3 RNA, but at 5 °C the motion became more anisotropic for the labeled RNAs, implying more order within the RNA lower stems. As observed by 9.5 GHz EPR, the slowing of nanosecond motions of large segments of the oligonucleotide was enhanced by increasing the ratio of the nucleocapsid protein NCp7 to mini c TAR DNA from zero to two. The slowing was most significant at labels in the loop and near the bulge. At a 4:1 ratio of NCp7 to mini c TAR DNA all labels reported tumbling times > 5 ns, indicating a condensation of NCp7 and TAR DNA. At the 4:1 ratio, pulse dipolar EPR spectroscopy of bi-labels attached near the 3′ and 5′ terminals showed evidence for an NCp7-induced increase in the 3′ - 5 ′end-to-end distance distribution and a partially melted stem. PMID:23009298

  15. Probing the effective nuclear-spin magnetic field in a single quantum dot via full counting statistics

    SciTech Connect

    Xue, Hai-Bin; Nie, Yi-Hang; Chen, Jingzhe; Ren, Wei

    2015-03-15

    We study theoretically the full counting statistics of electron transport through a quantum dot weakly coupled to two ferromagnetic leads, in which an effective nuclear-spin magnetic field originating from the configuration of nuclear spins is considered. We demonstrate that the quantum coherence between the two singly-occupied eigenstates and the spin polarization of two ferromagnetic leads play an important role in the formation of super-Poissonian noise. In particular, the orientation and magnitude of the effective field have a significant influence on the variations of the values of high-order cumulants, and the variations of the skewness and kurtosis values are more sensitive to the orientation and magnitude of the effective field than the shot noise. Thus, the high-order cumulants of transport current can be used to qualitatively extract information on the orientation and magnitude of the effective nuclear-spin magnetic field in a single quantum dot. - Highlights: • The effective nuclear-spin magnetic field gives rise to the off-diagonal elements of the reduced density matrix of single QD. • The off-diagonal elements of reduced density matrix of the QD have a significant impact on the high-order current cumulants. • The high-order current cumulants are sensitive to the orientation and magnitude of the effective nuclear-spin magnetic field. • The FCS can be used to detect the orientation and magnitude of the effective nuclear-spin magnetic field in a single QD.

  16. Probing the interactions between boronic acids and cis-diol-containing biomolecules by affinity capillary electrophoresis.

    PubMed

    Lü, Chenchen; Li, Hengye; Wang, Heye; Liu, Zhen

    2013-02-19

    The affinity of boronic acids to cis-diol-containing biomolecules has found wide applications in many fields, such as sensing, separation, drug delivery, and functional materials. A sound understanding of the binding interactions will greatly facilitate exquisite applications of this chemistry. Although a few analytical tools have been available for the characterization of the interactions, these techniques are associated with some apparent drawbacks, so they are only applicable to a limited range of boronic acids and cis-diol-containing biomolecules. Therefore, a widely applicable method is still greatly needed. In this work, an affinity capillary electrophoresis (ACE) method was established and validated to probe the interactions between boronic acids and cis-diol-containing biomolecules. The method was proven to be applicable to almost all types of cis-diol-containing biomolecules and boronic acids. Based on this method, a quantitative, comparative study on the interactions between 14 boronic acids that have important potentials for application with 5 typical monosaccharides of biological importance was carried out. The findings provided new insights into boronate affinity interactions, particularly the relationship between the binding strength with the molecular structures of the binding species. Besides, effects of pH and temperature on the binding strength were also investigated. This method exhibited several significant advantages, including (1) possibility of simultaneous study of multiple interactions, (2) low requirement on the purity of the binding species, (3) wide applicability, and (4) high accuracy and precision.

  17. Folic acid-conjugated europium complexes as luminescent probes for selective targeting of cancer cells.

    PubMed

    Quici, Silvio; Casoni, Alessandro; Foschi, Francesca; Armelao, Lidia; Bottaro, Gregorio; Seraglia, Roberta; Bolzati, Cristina; Salvarese, Nicola; Carpanese, Debora; Rosato, Antonio

    2015-02-26

    We report the synthesis of three optical probes (Eu(3+)⊂1, Eu(3+)⊂2, and Eu(3+)⊂3) having a luminescent Eu complex (signaling unit) bonded in different positions to folic acid (FA), the folate receptor (FR) targeting unit. The structures of the two regioisomers Eu(3+)⊂1 and Eu(3+)⊂2 were assigned by mass spectrometric experiments. The optical properties and stability of these probes were assessed in phosphate-buffered saline, cell culture medium, rat serum, and cellular lysate, and results indicated that they are chemically and photophysically stable. Cytotoxicity was studied with ovarian cancer cells having high (SKOV-3), intermediate (OVCAR-3), low (IGROV-1), or null (A2780) expression of FRs. The internalized probe, evaluated in SKOV-3, IGROV-1, and A2780 cells, was in the order Eu(3+)⊂2 > Eu(3+)⊂1 > Eu(3+)⊂3. No internalization was observed for A2780 cells. Such results, together with those obtained in competition experiments of FA versus Eu(3+)⊂2 and FA or Eu(3+)⊂2 versus (3)H-FA, indicate that internalization is receptor-mediated and that Eu(3+)⊂2 shows high selectivity and specificity for FR.

  18. Human leukocyte antigen haplotype phasing by allele-specific enrichment with peptide nucleic acid probes

    PubMed Central

    Murphy, Nicholas M; Pouton, Colin W; Irving, Helen R

    2014-01-01

    Targeted capture of large fragments of genomic DNA that enrich for human leukocyte antigen (HLA) system haplotypes has utility in haematopoietic stem cell transplantation. Current methods of HLA matching are based on inference or familial studies of inheritance; and each approach has its own inherent limitations. We have designed and tested a probe–target-extraction method for capturing specific HLA haplotypes by hybridization of peptide nucleic acid (PNA) probes to alleles of the HLA-DRB1 gene. Short target fragments contained in plasmids were initially used to optimize the method followed by testing samples of genomic DNA from human subjects with preselected HLA haplotypes and obtained approximately 10% enrichment for the specific haplotype. When performed with high-molecular-weight genomic DNA, 99.0% versus 84.0% alignment match was obtained for the specific haplotype probed. The allele-specific target enrichment that we obtained can facilitate the elucidation of haplotypes between the 65 kb separating the HLA-DRB1 and the HLA-DQA1 genes, potentially spanning a total distance of at least 130 kb. Allele-specific target enrichment with PNA probes is a straightforward technique that has the capability to improve the resolution of DNA and whole genome sequencing technologies by allowing haplotyping of enriched DNA and crucially, retaining the DNA methylation profile. PMID:24936514

  19. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1998-03-24

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration. 14 figs.

  20. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    1998-01-01

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration.

  1. Fluorescence energy transfer as a probe for nucleic acid structures and sequences.

    PubMed Central

    Mergny, J L; Boutorine, A S; Garestier, T; Belloc, F; Rougée, M; Bulychev, N V; Koshkin, A A; Bourson, J; Lebedev, A V; Valeur, B

    1994-01-01

    The primary or secondary structure of single-stranded nucleic acids has been investigated with fluorescent oligonucleotides, i.e., oligonucleotides covalently linked to a fluorescent dye. Five different chromophores were used: 2-methoxy-6-chloro-9-amino-acridine, coumarin 500, fluorescein, rhodamine and ethidium. The chemical synthesis of derivatized oligonucleotides is described. Hybridization of two fluorescent oligonucleotides to adjacent nucleic acid sequences led to fluorescence excitation energy transfer between the donor and the acceptor dyes. This phenomenon was used to probe primary and secondary structures of DNA fragments and the orientation of oligodeoxynucleotides synthesized with the alpha-anomers of nucleoside units. Fluorescence energy transfer can be used to reveal the formation of hairpin structures and the translocation of genes between two chromosomes. PMID:8152922

  2. Translational and rotational diffusion of flexible PEG and rigid dendrimer probes in sodium caseinate dispersions and acid gels.

    PubMed

    Salami, Souad; Rondeau-Mouro, Corinne; Barhoum, Myriam; van Duynhoven, John; Mariette, François

    2014-09-01

    The dynamics of rigid dendrimer and flexible PEG probes in sodium caseinate dispersions and acid gels, including both translational diffusion and rotational diffusion, were studied by NMR. Above the onset of the close-packing limit (C ∼ 10 g/100 g H2 O), translational diffusion of the probe depended on its flexibility and on the fluctuations of the matrix chains. The PEG probe diffused more rapidly than the spherical dendrimer probe of corresponding hydrodynamic radius. The greater conformational flexibility of PEG facilitated its motion through the crowded casein matrix. Rotational diffusion was, however, substantially less hindered than the translational diffusion and depended on the local protein-probe friction which became high when the casein concentration increased. The coagulation of the matrix led to the formation of large voids, which resulted in an increase in the translational diffusion of the probes, whereas the rotational diffusion of the probes was retarded in the gel, which could be attributed to the immobilized environment surrounding the probe. Quantitative information from PFG-NMR and SEM micrographs have been combined for characterizing microstructural details in SC acid gels.

  3. Boronic Acid: A Bio-Inspired Strategy To Increase the Sensitivity and Selectivity of Fluorescent NADH Probe.

    PubMed

    Wang, Lu; Zhang, Jingye; Kim, Beomsue; Peng, Juanjuan; Berry, Stuart N; Ni, Yong; Su, Dongdong; Lee, Jungyeol; Yuan, Lin; Chang, Young-Tae

    2016-08-24

    Fluorescent probes have emerged as an essential tool in the molecular recognition events in biological systems; however, due to the complex structures of certain biomolecules, it remains a challenge to design small-molecule fluorescent probes with high sensitivity and selectivity. Inspired by the enzyme-catalyzed reaction between biomolecule and probe, we present a novel combination-reaction two-step sensing strategy to improve sensitivity and selectivity. Based on this strategy, we successfully prepared a turn-on fluorescent reduced nicotinamide adenine dinucleotide (NADH) probe, in which boronic acid was introduced to bind with NADH and subsequently accelerate the sensing process. This probe shows remarkably improved sensitivity (detection limit: 0.084 μM) and selectivity to NADH in the absence of any enzymes. In order to improve the practicality, the boronic acid was further modified to change the measurement conditions from alkalescent (pH 9.5) to physiological environment (pH 7.4). Utilizing these probes, we not only accurately quantified the NADH weight in a health care product but also evaluated intracellular NADH levels in live cell imaging. Thus, these bio-inspired fluorescent probes offer excellent tools for elucidating the roles of NADH in biological systems as well as a practical strategy to develop future sensitive and selective probes for complicated biomolecules.

  4. Electron spin resonance studies on reduction process of nitroxyl spin radicals used in molecular imaging

    SciTech Connect

    Dhas, M. Kumara; Benial, A. Milton Franklin; Jawahar, A.

    2014-04-24

    The Electron spin resonance studies on the reduction process of nitroxyl spin probes were carried out for 1mM {sup 14}N labeled nitroxyl radicals in pure water and 1 mM concentration of ascorbic acid as a function of time. The electron spin resonance parameters such as signal intensity ratio, line width, g-value, hyperfine coupling constant and rotational correlation time were determined. The half life time was estimated for 1mM {sup 14}N labeled nitroxyl radicals in 1 mM concentration of ascorbic acid. The ESR study reveals that the TEMPONE has narrowest line width and fast tumbling motion compared with TEMPO and TEMPOL. From the results, TEMPONE has long half life time and high stability compared with TEMPO and TEMPOL radical. Therefore, this study reveals that the TEMPONE radical can act as a good redox sensitive spin probe for molecular imaging.

  5. Selective local lysis and sampling of live cells for nucleic acid analysis using a microfluidic probe

    PubMed Central

    Kashyap, Aditya; Autebert, Julien; Delamarche, Emmanuel; Kaigala, Govind V.

    2016-01-01

    Heterogeneity is inherent to biology, thus it is imperative to realize methods capable of obtaining spatially-resolved genomic and transcriptomic profiles of heterogeneous biological samples. Here, we present a new method for local lysis of live adherent cells for nucleic acid analyses. This method addresses bottlenecks in current approaches, such as dilution of analytes, one-sample-one-test, and incompatibility to adherent cells. We make use of a scanning probe technology - a microfluidic probe - and implement hierarchical hydrodynamic flow confinement (hHFC) to localize multiple biochemicals on a biological substrate in a non-contact, non-destructive manner. hHFC enables rapid recovery of nucleic acids by coupling cell lysis and lysate collection. We locally lysed ~300 cells with chemical systems adapted for DNA or RNA and obtained lysates of ~70 cells/μL for DNA analysis and ~15 cells/μL for mRNA analysis. The lysates were introduced into PCR-based workflows for genomic and transcriptomic analysis. This strategy further enabled selective local lysis of subpopulations in a co-culture of MCF7 and MDA-MB-231 cells, validated by characteristic E-cadherin gene expression in individually extracted cell types. The developed strategy can be applied to study cell-cell, cell-matrix interactions locally, with implications in understanding growth, progression and drug response of a tumor. PMID:27411740

  6. Exploring 12'-apo-beta-carotenoic-12'-acid as an ultrafast polarity probe for ionic liquids.

    PubMed

    Lohse, Peter W; Bürsing, Reinhard; Lenzer, Thomas; Oum, Kawon

    2008-03-13

    The ultrafast excited-state dynamics of the carbonyl-containing carotenoid 12'-apo-beta-carotenoic-12'-acid (12'CA) have been used for probing the microscopic environment in various ionic liquids (ILs). The following IL cations were investigated: 1,3-di-n-alkyl-imidazolium featuring different n-alkyl chain lengths and also additional methylation at the C2 position, triethylsulfonium, as well as two tetraalkylammonium ions. These were combined with different anions: [BF4]-, [PF6]-, ethyl sulfate ([EtOSO3]-), and bis(trifluoromethylsulfonyl)amide ([Tf2N]-). The probe molecule was excited via the S0 --> S2 transition at 425 or 430 nm, and the characteristic stimulated emission decay of the low-lying excited electronic S1/ICT (intramolecular charge transfer) state of 12'CA was monitored in the near IR (850 or 860 nm). Its lifetime tau1 is sensitive to the micropolarity-induced stabilization of S1/ICT relative to S0. The lifetime tau1 of the S1/ICT state varies only moderately in all ionic liquids studied here ( approximately 40-110 ps), which lies in the range between ethanol (109 ps) and methanol (49 ps). While organic solvents show an excellent correlation of tau1 with the solvent polarity function Deltaf = (epsilon - 1)/(epsilon + 2) - (n2 - 1)/(n2 + 2), where epsilon and n are the static dielectric constant and the refractive index of the solvent, respectively, this is not the case for ILs. This is due to dominant local electrostatic probe-cation interactions which cannot be easily quantified by macroscopic quantities. Methylation at the C2 position of 1,3-di-n-alkyl-imidazolium reduces the accessibility of the cation and therefore the electrostatic stabilization of the probe, resulting in an increase of tau1. A similar increase is observed upon extension of one of the n-alkyl chains from ethyl to n-decyl. Tetraalkylammonium ILs show an increased tau1 probably due to their more delocalized positive charge which cannot interact so favorably with the probe, in

  7. Two-Dimensional Field-Step ELDOR. A Method for Characterizing the Motion of Spin Probes and Spin Labels in Glassy Solids

    NASA Astrophysics Data System (ADS)

    Saalmueller, J. W.; Long, H. W.; Maresch, G. G.; Spiess, H. W.

    A practical route for obtaining two-dimensional electron double-resonance spectra of radicals in disordered solids is presented in detail. It involves narrow-band pulse excitation during a magnetic field step combined with echo detection after a mixing time. The equipment and experimental procedures are described, and factors affecting the performance of the field-jump coil, spectral resolution, and sensitivity are thoroughly discussed. Simulated spectra, which take into account distributions of correlation times, show the spectral features that can be observed with this technique. These simulations have been improved over previous work by taking into account g-tensor fluctuations, which is the dominant effect in determining the anisotropy of the electron spin-lattice relaxation. Data for nitroxide radicals in polycarbonate at 110 K are analyzed and an orientation averaged nuclear spin-lattice relaxation time of 82 ± 13 μs and an electron spin-lattice relaxation time for radicals oriented along the zdirection (slowest relaxation) of 23 ± 4 μs are measured. Simulations show that this relaxation is caused by highly restricted liberational motion with a distribution of correlation times having mean of 0.1 μs and a width of about 0.8 decades in combination with a very narrow mode having a correlation time of 10 ps.

  8. A two-dimensional Fourier transform electron-spin resonance (ESR) study of nuclear modulation and spin relaxation in irradiated malonic acid

    NASA Astrophysics Data System (ADS)

    Lee, Sanghyuk; Patyal, Baldev R.; Freed, Jack H.

    1993-03-01

    Nuclear modulation in electron-spin-echo spectroscopy is conventionally studied by one-dimensional electron-spin-echo envelope modulation (1D-ESEEM). Two-dimensional Fourier transform electron-spin resonance (2D-FTESR) studies of nuclear modulation have the promise of enhancing the spectral resolution and clarifying the key details of the relaxation processes. We present a 2D-FTESR study on single proton nuclear modulation from γ-irradiated malonic acid single crystals to test the validity of the Gamliel-Freed theory and to assess the value of the new methods. The two pulse spin-echo correlation spectroscopy (SECSY) spectra as a function of orientation of the single crystal show very good agreement with the Gamliel-Freed theory extended to the general case of nonaxially symmetric hyperfine interaction. It is very simply affected by spin relaxation, such that relative intensities are essentially unaffected. Thus SECSY-ESR can most reliably be utilized for studying nuclear modulation. Stimulated SECSY provides the simplest nuclear modulation patterns, which, however, do exhibit the suppression effect well known in three-pulse ESEEM studies. Two-dimensional electron-electron double resonance (2D-ELDOR) provides nuclear modulation patterns similar to that of SECSY-ESR, so the suppression effect is absent. Both three-pulse methods exhibit complex relaxation behavior which can affect relative intensities. This is a feature characteristic of three-pulse ESEEM, but is not well understood. It is shown how the 2D-FTESR methods enable one to obtain the details of the complex spin relaxation, and in the process, obtain very good agreement between experiment and theory. 2D-ELDOR exhibits exchange cross peaks as well as coherence peaks from the nuclear modulation. It is shown how experiments, as a function of mixing time, enable one to separate the effects of the two. It is pointed out that such experiments are in the spirit of 3D spectroscopy. A new observation of the

  9. Complexation of malic acid with cadmium(II) probed by electrospray ionization mass spectrometry.

    PubMed

    Jaklová Dytrtová, Jana; Jakl, Michal; Schröder, Detlef

    2012-02-15

    Electrospray ionization was used as a technique for the characterization of the interactions between cadmium(II) ions and malic acid (1) in aqueous solution. Particular attention was paid to the nature of the species formed, which generally correspond to complexes of CdX(+) cations with neutral malic acid, where X either is the counterion of the metal salt used as a precursor (i.e. X=Cl, I) or corresponds to singly deprotonated malic acid. In pure water solutions, also highly coordinated complexes [Cd(1-H)(1)(2)](+) and [CdCl(1)(2)](+) were detected, whereas the most abundant complexes detected in a sample of soil solution were: [Cd(1-H)(1)](+) and [CdCl(1)](+). With respect to possible application in environmental analysis, the effects of (i) metal salts present in solution, (ii) modest mineralization, and (iii) the matrices of real soil solutions were probed. While the presence of other metals leads to additional complexes, the characteristic species containing both cadmium(II) and malic acid can still be detected with good sensitivity.

  10. Magic-angle-spinning NMR studies of acid sites in zeolite H-ZSM-5

    SciTech Connect

    Brunner, E.; Ernst, H.; Freude, D.; Froehlich, T.; Hunger, M.; Pfeifer, H. )

    1991-01-01

    {sup 1}H, {sup 13}C, {sup 27}Al, and {sup 29}Si magic-angle-spinning (MAS) NMR was used to elucidate the nature of the catalytic activity of zeolite H-ZSM-5. {sup 1}H MAS NMR of sealed samples after mild hydrothermal dealumination shows that the enhanced activity for n-hexane cracking is not due to an enhanced Bronstead acidity. The concentrations of the various OH groups and aluminous species suggest that the reason for the enhanced catalytic activity is the interaction of the n-hexane molecule with a bridging hydroxyl group and with extra-framework aluminium species, which give rise to the enhanced activity, cannot be easily removed from their positions, and are therefore immobilized by the zeolitic framework.

  11. Using spin labels to study molecular processes in soils: Covalent binding of aromatic amines to humic acids of soils

    NASA Astrophysics Data System (ADS)

    Aleksandrova, O. N.; Kholodov, V. A.; Perminova, I. V.

    2015-08-01

    Interactions of aliphatic and aromatic amines with soil and humic acids isolated from it are studied by means of spin labels and electron paramagnetic resonance (EPR) spectroscopy. Nitroxyl radicals containing amino groups are used as spin labels. It is found experimentally that aromatic amines are instantaneously converted to the bound state. It is shown that the microareas of their incorporation are characterized by a significant delay in the reduction of the nitroxyl fragment of spin-label molecules, indicating the formation of condensed structures typical of an oxidative binding mechanism. It is concluded that aliphatic amines do not bind to humic acids. It is noted that the studied process allows elucidating the formation of bound xenobiotic residues in soils.

  12. Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

    PubMed Central

    2011-01-01

    Background The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH) probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to Abiotrophia/Granulicatella. Results As lactobacilli are known for notorious resistance to probe penetration, probe-specific assay protocols were experimentally developed to provide maximum cell wall permeability, probe accessibility, hybridization stringency, and fluorescence intensity. The new assays were then applied in a pilot study to three biofilm samples harvested from variably demineralized bovine enamel discs that had been carried in situ for 10 days by different volunteers. Best probe penetration and fluorescent labeling of reference strains were obtained after combined lysozyme and achromopeptidase treatment followed by exposure to lipase. Hybridization stringency had to be established strictly for each probe. Thereafter all probes showed the expected specificity with reference strains and labeled the anticipated morphotypes in dental plaques. Applied to in situ grown biofilms the set of probes detected only Lactobacillus fermentum and bacteria of the Lactobacillus casei group. The most cariogenic biofilm contained two orders of magnitude higher L. fermentum cell numbers than the other biofilms. Abiotrophia/Granulicatella and streptococci from the mitis group were found in all samples at high levels, whereas Streptococcus mutans was detected in only one sample in very low numbers. Conclusions Application of these new group- and species-specific FISH probes to oral biofilm-forming lactic acid bacteria will allow a clearer understanding of the supragingival biome, its spatial architecture and of structure-function relationships implicated during plaque homeostasis and caries development. The probes should prove of value far beyond the field of oral microbiology, as many of

  13. Identification of Dekkera bruxellensis (Brettanomyces) from Wine by Fluorescence In Situ Hybridization Using Peptide Nucleic Acid Probes

    PubMed Central

    Stender, Henrik; Kurtzman, Cletus; Hyldig-Nielsen, Jens J.; Sørensen, Ditte; Broomer, Adam; Oliveira, Kenneth; Perry-O'Keefe, Heather; Sage, Andrew; Young, Barbara; Coull, James

    2001-01-01

    A new fluorescence in situ hybridization method using peptide nucleic acid (PNA) probes for identification of Brettanomyces is described. The test is based on fluorescein-labeled PNA probes targeting a species-specific sequence of the rRNA of Dekkera bruxellensis. The PNA probes were applied to smears of colonies, and results were interpreted by fluorescence microscopy. The results obtained from testing 127 different yeast strains, including 78 Brettanomyces isolates from wine, show that the spoilage organism Brettanomyces belongs to the species D. bruxellensis and that the new method is able to identify Brettanomyces (D. bruxellensis) with 100% sensitivity and 100% specificity. PMID:11157265

  14. Exploring the Hybridization Thermodynamics of Spherical Nucleic Acids to Tailor Probes for Diagnostic and Therapeutic Applications

    NASA Astrophysics Data System (ADS)

    Randeria, Pratik Shailesh

    Spherical nucleic acids (SNAs), three-dimensional nanoparticle conjugates composed of densely packed and highly oriented oligonucleotides around organic or inorganic nanoparticles, are an emergent class of nanostructures that show promise as single-entity agents for intracellular messenger RNA (mRNA) detection and gene regulation. SNAs exhibit superior biocompatibility and biological properties compared to linear oligonucleotides, enabling them to overcome many of the limitations of linear oligonucleotides for use in biomedical applications. However, the origins of these biologically attractive properties are not well understood. In this dissertation, the chemistry underlying one such property is studied in detail, and the findings are applied towards the rational design of more effective SNAs for diagnostic and therapeutic applications. Chapter 1 introduces the synthesis of SNAs, the unique properties that make them superior to linear nucleic acids for biomedicine, and previously studied applications of these structures. Chapter 2 focuses on quantitatively studying the impact of the chemical structure of the SNA on its ability to hybridize multiple complementary nucleic acids. This chapter lays the groundwork for understanding the factors that govern SNA hybridization thermodynamics and how to tailor SNAs to increase their binding affinity to target mRNA strands. Chapters 3 and 4 capitalize on this knowledge to engineer probes for intracellular mRNA detection and gene regulation applications. Chapter 3 reports the development of an SNA-based probe that can simultaneously report the expression level of two different mRNA transcripts in live cells and differentiate diseased cells from non-diseased cells. Chapter 4 investigates the use of topically-applied SNAs to down-regulate a critical mediator of impaired wound healing in diabetic mice to accelerate wound closure. This study represents the first topical therapeutic application of SNA nanotechnology to treat open

  15. Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton

    PubMed Central

    Bryson, Samuel; Li, Zhou; Pett-Ridge, Jennifer; Hettich, Robert L.; Mayali, Xavier; Pan, Chongle

    2016-01-01

    ABSTRACT Heterotrophic marine bacterioplankton are a critical component of the carbon cycle, processing nearly a quarter of annual primary production, yet defining how substrate utilization preferences and resource partitioning structure microbial communities remains a challenge. In this study, proteomic stable isotope probing (proteomic SIP) was used to characterize population-specific assimilation of dissolved free amino acids (DFAAs), a major source of dissolved organic carbon for bacterial secondary production in aquatic environments. Microcosms of seawater collected from Newport, Oregon, and Monterey Bay, California, were incubated with 1 µM 13C-labeled amino acids for 15 and 32 h. The taxonomic compositions of microcosm metaproteomes were highly similar to those of the sampled natural communities, with Rhodobacteriales, SAR11, and Flavobacteriales representing the dominant taxa. Analysis of 13C incorporation into protein biomass allowed for quantification of the isotopic enrichment of identified proteins and subsequent determination of differential amino acid assimilation patterns between specific bacterioplankton populations. Proteins associated with Rhodobacterales tended to have a significantly high frequency of 13C-enriched peptides, opposite the trend for Flavobacteriales and SAR11 proteins. Rhodobacterales proteins associated with amino acid transport and metabolism had an increased frequency of 13C-enriched spectra at time point 2. Alteromonadales proteins also had a significantly high frequency of 13C-enriched peptides, particularly within ribosomal proteins, demonstrating their rapid growth during incubations. Overall, proteomic SIP facilitated quantitative comparisons of DFAA assimilation by specific taxa, both between sympatric populations and between protein functional groups within discrete populations, allowing an unprecedented examination of population level metabolic responses to resource acquisition in complex microbial communities

  16. Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton.

    PubMed

    Bryson, Samuel; Li, Zhou; Pett-Ridge, Jennifer; Hettich, Robert L; Mayali, Xavier; Pan, Chongle; Mueller, Ryan S

    2016-01-01

    Heterotrophic marine bacterioplankton are a critical component of the carbon cycle, processing nearly a quarter of annual primary production, yet defining how substrate utilization preferences and resource partitioning structure microbial communities remains a challenge. In this study, proteomic stable isotope probing (proteomic SIP) was used to characterize population-specific assimilation of dissolved free amino acids (DFAAs), a major source of dissolved organic carbon for bacterial secondary production in aquatic environments. Microcosms of seawater collected from Newport, Oregon, and Monterey Bay, California, were incubated with 1 µM (13)C-labeled amino acids for 15 and 32 h. The taxonomic compositions of microcosm metaproteomes were highly similar to those of the sampled natural communities, with Rhodobacteriales, SAR11, and Flavobacteriales representing the dominant taxa. Analysis of (13)C incorporation into protein biomass allowed for quantification of the isotopic enrichment of identified proteins and subsequent determination of differential amino acid assimilation patterns between specific bacterioplankton populations. Proteins associated with Rhodobacterales tended to have a significantly high frequency of (13)C-enriched peptides, opposite the trend for Flavobacteriales and SAR11 proteins. Rhodobacterales proteins associated with amino acid transport and metabolism had an increased frequency of (13)C-enriched spectra at time point 2. Alteromonadales proteins also had a significantly high frequency of (13)C-enriched peptides, particularly within ribosomal proteins, demonstrating their rapid growth during incubations. Overall, proteomic SIP facilitated quantitative comparisons of DFAA assimilation by specific taxa, both between sympatric populations and between protein functional groups within discrete populations, allowing an unprecedented examination of population level metabolic responses to resource acquisition in complex microbial communities

  17. Probing titanate nanowire surface acidity through methylene blue adsorption in colloidal suspension and on thin films.

    PubMed

    Horváth, Endre; Szilágyi, István; Forró, László; Magrez, Arnaud

    2014-02-15

    The interaction of the cationic dye methylene blue (MB) with titanate nanowires (TiONWs) was investigated in different pH environments using visible spectroscopy and electrophoresis on thin films as well as in aqueous suspension. The surface charge of the TiONWs depends on the pH and ionic strength leading to positive charge under acidic and negative under alkaline conditions. The TiONWs have the same adsorption capacity on films and in suspensions at neutral pH while under alkaline conditions they are able to adsorb significantly more MB in suspension due to their higher surface area. Detailed adsorption studies in water revealed that dye cations form monomers, dimers and larger aggregates of H-type (face-to-face) on the TiONW films. The results indicate that below pH = 4.0 the TiONWs' external surface consists of Brøntsted acid sites capable of protonating MB. It was suggested that reversible indicator role of MB molecule dimers probes the TiONW surface acidity (Brøntsted sites).

  18. Spin Labeling ESR Investigation of a Role of Humic Acids at Covalent Binding of Xenobiotics to Soil

    NASA Astrophysics Data System (ADS)

    Aleksandrova, Olga

    2014-05-01

    The environmental risk of organic xenobiotic chemicals released into soils is controlled by their sorption and binding processes. However, the molecular mechanisms of reversible and irreversible interactions of xenobiotics with soil constituents and an influence of humic substances on this interaction are only partly understood. New methods and approaches aimed at understanding of molecular mechanisms in the soil environment and a role of humic substances in the sorption and binding processes are today required to manage and keep the quality of soil used and fertilized in agricultural industry. The paper presents a new approach of using stable ESR spin labels to investigate a role of humic substances in the interactions of organic xenobiotic chemicals with constituents of natural soil via the typical functional groups of xenobiotics, such as Amines. At the experiment, the nitroxide spin labels, such as TEMPO (2,2,6,6-Tetramethylpiperidin-1-oxyl), Amino-TEMPO (4-amino-2,2,6,6-Tetramethylpiperidin-1-oxyl) and Aniline spin labels (2,5,5-Trimethyl-2-(3-aminophenyl)pyrrolidin-1-oxyl), were added to samples of different natural soils, such luvisol, cambisol and chernozem. Amino-TEMPO and Aniline spin labels include the aliphatic amino and aromatic amino functional groups, respectively. A significant broadening of the ESR spectrum of Aniline spin labels incubated in different soils indicated a stable effect of covalent binding of the spin labels to soil constituents via the aromatic amino, whereas the ESR spectra of the other two spin labels were not broadened that pointed at the absence of covalent binding of spin labels via the aliphatic amino. As shown, a part of bound spin labels via the aromatic amino increased with increasing of the concentration of humic acids in soil. The same broadened signals were also be detected with the humic acids extracted from the investigated soils. A strong covalent binding of spin labels to humic substances via the aromatic amines was

  19. Location and binding mechanism of an ESIPT probe 3-hydroxy-2-naphthoic acid in unsaturated fatty acid bound serum albumins.

    PubMed

    Ghorai, Shyamal Kr; Tripathy, Debi Ranjan; Dasgupta, Swagata; Ghosh, Sanjib

    2014-02-05

    The binding site and the binding mechanism of 3-hydroxy-2-naphthoic acid (3HNA) in oleic acid (OA) bound serum albumins (bovine serum albumin (BSA) and human serum albumin (HSA)) have been determined using steady state and time resolved emission of tryptophan residues (Trp) in proteins and the ESIPT emission of 3HNA. Time resolved anisotropy of the probe 3HNA and low temperature phosphorescence of Trp residues of BSA in OA bound BSA at 77K reveals a drastic change of the binding site of 3HNA in the ternary system compared to that in the free protein. 3HNA binds near Trp213 in the ternary system whereas 3HNA binds near Trp134 in the free protein. The structure of OA bound BSA generated using docking methodology exhibits U-bend configuration of all bound OA. The docked pose of 3HNA in the free protein and in OA bound albumins (ternary systems) and the concomitant perturbation of the structure of proteins around the binding region of 3HNA corroborate the enhanced ESIPT emission of 3HNA and the energy transfer efficiency from the donor Trp213 of BSA to 3HNA acceptor in 3HNA-OA-BSA system.

  20. Neutrophil chemotaxis and arachidonic acid metabolism are not linked: evidence from metal ion probe studies

    SciTech Connect

    Turner, S.R.; Turner, R.A.; Smith, D.M.; Johnson, J.A.

    1986-03-05

    Heavy metal ions can inhibit arachidonic acid (AA) metabolism protect against ionophore cytotoxicity (ibid) and inhibit neutrophil chemotaxis. In this study they used Au/sup 3 +/, Zn/sup 2 +/, Cr/sup 3 +/, Mn/sup 2 +/ and Cu/sup 2 +/ as probes of the interrelationships among AA metabolism, ionophore-mediated cytotoxicity, and chemotaxis. Phospholipid deacylation was measured in ionophore-treated cells prelabeled with /sup 3/H-AA. Eicosanoid release from ionophore-treated cells was monitored by radioimmunoassay. Cytoprotection was quantitated as ability to exclude trypan blue. Chemotaxis toward f-met-leu-phe was measured by leading front analysis. The results imply that metal ions attenuate ionophore cytotoxicity by blocking phospholipid deacylation and eicosanoid release. In contrast to previous reports, no correlation between AA metabolism and chemotaxis was demonstrated, suggesting that these 2 processes are not linked.

  1. Collective dynamics of a photosynthetic protein probed by neutron spin-echo spectroscopy and molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Dellerue, S.; Petrescu, A.; Smith, J. C.; Longeville, S.; Bellissent-Funel, M.-C.

    2000-03-01

    We have studied the collective dynamics of an hydrated soluble protein, the C-phycocyanin by using neutron spin-echo spectroscopy. Molecular dynamics simulations, performed with the same system, showed that the main dynamic contribution comes from backbone and side-chain motions. Both the experimental and spectra exhibit a dynamic relaxation with a characteristic time of about 10 ps.

  2. Infrared phonons as a probe of spin-liquid states in herbertsmithite ZnCu3(OH)6Cl2

    NASA Astrophysics Data System (ADS)

    Sushkov, A. B.; Jenkins, G. S.; Han, Tian-Heng; Lee, Young S.; Drew, H. D.

    2017-03-01

    We report on temperature dependence of the infrared reflectivity spectra of a single crystalline herbertsmithite in two polarizations—parallel and perpendicular to the kagome plane of Cu atoms. We observe anomalous broadening of the low frequency phonons possibly caused by fluctuations in the exotic dynamical magnetic order of the spin liquid.

  3. Probing current-induced magnetic fields in Au|YIG heterostructures with low-energy muon spin spectroscopy

    NASA Astrophysics Data System (ADS)

    Aqeel, A.; Vera-Marun, I. J.; Salman, Z.; Prokscha, T.; Suter, A.; van Wees, B. J.; Palstra, T. T. M.

    2017-02-01

    We investigated the depth dependence of current-induced magnetic fields in a bilayer of a normal metal (Au) and a ferrimagnetic insulator (Yttrium Iron Garnet—YIG) by using low energy muon spin spectroscopy (LE-μSR). This allows us to explore how these fields vary from the Au surface down to the buried Au|YIG interface, which is relevant to study physics like the spin-Hall effect. We observed a maximum shift of 0.4 G in the internal field of muons at the surface of Au film which is in close agreement with the value expected for Oersted fields. As muons are implanted closer to the Au|YIG interface, the shift is strongly suppressed, which we attribute to the dipolar fields present at the Au|YIG interface. Combining our measurements with modeling, we show that dipolar fields caused by the finite roughness of the Au|YIG interface consistently explain our observations. Our results, therefore, gauge the limits on the spatial resolution and the sensitivity of LE-μSR to the roughness of the buried magnetic interfaces, a prerequisite for future studies addressing current induced fields caused by the spin-accumulations due to the spin-Hall effect.

  4. Probing the accretion disc structure by the twin kHz QPOs and spins of neutron stars in LMXBs

    NASA Astrophysics Data System (ADS)

    Wang, D. H.; Zhang, C. M.; Lei, Y. J.; Chen, L.; Qu, J. L.; Zhi, Q. J.

    2017-04-01

    We analyse the relation between the emission radii of twin kilohertz quasi-periodic oscillations (kHz QPOs) and the co-rotation radii of the 12 neutron star low-mass X-ray binaries (NS-LMXBs), which are simultaneously detected with the twin kHz QPOs and NS spins. We find that the average co-rotation radius of these sources is ∼ 32 km, and all the emission positions of twin kHz QPOs lie inside the co-rotation radii, indicating that the twin kHz QPOs are formed in the spin-up process. It is noticed that the upper frequency of twin kHz QPOs is higher than NS spin frequency by ≥10 per cent, which may account for a critical velocity difference between the Keplerian motion of accretion matter and NS spin that is corresponding to the production of twin kHz QPOs. In addition, we also find that ∼83 per cent of twin kHz QPOs cluster around the radius range of 15-20 km, which may be affected by the hard surface or the local strong magnetic field of the NS. As a special case, SAX J1808.4-3658 shows the larger emission radii of twin kHz QPOs of r ∼ 21-24 km, which may be due to its low accretion rate or small measured NS mass (<1.4 M⊙).

  5. An Activity-Based Probe for N-Acylethanolamine Acid Amidase

    PubMed Central

    Armirotti, Andrea; Summa, Maria; Bertozzi, Fabio; Garau, Gianpiero; Bandiera, Tiziano; Piomelli, Daniele

    2015-01-01

    N-Acylethanolamine acid amidase (NAAA) is a lysosomal cysteine hydrolase involved in the degradation of saturated and monounsaturated fatty acid ethanolamides (FAEs), a family of endogenous lipid signaling molecules that includes oleoylethanolamide (OEA) and palmitoylethanolamide (PEA). Among the reported NAAA inhibitors, α–amino–β–lactone (3–aminooxetan–2–one) derivatives have been shown to prevent FAE hydrolysis in innate-immune and neural cells and to reduce reactions to inflammatory stimuli. Recently, we disclosed two potent and selective NAAA inhibitors, the compounds ARN077 (5-phenylpentyl N-[(2S,3R)-2-methyl-4-oxo-oxetan-3-yl]carbamate) and ARN726 (4-cyclohexylbutyl-N-[(S)-2-oxoazetidin-3-yl]carbamate). The former is active in vivo by topical administration in rodent models of hyperalgesia and allodynia, while the latter exerts systemic anti-inflammatory effects in mouse models of lung inflammation. In the present study, we designed and validated a derivative of ARN726 as the first activity-based protein profiling (ABPP) probe for the in vivo detection of NAAA. The newly synthesized molecule 1 is an effective in vitro and in vivo click-chemistry activity based probe (ABP), which is able to capture the catalytically active form of NAAA in Human Embryonic Kidney 293 (HEK293) cells overexpressing human NAAA as well as in rat lung tissue. Competitive ABPP with 1 confirmed that ARN726 and ARN077 inhibit NAAA in vitro and in vivo. Compound 1 is a useful new tool to identify activated NAAA both in vitro and in vivo, and to investigate the physiological and pathological roles of this enzyme. PMID:26102511

  6. Amperometric microsensor for direct probing of ascorbic acid in human gastric juice.

    PubMed

    Hutton, Emily A; Pauliukaitė, Rasa; Hocevar, Samo B; Ogorevc, Božidar; Smyth, Malcolm R

    2010-09-30

    This article reports on a novel microsensor for amperometric measurement of ascorbic acid (AA) under acidic conditions (pH 2) based on a carbon fiber microelectrode (CFME) modified with nickel oxide and ruthenium hexacyanoferrate (NiO-RuHCF). This sensing layer was deposited electrochemically in a two-step procedure involving an initial galvanostatic NiO deposition followed by a potentiodynamic RuHCF deposition from solutions containing the precursor salts. Several important parameters were examined to characterize and optimize the NiO-RuHCF sensing layer with respect to its current response to AA by using cyclic voltammetry, and scanning electron microscopy-energy dispersive X-ray spectroscopy methods. With the NiO-RuHCF coated CFME, the AA oxidation potential under acidic conditions was shifted to a less positive value for about 0.2 V (E(p) of ca. 0.23 V vs. Ag/AgCl) as compared to a bare CFME, which greatly improves the electrochemical selectivity. Using the hydrodynamic amperometry mode, the current vs. AA concentration in 0.01 M HCl, at a selected operating potential of 0.30 V, was found to be linear over a wide range of 10-1610 μM (n=22, r=0.999) with a calculated limit of detection of 1.0 μM. The measurement repeatability was satisfactory with a relative standard deviation (r.s.d.) ranging from 4% to 5% (n=6), depending on the AA concentration, and with a sensor-to-sensor reproducibility (r.s.d.) of 6.9% at 100 μM AA. The long-term reproducibility, using the same microsensor for 112 consecutive measurements of 20 μM AA over 11 h of periodic probing sets over 4 days, was 16.1% r.s.d., thus showing very good stability at low AA levels and suitability for use over a prolonged period of time. Moreover, using the proposed microsensor, additionally coated with a protective cellulose acetate membrane, the calibration plot obtained in the extremely complex matrix of real undiluted gastric juice was linear from 10 to 520 μM (n=14, r=0.998). These results

  7. New fluorescent octadecapentaenoic acids as probes of lipid membranes and protein-lipid interactions.

    PubMed Central

    Mateo, C R; Souto, A A; Amat-Guerri, F; Acuña, A U

    1996-01-01

    The chemical and spectroscopic properties of the new fluorescent acids all(E)-8, 10, 12, 14, 16-octadecapentaenoic acid (t-COPA) and its (8Z)-isomer (c-COPA) have been characterized in solvents of different polarity, synthetic lipid bilayers, and lipid/protein systems. These compounds are reasonably photostable in solution, present an intense UV absorption band (epsilon(350 nm) approximately 10(5) M(-1) cm(-1)) strongly overlapped by tryptophan fluorescence and their emission, centered at 470 nm, is strongly polarized (r(O) = 0.385 +/- 0.005) and decays with a major component (85%) of lifetime 23 ns and a faster minor one of lifetime 2 ns (D,L-alpha-dimyristoylphosphatidylcholine (DMPC), 15 degrees C). Both COPA isomers incorporate readily into vesicles and membranes (K(p) approximately 10(6)) and align parallel to the lipids. t-COPA distributes homogeneously between gel and fluid lipid domains and the changes in polarization accurately reflect the lipid T(m) values. From the decay of the fluorescence anisotropy in spherical bilayers of DMPC and POPC it is shown that t-COPA also correctly reflects the lipid order parameters, determined by 2H NMR techniques. Resonance energy transfer from tryptophan to the bound pentaenoic acid in serum albumin in solution, and from the tryptophan residues of gramicidin in lipid bilayers also containing the pentaenoic acid, show that this probe is a useful acceptor of protein tryptophan excitation, with R(O) values of 30-34 A. Images FIGURE 10 PMID:8889194

  8. First observation of high-spin states in {sup 214}Po: Probing the valence space beyond {sup 208}Pb

    SciTech Connect

    Astier, Alain; Porquet, Marie-Genevieve

    2011-01-15

    Excited states in {sup 214}Po have been populated using the {sup 18}O + {sup 208}Pb reaction at 85-MeV beam energy and studied with the Euroball IV {gamma}-multidetector array. The level scheme has been built up to {approx}2.7-MeV excitation energy and spin I=12({h_bar}/2{pi}) from the triple-{gamma} coincidence data. Spin and parity values of most of the observed states have been assigned from the {gamma}-angular properties. The configurations of the yrast states are discussed using results of empirical shell-model calculations and by analogy with the neighboring nuclei. The {sup 214}Po level scheme established in this work constitutes an important step for the determination of the effective nucleon-nucleon interactions beyond N=126.

  9. A triterpene oleanolic acid conjugate with 3-hydroxyflavone derivative as a new membrane probe with two-color ratiometric response.

    PubMed

    Turkmen, Zeynep; Klymchenko, Andrey S; Oncul, Sule; Duportail, Guy; Topcu, Gulacti; Demchenko, Alexander P

    2005-07-29

    We report on the synthesis by coupling of a triterpenoid oleanolic acid with 4'-diethylamino-3-hydroxyflavone (FE) to produce an environment-sensitive biomembrane probe with two-band ratiometric response in fluorescence emission. The synthesized compound (probe FOT) was tested in a series of model solvents and demonstrated the response to solvent polarity and intermolecular hydrogen bonding very similar to that of parent probe FE. Meantime when incorporated into lipid bilayer membranes, it showed new features differing in response between lipids of different surface charges as well as between glycerophospholipids and sphingomyelin. We observed that in the conditions of coexistence of rafts and non-raft structures the probe is excluded from the rafts.

  10. Determination of bismuth in pharmaceutical products using phosphoric acid as molecular probe by resonance light scattering.

    PubMed

    Yun, Yanru; Cui, Fengling; Geng, Shaoguang; Jin, Jianhua

    2012-01-01

    A novel method for the sensitive determination of bismuth(III) in pharmaceutical products using phosphoric acid as a molecular probe by resonance light scattering (RLS) is discussed. In 0.5 mol/L phosphoric acid (H3 PO4) medium, bismuth(III) reacted with PO4 (3-) to form an ion association compound, which resulted in the significant enhancement of RLS intensity and the appearance of the corresponding RLS spectral characteristics. The maximum scattering peak of the system existed at 364 nm. Under optimal conditions, there was linear relationship between the relative intensity of RLS and concentration of bismuth(III) in the range of 0.06-10.0 µg/mL for the system. A low detection limit for bismuth(III) of 3.22 ng/mL was achieved. The relative standard deviations (RSD) for the determination of 0.40 and 0.80 µg/mL bismuth(III) were 2.1% and 1.1%, respectively, for five determinations. Based on this fact, a simple, rapid, and sensitive method was developed for the determination of bismuth(III) at nanogram level by RLS technique with a common spectrofluorimeter. This analytical system was successfully applied to determine the trace amounts of bismuth(III) in pharmaceutical products, which was in good agreement with the results obtained by atomic absorption spectrometry (AAS).

  11. Interplay of stereoelectronic and enviromental effects in tuning the structural and magnetic properties of a prototypical spin probe: further insights from a first principle dynamical approach.

    PubMed

    Pavone, Michele; Cimino, Paola; De Angelis, Filippo; Barone, Vincenzo

    2006-04-05

    The nitrogen isotropic hyperfine coupling constant (hcc) and the g tensor of a prototypical spin probe (di-tert-butyl nitroxide, DTBN) in aqueous solution have been investigated by means of an integrated computational approach including Car-Parrinello molecular dynamics and quantum mechanical calculations involving a discrete-continuum embedding. The quantitative agreement between computed and experimental parameters fully validates our integrated approach. Decoupling of the structural, dynamical, and environmental contributions acting onto the spectral observables allows an unbiased judgment of the role played by different effects in determining the overall experimental observables and highlights the importance of finite-temperature vibrational averaging. Together with their intrinsic interest, our results pave the route toward more reliable interpretations of EPR parameters of complex systems of biological and technological relevance.

  12. Influence of static and dynamic dipolar fields in bulk YIG/thin film NiFe systems probed via spin rectification effect

    NASA Astrophysics Data System (ADS)

    Soh, Wee Tee; Tay, Z. J.; Yakovlev, N. L.; Peng, Bin; Ong, C. K.

    2017-03-01

    The characteristics of the static and dynamic components of the dipolar fields originating from a bulk polycrystalline yttrium iron garnet (YIG) substrate are probed by depositing a NiFe (Permalloy) layer on it, which acts as a detector. By measuring dc voltages generated via spin rectification effect (SRE) within the NiFe layer under microwave excitation, we characterize the influence of dipolar fields from bulk YIG on the NiFe layer. It is found that the dynamic YIG dipolar fields modify the self-SRE of NiFe, driving its own rectification voltages within the NiFe layer, an effect we term as non-local SRE. This non-local SRE only occurs near the simultaneous resonance of both YIG and NiFe. On the other hand, the static dipolar field from YIG manifests itself as a negative anisotropy in the NiFe layer which shifts the latter's ferromagnetic resonance frequency.

  13. Difference between ²JC2H3 and ²JC3H2 spin-spin couplings in heterocyclic five- and six-membered rings as a probe for studying σ-ring currents: a quantum chemical analysis.

    PubMed

    Contreras, Rubén H; dos Santos, Francisco P; Ducati, Lucas C; Tormena, Cláudio F

    2010-12-01

    Adequate analyses of canonical molecular orbitals (CMOs) can provide rather detailed information on the importance of different σ-Fermi contact (FC) coupling pathways (FC term transmitted through the σ-skeleton). Knowledge of the spatial distribution of CMOs is obtained by expanding them in terms of natural bond orbitals (NBOs). Their relative importance for transmitting the σ-FC contribution to a given spin-spin coupling constants (SSCCs) is estimated by resorting to the expression of the FC term given by the polarisation propagator formalism. In this way, it is possible to classify the effects affecting such couplings in two different ways: delocalisation interactions taking place in the neighbourhood of the coupling nuclei and 'round the ring' effects. The latter, associated with σ-ring currents, are observed to yield significant differences between the FC terms of (2)J(C2H3) and (2)J(C3H2) SSCCs which, consequently, are taken as probes to gauge the differences in σ-ring currents for the five-membered rings (furan, thiophene, selenophene and pyrrol) and also for the six-membered rings (benzene, pyridine, protonated pyridine and N-oxide pyridine) used in the present study.

  14. Alginic acid-based macromolecular chemiluminescent probe for universal protein assay on a solid-phase membrane.

    PubMed

    Krawczyk, Tomasz; Kondo, Midori; Azam, Md Golam; Zhang, Huan; Shibata, Takayuki; Kai, Masaaki

    2010-11-01

    A novel chemiluminescent (CL) technique for the rapid determination of proteins on a membrane is described. The method utilizes an interaction between luminol-labeled alginic acid macromolecule and proteins. The synthesis of the macromolecular probe consists of the oxidation of alginic acid with NaIO(4), the introduction of luminol through imine formation as a CL tag, and the reduction of the conjugate with NaBH(4) to obtain the stable probe. The analytical protocol consists of adsorbing proteins on a poly(vinylidene difluoride) (PVDF) membrane, incubating the membrane for 30 min with the probe solution in the presence of boric acid and a surfactant, two short washing steps in order to remove an excess of the probe, and detection of CL intensity with hemin, tetra-n-propylammonium hydroxide and H(2)O(2). This proposed CL assay for proteins can be finished within 1 h, and indicates the detection limit of 15-250 ng of proteins on the membrane. The CL signals in the calibration curves for some proteins such as albumin show proportional intensities against the amounts of the proteins less than ca. 125 ng, though there is a logarithmic relationship between the CL signals and the protein amounts larger than ca. 125 ng. However, some other proteins indicate the proportional CL intensities against the increasing amounts in wider range up to 500 ng of the proteins. The synthesised alginic acid-based probe indicates specific selectivity towards proteins, and should be used as a CL probe for the universal detection of various proteins on a solid-phase membrane even in the presence of DNA and RNA.

  15. Probe depth matters in dermal microdialysis sampling of benzoic acid after topical application: an ex vivo study in human skin.

    PubMed

    Holmgaard, R; Benfeldt, E; Bangsgaard, N; Sorensen, J A; Brosen, K; Nielsen, F; Nielsen, J B

    2012-01-01

    Microdialysis (MD) in the skin - dermal microdialysis (DMD) - is a unique technique for sampling of topically as well as systemically administered drugs at the site of action, e.g. sampling of dermatological drug concentrations in the dermis. Debate has concerned the existence of a correlation between the depth of the sampling device - the probe - in the dermis and the amount of drug sampled following topical drug administration. This study evaluates the relation between probe depth and drug sampling using dermal DMD sampling ex vivo in human skin. We used superficial (<1 mm), intermediate (1-2 mm) and deep (>2 mm) positioning of the linear MD probe in the dermis of human abdominal skin, followed by topical application of 4 mg/ml of benzoic acid (BA) in skin chambers overlying the probes. Dialysate was sampled every hour for 12 h and analysed for BA content by high-performance liquid chromatography. Probe depth was measured by 20-MHz ultrasound scanning. The area under the time-versus-concentration curve (AUC) describes the drug exposure in the tissue during the experiment and is a relevant parameter to compare for the 3 dermal probe depths investigated. The AUC(0-12) were: superficial probes: 3,335 ± 1,094 μg·h/ml (mean ± SD); intermediate probes: 2,178 ± 1,068 μg·h/ml, and deep probes: 1,159 ± 306 μg·h/ml. AUC(0-12) sampled by the superficial probes was significantly higher than that of samples from the intermediate and deeply positioned probes (p value <0.05). There was a significant inverse correlation between probe depth and AUC(0-12) sampled by the same probe (p value <0.001, r(2) value = 0.5). The mean extrapolated lag-times (±SD) for the superficial probes were 0.8 ± 0.1 h, for the intermediate probes 1.7 ± 0.5 h, and for the deep probes 2.7 ± 0.5 h, which were all significantly different from each other (p value <0.05). In conclusion, this paper demonstrates that there is an inverse relationship between the depth of the probe in the dermis

  16. Polymer dynamics near the surface and in the bulk of poly(tetrafluoroethylene) probed by zero-field muon-spin-relaxation spectroscopy.

    PubMed

    McKenzie, Iain; Salman, Zaher; Giblin, Sean R; Han, Yun Yu; Leach, Gary W; Morenzoni, Elvezio; Prokscha, Thomas; Suter, Andreas

    2014-02-01

    The results of many experiments on polymers such as polystyrene indicate that the polymer chains near a free surface exhibit enhanced dynamics when compared with the bulk. We have investigated whether this is the case for poly(tetrafluoroethylene) (PTFE) by using zero-field muon-spin-relaxation spectroscopy to characterize a local probe, the F-Mu(+)-F state, which forms when spin-polarized positive muons are implanted in PTFE. Low-energy muons (implantation energies from 2.0 to 23.0 keV) were used to study the F-Mu(+)-F state between ∼ 23 and 191 nm from the free surface of PTFE. Measurements were also made with surface muons (4.1 MeV) where the mean implantation depth is on the order of ∼ 0.6 mm. The relaxation rate of the F-Mu(+)-F state up to ∼ 150 K was found to be significantly higher for muons implanted at 2.0 keV than for higher implantation energies, which suggests that the polymer chains in a region on the order of a few tens of nanometers from the free surface are more mobile than those in the bulk.

  17. Novel molecular beacon DNA probes for protein-nucleic acid interaction studies

    NASA Astrophysics Data System (ADS)

    Li, Jianwei J.; Perlette, John; Fang, Xiaohong; Kelley, Shannon; Tan, Weihong

    2000-03-01

    We report a novel approach to study protein-nucleic acid interactions by using molecular beacons (MBs). Molecular beacons are hairpin-shaped DNA oligonucleotide probes labeled with a fluorophore and a quencher, and can report the presence of target DNA/RNA sequences. MBs can also report the existence of single-stranded DNA binding proteins (SSB) through non-sequence specific binding. The interaction between SSB and MB has resulted in significant fluorescence restoration of the MB. The fluorescence enhancement brought by SSB and by complementary DNA is very comparable. The molar ratio of the binding between SSB and the molecular beacon is 1:1 with a binding constant of 2 X 107 M-1. Using the MB-SSB binding, we are able to determine SSB at 2 X 10-10 M with a conventional spectrometer. We have also applied MB DNA probes for the analysis of an enzyme lactic dehydrogenase (LDH), and for the investigation of its binding properties with ssDNA. The biding process between MB and different isoenzymes of LDH has been studied. We also show that there are significant differences in MB binding affinity to different proteins, which will enable selective binding studies of a variety of proteins. This new approach is potentially useful for protein-DNA/RNA interaction studies that require high sensitivity, speed and convenience. The results also open the possibility of using easily obtainable, custom designed, modified DNA molecules for studies of drug interactions and targeting. Our results demonstrate that MB can be effectively used for sensitive protein quantitation and for efficient protein-DNA interaction studies. MB has the signal transduction mechanism built within the molecule, and can thus be used for quick protein assay development and for real-time measurements.

  18. Peptide nucleic acid probe for protein affinity purification based on biotin-streptavidin interaction and peptide nucleic acid strand hybridization.

    PubMed

    Tse, Jenny; Wang, Yuanyuan; Zengeya, Thomas; Rozners, Eriks; Tan-Wilson, Anna

    2015-02-01

    We describe a new method for protein affinity purification that capitalizes on the high affinity of streptavidin for biotin but does not require dissociation of the biotin-streptavidin complex for protein retrieval. Conventional reagents place both the selectively reacting group (the "warhead") and the biotin on the same molecule. We place the warhead and the biotin on separate molecules, each linked to a short strand of peptide nucleic acid (PNA), synthetic polymers that use the same bases as DNA but attached to a backbone that is resistant to attack by proteases and nucleases. As in DNA, PNA strands with complementary base sequences hybridize. In conditions that favor PNA duplex formation, the warhead strand (carrying the tagged protein) and the biotin strand form a complex that is held onto immobilized streptavidin. As in DNA, the PNA duplex dissociates at moderately elevated temperature; therefore, retrieval of the tagged protein is accomplished by a brief exposure to heat. Using iodoacetate as the warhead, 8-base PNA strands, biotin, and streptavidin-coated magnetic beads, we demonstrate retrieval of the cysteine protease papain. We were also able to use our iodoacetyl-PNA:PNA-biotin probe for retrieval and identification of a thiol reductase and a glutathione transferase from soybean seedling cotyledons.

  19. Antimicrobial Poly(lactic acid)-Based Nanofibres Developed by Solution Blow Spinning.

    PubMed

    Martínez-Sanz, Marta; Bilbao-Sainz, Cristina; Du, Wen-Xian; Chiou, Bor-Sen; Williams, Tina G; Wood, Delilah F; Imam, Syed H; Orts, William J; Lopez-Rubio, Amparo; Lagaron, Jose M

    2015-01-01

    The present study reports on the development of hybrid poly(lactic acid) (PLA) fibres loaded with highly crystalline bacterial cellulose nanowhiskers (BCNW) by the novel solution blow spinning method. Furthermore, fibres with antimicrobial properties were generated by incorporating carvacrol and THC as antimicrobial agents and the biocide effect against Listeria monocytogenes was studied. Initially, PLA blow spun fibres containing BCNW were optimized in terms of morphology and thermal properties. The addition of BCNW was seen to significantly increase the viscosity and surface tension of solutions, restricting the capacity to form fibres for concentrations greater than 30 wt.-% BCNW. 15 wt.-% BCNW was selected as the optimum nanofiller loading as it led to the most uniform fibres morphology, with BCNW homogeneously distributed along the fibres' axis. Subsequently, carvacrol and THC were incorporated into the fibres to confer them with antimicrobial properties, although the hydrophobic PLA matrix did not provide an efficient release of the antimicrobials. Thus, hydrophilic substances were added in order to trigger the antimicrobials release through water sorption mechanisms. The addition of the BCNW filler was not seen to significantly increase the antimicrobial capacity of the fibres by itself and, hence, gelatin was added to help promoting further the hydrophylicity and biocide performance of the fibres. Nevertheless, for the more hydrophilic THC, the biocide capacity of the fibres with gelatin was accentuated further by the presence of the BCNW.

  20. ProbingSpin-Forbidden’ Oxygen Atom Transfer: Gas-Phase Reactions of Chromium-Porphyrin Complexes

    PubMed Central

    Fornarini, Simonetta; Lanucara, Francesco; Warren, Jeffrey J.

    2010-01-01

    Oxygen-atom transfer reactions of metalloporphyrin species play an important role in biochemical and synthetic oxidation reactions. An emerging theme in this chemistry is that spin-state changes can play important roles, and a ‘two-state’ reactivity model has been extensively applied especially in iron-porphyrin systems. Herein we explore the gas phase oxygen-atom transfer chemistry of meso-tetrakis(pentafluorophenyl)porphyrin (TPFPP) chromium complexes, as well as some other tetradentate macrocyclic ligands. Electrospray ionization in concert with Fourier transform ion cyclotron resonance (FT-ICR) spectrometry has been used to characterize and observe reactivity of the ionic species [(TPFPP)CrIII]+ (1) and [(TPFPP)CrVO]+ (2). These are an attractive system to examine the effects of spin state change on oxygen atom transfer because the d1 CrV species are doublets while the CrIII complexes have quartet ground states with high-lying doublet excited states. In the gas phase, [(TPFPP)CrIII]+ forms adducts with a variety of neutral donors but O-atom transfer is only observed for NO2. Pyridine N-oxide adducts of 1 do yield 2 upon collision induced dissociation (CID), but the ethylene oxide, DMSO, and TEMPO analogs do not. [(TPFPP)CrVO]+ is shown by its reactivity and by CID experiments to be a terminal metal-oxo with a single vacant coordination site. It also displays limited reaction chemistry, being deoxygenated only by the very potent reductant P(OMe)3. In general, [(TPFPP)CrVO]+ species are much less reactive than the Fe and Mn analogs. Thermochemical analysis of the reactions points towards the involvement of spin issues in the lower observed reactivity of the chromium complexes. PMID:20218631

  1. Spin-wave resonance in (Ga,Mn)As thin films: Probing in-plane surface magnetic anisotropy

    NASA Astrophysics Data System (ADS)

    Puszkarski, H.; Tomczak, P.

    2015-05-01

    We show that recent spin-wave resonance studies of (Ga,Mn)As thin films performed by Liu et al. [Phys. Rev. B 75, 195220 (2007), 10.1103/PhysRevB.75.195220] reveal a substantial increase in the in-plane uniaxial anisotropy at the film surface with respect to the bulk value (surface uniaxial anisotropy field H2∥ surf=305 Oe against the bulk value H2∥ bulk=77 Oe). At the same time, the cubic anisotropy at the film surface proves substantially lower than in the bulk (H4∥ surf=39 Oe against H4∥ bulk=197 Oe).

  2. Ultrafast supercontinuum fiber-laser based pump-probe scanning magneto-optical Kerr effect microscope for the investigation of electron spin dynamics in semiconductors at cryogenic temperatures with picosecond time and micrometer spatial resolution

    SciTech Connect

    Henn, T.; Kiessling, T. Ossau, W.; Molenkamp, L. W.; Biermann, K.; Santos, P. V.

    2013-12-15

    We describe a two-color pump-probe scanning magneto-optical Kerr effect microscope which we have developed to investigate electron spin phenomena in semiconductors at cryogenic temperatures with picosecond time and micrometer spatial resolution. The key innovation of our microscope is the usage of an ultrafast “white light” supercontinuum fiber-laser source which provides access to the whole visible and near-infrared spectral range. Our Kerr microscope allows for the independent selection of the excitation and detection energy while avoiding the necessity to synchronize the pulse trains of two separate picosecond laser systems. The ability to independently tune the pump and probe wavelength enables the investigation of the influence of excitation energy on the optically induced electron spin dynamics in semiconductors. We demonstrate picosecond real-space imaging of the diffusive expansion of optically excited electron spin packets in a (110) GaAs quantum well sample to illustrate the capabilities of the instrument.

  3. [Oligonucleotide derivatives in the nucleic acid hybridization analysis. I. Covalent immobilization of oligonucleotide probes onto the nylon].

    PubMed

    Dmitrienko, E V; Pyshnaia, I A; Pyshnyĭ, D V

    2010-01-01

    The features of UV-induced immobilization of oligonucleotides on a nylon membranes and the effectiveness of enzymatic labeling of immobilized probes at heterophase detection of nucleic acids are studied. Short terminal oligothymidilate (up to 10 nt) sequences are suggested to attach to the probe via a flexible ethylene glycol based linker. The presence of such fragment enhances the intensity of immobilization and reduces UV-dependent degradation of the targeted (sequence-specific) part of the probe by reducing the dose needed for the immobilization of DNA. The optimum dose of UV-irradiation is determined to be ~0.4 J/cm(2) at the wavelength 254 nm. This dose provides high level of hybridization signal for immobilized probes with various nucleotide composition of the sequence specific moiety. The amide groups of the polyamide are shown to play the key role in the photoinduced immobilization of nucleic acids, whereas the primary amino groups in the structure of PA is not the center responsible for the covalent binding of DNA by UV-irradiation, as previously believed. Various additives in the soaking solution during the membrane of UV-dependent immobilization of probes are shown to influence its effectiveness. The use of alternative to UV-irradiation system of radical generation are shown to provide the immobilization of oligonucleotides onto the nylon membrane.

  4. Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm.

    PubMed

    Ohrmalm, Christina; Jobs, Magnus; Eriksson, Ronnie; Golbob, Sultan; Elfaitouri, Amal; Benachenhou, Farid; Strømme, Maria; Blomberg, Jonas

    2010-11-01

    One of the main problems in nucleic acid-based techniques for detection of infectious agents, such as influenza viruses, is that of nucleic acid sequence variation. DNA probes, 70-nt long, some including the nucleotide analog deoxyribose-Inosine (dInosine), were analyzed for hybridization tolerance to different amounts and distributions of mismatching bases, e.g. synonymous mutations, in target DNA. Microsphere-linked 70-mer probes were hybridized in 3M TMAC buffer to biotinylated single-stranded (ss) DNA for subsequent analysis in a Luminex® system. When mismatches interrupted contiguous matching stretches of 6 nt or longer, it had a strong impact on hybridization. Contiguous matching stretches are more important than the same number of matching nucleotides separated by mismatches into several regions. dInosine, but not 5-nitroindole, substitutions at mismatching positions stabilized hybridization remarkably well, comparable to N (4-fold) wobbles in the same positions. In contrast to shorter probes, 70-nt probes with judiciously placed dInosine substitutions and/or wobble positions were remarkably mismatch tolerant, with preserved specificity. An algorithm, NucZip, was constructed to model the nucleation and zipping phases of hybridization, integrating both local and distant binding contributions. It predicted hybridization more exactly than previous algorithms, and has the potential to guide the design of variation-tolerant yet specific probes.

  5. Sucrose esters of carboxylic acids in glandular trichomes ofSolanum berthaultii deter settling and probing by green peach aphid.

    PubMed

    Neal, J J; Tingey, W M; Steffens, J C

    1990-02-01

    Removal of type B trichome exudate fromSolanum berthaultii leaflets leads to a decrease in tarsal gumming and mortality and an increase in feeding by the green peach aphid,Myzus persicae. Type B trichome exudate of theS. berthaultii accession PI 473331 is composed of a complex of 3',3,4,6-tetra-O-acyl sucroses containing primarily short-chain branched carboxylic acids. The acyl constituents are primarily derived from 2-methylpropanoic, 2-methylbutyric, and 8-methylnonanoic acids but constituents derived fromn-decanoic and dodecanoic acids are also present. Sucrose esters inhibit settling and probing by aphids in glass feeding cages.

  6. Resonant soft X-ray scattering—a new probe of charge, spin and orbital ordering in the manganites

    NASA Astrophysics Data System (ADS)

    Hatton, P. D.; Wilkins, S. B.; Beale, T. A. W.; Johal, T. K.; Prabhakaran, D.; Boothroyd, A. T.

    2005-04-01

    Soft X-ray resonant diffraction is a new technique pioneered by our group. We have published examples of the huge resonant enhancements of charge and magnetic scattering that can be obtained at the L-edges of 3d transition metal oxides. In this paper we will also show how resonant soft X-ray scattering enables direct observation of orbital ordering. We have studied the low temperature phase of La0.5Sr1.5MnO4 that displays charge, spin and orbital ordering. We have employed resonant soft X-ray scattering at the manganese L edges which provide a direct measurement of the orbital ordering. Energy scans at constant wavevector have been compared to theoretical predictions and show that at all temperatures there are two separate contributions to the observed scattering, direct Goodenough orbital ordering and strong cooperative Jahn-Teller distortions of the Mn ions. Finally, we will show how that the spin and orbital degrees of freedom are strongly correlated in these materials.

  7. Vogel-Fulcher-Tammann freezing of a thermally fluctuating artificial spin ice probed by x-ray photon correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Morley, S. A.; Alba Venero, D.; Porro, J. M.; Riley, S. T.; Stein, A.; Steadman, P.; Stamps, R. L.; Langridge, S.; Marrows, C. H.

    2017-03-01

    We report on the crossover from the thermal to the athermal regime of an artificial spin ice formed from a square array of magnetic islands whose lateral size, 30 nm × 70 nm, is small enough that they are dynamic at room temperature. We used resonant magnetic soft x-ray photon correlation spectroscopy as a method to observe the time-time correlations of the fluctuating magnetic configurations of spin ice during cooling, which are found to slow abruptly as a freezing temperature of T0=178 ±5 K is approached. This slowing is well described by a Vogel-Fulcher-Tammann law, implying that the frozen state is glassy, with the freezing temperature being commensurate with the strength of magnetostatic interaction energies in the array. The activation temperature, TA=40 ±10 K, is much less than that expected from a Stoner-Wohlfarth coherent rotation model. Zero-field-cooled/field-cooled magnetometry reveals a freeing up of fluctuations of states within islands above this temperature, caused by variation in the local anisotropy axes at the oxidised edges. This Vogel-Fulcher-Tammann behavior implies that the system enters a glassy state upon freezing, which is unexpected for a system with a well-defined ground state.

  8. Quantification of Syntrophic Fatty Acid-β-Oxidizing Bacteria in a Mesophilic Biogas Reactor by Oligonucleotide Probe Hybridization

    PubMed Central

    Hansen, Kaare H.; Ahring, Birgitte K.; Raskin, Lutgarde

    1999-01-01

    Small-subunit rRNA sequences were obtained for two saturated fatty acid-β-oxidizing syntrophic bacteria, Syntrophomonas sapovorans and Syntrophomonas wolfei LYB, and sequence analysis confirmed their classification as members of the family Syntrophomonadaceae. S. wolfei LYB was closely related to S. wolfei subsp. wolfei, but S. sapovorans did not cluster with the other members of the genus Syntrophomonas. Five oligonucleotide probes targeting the small-subunit rRNA of different groups within the family Syntrophomonadaceae, which contains all currently known saturated fatty acid-β-oxidizing syntrophic bacteria, were developed and characterized. The probes were designed to be specific at the family, genus, and species levels and were characterized by temperature-of-dissociation and specificity studies. To demonstrate the usefulness of the probes for the detection and quantification of saturated fatty acid-β-oxidizing syntrophic bacteria in methanogenic environments, the microbial community structure of a sample from a full-scale biogas plant was determined. Hybridization results with probes for syntrophic bacteria and methanogens were compared to specific methanogenic activities and microbial numbers determined with most-probable-number estimates. Most of the methanogenic rRNA was comprised of Methanomicrobiales rRNA, suggesting that members of this order served as the main hydrogen-utilizing microorganisms. Between 0.2 and 1% of the rRNA was attributed to the Syntrophomonadaceae, of which the majority was accounted for by the genus Syntrophomonas. PMID:10543784

  9. Exciton spin coherence in InGaAs/GaAs quantum dots revisited by heterodyne pump-probe experiment

    NASA Astrophysics Data System (ADS)

    Eble, B.; Siarry, B.; Bernardot, F.; Grinberg, P.; Testelin, C.; Lemaître, A.

    2016-10-01

    We demonstrate here the phase control of the neutral exciton quantum beats in InGaAs/GaAs quantum dots. A longitudinal magnetic field is used as a tuning parameter to change the phase of the oscillations in a deterministic way. This effect arises from the competition between the Zeeman splitting and the electron/hole exchange interaction on the exciton dipole symmetry. To explore this mechanism, we have developed a pump-probe setup based on the optical heterodyne detection of the quantum dots reflectivity allowing one to measure the exciton dynamics from a small quantum dots ensemble (˜300).

  10. Probing the neutron star spin evolution in the young Small Magellanic Cloud Be/X-ray binary SXP 1062

    NASA Astrophysics Data System (ADS)

    Popov, S. B.; Turolla, R.

    2012-03-01

    The newly discovered Be/X-ray binary in the Small Magellanic Cloud, SXP 1062, provides the first example of a robust association with a supernova remnant (SNR). The short age estimated for the SNR qualifies SXP 1062 as the youngest known source in its class, ?. As such, it allows us to test current models of magnetorotational evolution of neutron stars in a still unexplored regime. Here we discuss possible evolutionary scenarios for SXP 1062 in an attempt to reconcile its long spin period, ?, and short age. Although several options can be considered, like an anomalously long initial period or the presence of a fossil disc, our results indicate that SXP 1062 may host a neutron star born with a large initial magnetic field, typically in excess of ˜ 1014 G, which then decayed to ˜ 1013 G.

  11. Probing the Spin Structure of the Proton Using Polarized Proton-Proton Collisionsand the Production of W Bosons

    SciTech Connect

    Beaumier, Michael J.

    2016-08-01

    This thesis discusses the process of extracting the longitudinal asymmetry, A$W±\\atop{L}$ describing W → μ production in forward kinematic regimes. This asymmetry is used to constrain our understanding of the polarized parton distribution functions characterizing $\\bar{u}$ and $\\bar{d}$ sea quarks in the proton. This asymmetry will be used to constrain the overall contribution of the sea-quarks to the total proton spin. The asymmetry is evaluated over the pseudorapidity range of the PHENIX Muon Arms, 2.1 < |η| 2.6, for longitudinally polarized proton-proton collisions at 510 GeV √s. In particular, I will discuss the statistical methods used to characterize real muonic W decays and the various background processes is presented, including a discussion of likelihood event selection and the Extended Unbinned Maximum Likelihood t. These statistical methods serve estimate the yields of W muonic decays, which are used to calculate the longitudinal asymmetry.

  12. Differentiation of Candida albicans and Candida dubliniensis by Fluorescent In Situ Hybridization with Peptide Nucleic Acid Probes

    PubMed Central

    Oliveira, Kenneth; Haase, Gerhard; Kurtzman, Cletus; Hyldig-Nielsen, Jens Jo/rgen; Stender, Henrik

    2001-01-01

    The recent discovery of Candida dubliniensis as a separate species that traditionally has been identified as Candida albicans has led to the development of a variety of biochemical and molecular methods for the differentiation of these two pathogenic yeasts. rRNA sequences are well-established phylogenetic markers, and probes targeting species-specific rRNA sequences have been used in diagnostic assays for the detection and identification of microorganisms. Peptide nucleic acid (PNA) is a DNA mimic with improved hybridization characteristics, and the neutral backbone of PNA probes offers significant advantages in whole-cell in situ hybridization assays. In this study, we developed PNA probes targeting the rRNAs of C. albicans and C. dubliniensis and applied them to a fluorescence in situ hybridization method (PNA FISH) for differentiation between C. albicans and C. dubliniensis. Liquid cultures were smeared onto microscope slides, heat fixed, and then hybridized for 30 min. Unhybridized PNA probe was removed by washing, and smears were examined by fluorescence microscopy. Evaluation of the PNA FISH method using smears of 79 C. dubliniensis and 70 C. albicans strains showed 100% sensitivity and 100% specificity for both PNA probes. We concluded that PNA FISH is a powerful tool for the differentiation of C. albicans and C. dubliniensis. PMID:11682542

  13. Intracellular surface-enhanced Raman scattering probe based on gold nanorods functionalized with mercaptohexadecanoic acid with reduced cytotoxicity.

    PubMed

    Liu, Min; Wang, Zhuyuan; Zong, Shenfei; Zhang, Ruohu; Yang, Jing; Cui, Yiping

    2012-01-01

    A surface-enhanced Raman scattering (SERS) probe for intracellular detection was demonstrated by utilizing gold nanorods (GNRs) coated with p-aminothiophenol as the Raman reporters. In this probe, to reduce the cytotoxicity of GNRs, cetyltrimethylammonium bromide (CTAB) molecules adsorbed on the surfaces of GNRs as ligands were replaced by mercaptohexadecanoic acid via a "round-trip" phase change method. Such a ligand exchange can reduce the toxicity of the probe compared to the original CTAB-stabilized GNRs, which were confirmed by both 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and bright field view of HeLa cells. Meanwhile, the transmission electron microscopy images indicated that there is no significant morphologic change of GNRs before and after the ligand exchange. Moreover, its SERS performance was adequately retained after the incorporation of the probe into living HeLa cells. This new type of SERS probe is expected to have great potential in intracellular imaging or sensing applications.

  14. Detection and quantification of genetically modified organisms using very short, locked nucleic acid TaqMan probes.

    PubMed

    Salvi, Sergio; D'Orso, Fabio; Morelli, Giorgio

    2008-06-25

    Many countries have introduced mandatory labeling requirements on foods derived from genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (PCR) based upon the TaqMan probe chemistry has become the method mostly used to support these regulations; moreover, event-specific PCR is the preferred method in GMO detection because of its high specificity based on the flanking sequence of the exogenous integrant. The aim of this study was to evaluate the use of very short (eight-nucleotide long), locked nucleic acid (LNA) TaqMan probes in 5'-nuclease PCR assays for the detection and quantification of GMOs. Classic TaqMan and LNA TaqMan probes were compared for the analysis of the maize MON810 transgene. The performance of the two types of probes was tested on the maize endogenous reference gene hmga, the CaMV 35S promoter, and the hsp70/cryIA(b) construct as well as for the event-specific 5'-integration junction of MON810, using plasmids as standard reference molecules. The results of our study demonstrate that the LNA 5'-nuclease PCR assays represent a valid and reliable analytical system for the detection and quantification of transgenes. Application of very short LNA TaqMan probes to GMO quantification can simplify the design of 5'-nuclease assays.

  15. Physical characterization of the state of motion of the phenalenyl spin probe in cation-exchanged faujasite zeolite supercages with pulsed EPR

    NASA Astrophysics Data System (ADS)

    Doetschman, D. C.; Dwyer, D. W.; Fox, J. D.; Frederick, C. K.; Scull, S.; Thomas, G. D.; Utterback, S. G.; Wei, J.

    1994-08-01

    The molecular motion of the phenalenyl (PNL) spin probe in the supercages of cation-exchanged X and Y zeolites (faujasites) has been physically characterized by pulsed and continuous wave (CW) electron paramagnetic resonance (EPR). Both X and Y zeolites, whose cation sites were exchanged with the alkali metal ions, Li +, Na +, K +, Rb + and Cs + were examined. There is a good correspondence between the temperature dependences of the PNL electron spin phase memory time and the CW EPR spectra. Both display evidence of a thermal activation from a stationary, non-rotating molecular state to a low-temperature state of in-plane rotation (Das et al., Chem Phys. 143 (1990) 253). The rate of in-plane rotation is an activated process, with E* | / R=1289 |+- 35 K and 1462 ± 47 K in NaX and KX zeolites, respectively. The rotation appears to be about an axis along which the half-filled, non-bonding π orbital interacts with the exchanged cation in the supercage. Both CW and pulsed EPR also show a higher temperature activation from the in-plane rotating state to an effectively isoptropic state of rotation of PNL in which the PNL-cation bond is thought to be broken, with E* ⊥ / R=2050 ± 110 K, 1956 ± 46K, 1335 ± 97 K in LiX, NaX and KX zeolites, respectively. The strength of the PNL-cation bonding decreases with increasing cation atomic number as indicated by E* ⊥ and the peripheral repulsion (crowding) of PNL increases with cation size as indicated E* |. There are qualitative indications that the binding of PNL to the cations in the Y zeolite is stronger than in the X zeolite.

  16. Spin Hall Magnetoresistance as a Probe for Surface Magnetization in Pt /Co Fe2O4 Bilayers

    NASA Astrophysics Data System (ADS)

    Isasa, Miren; Vélez, Saül; Sagasta, Edurne; Bedoya-Pinto, Amilcar; Dix, Nico; Sánchez, Florencio; Hueso, Luis E.; Fontcuberta, Josep; Casanova, Fèlix

    2016-09-01

    We study the spin Hall magnetoresistance (SMR) in Pt grown in situ on CoFe2O4 (CFO) ferrimagnetic insulating films. A careful analysis of the angle-dependent and field-dependent longitudinal magnetoresistance indicates that the SMR contains a contribution that does not follow the bulk magnetization of CFO, but it is a fingerprint of the complex magnetism at the surface of the CFO layer, thus signaling SMR as a tool for mapping surface magnetization. A systematic study of the SMR for different temperatures and CFO thicknesses gives us information impossible to obtain with any standard magnetometry technique. On one hand, the surface magnetization behaves independently of the CFO thickness and does not saturate up to high fields, evidencing that the surface has its own anisotropy. On the other hand, characteristic zero-field magnetization steps are not present at the surface while they are relevant in the bulk, strongly suggesting that antiphase boundaries are responsible for such intriguing features. In addition, a contribution from the ordinary magnetoresistance of Pt is identified, which is distinguishable only due to the low resistivity of the in situ grown Pt.

  17. Probing protein hydration and aging of food materials by the magnetic field dependence of proton spin-lattice relaxation times.

    PubMed

    Godefroy, Sophie; Korb, Jean-Pierre; Creamer, Lawrence K; Watkinson, Philip J; Callaghan, Paul T

    2003-11-15

    Most cheeses can be considered as solid emulsions of milk fat in a matrix of water and proteins. Regions of each of the phases can be liquid during processing and maturation. Identifying these regions and monitoring changes in them is important as a prelude to controlling the structure of the final cheese. We concentrate on the behavior of water in the vicinity of proteins as a function of cheese aging. Our method utilizes nuclear magnetic relaxation dispersion (NMRD) associated with the frequency dependence of water spin-lattice relaxation rates using the field cycling NMR technique. This method provides insight into the dynamical behavior of water molecules on a very large time scale. Moreover, we can distinguish between molecular motion in bulk and motion in the vicinity of a source of relaxation, such as proteins. A fit of our dispersion data using a theory developed by J.-P. Korb and R.G. Bryant (J. Chem. Phys. 115 (2001) 23) allowed us to determine the degree of hydration of proteins as a function of aging. In particular, we find that protein hydration increases with ripening.

  18. 1H and 2H NMR spin-lattice relaxation probing water: PEG molecular dynamics in solution.

    PubMed

    Clop, Eduardo M; Perillo, María A; Chattah, Ana K

    2012-10-04

    Nuclear magnetic resonance spin-lattice relaxation times (T(1)) measurements were performed in aqueous solutions of poly(ethylene glycol) (PEG) of 6000 Da molecular mass to study the dynamical relation between PEG and water molecules at different solute concentrations. (1)H-T(1) experiments were carried on at a low magnetic field in the time domain (20 MHz) and at a high field (400 MHz) to obtain spectral resolution. Two contributing components were identified in each proton system, PEG and water, presenting values of T(1) with very different orders of magnitude. The approximate matching between the shorter (1)H-T(1) values associated with water and PEG has lead us to conclude that there exists a network of interactions (hydrogen bonds) between the solute and the solvent, which results in the presence of an ordered and dehydrated structure of PEG folded or self-assembled in equilibrium with a more flexible monomer structure. Dynamic light scattering results were consistent with the formation of PEG aggregates, showing a mean size between 40 and 100 nm.

  19. Visualization of the mycelia of wood-rotting fungi by fluorescence in situ hybridization using a peptide nucleic acid probe.

    PubMed

    Nakada, Yuji; Nakaba, Satoshi; Matsunaga, Hiroshi; Funada, Ryo; Yoshida, Makoto

    2013-01-01

    White rot fungus, Phanerochaete chrysosporium, and brown rot fungus, Postia placenta, grown on agar plates, were visualized by fluorescence in situ hybridization (FISH) using a peptide nucleic acid (PNA) probe. Mycelia grown on wood chips were also clearly detected by PNA-FISH following blocking treatment. To the best of our knowledge, this is the first report on the visualization of fungi in wood by FISH.

  20. A high-resolution mitochondria-targeting ratiometric fluorescent probe for detection of the endogenous hypochlorous acid

    NASA Astrophysics Data System (ADS)

    Zhou, Liyi; Lu, Dan-Qing; Wang, Qianqian; Hu, Shunqin; Wang, Haifei; Sun, Hongyan; Zhang, Xiaobing

    2016-09-01

    Hypochlorite anion, one of the biologically important reactive oxygen species, plays an essential role in diverse normal biochemical functions and abnormal pathological processes. Herein, an efficient high-resolution mitochondria-targeting ratiometric fluorescent probe for hypochlorous acid detection has been designed, synthesized and characterized. It is easily synthesized by the condensation reaction (Cdbnd C) of a 2-(2-hydroxyphenyl) quinazolin-4(3H)-one fluorophore and a cyanine group (mitochondria-targeting), which made the whole molecular a large Stokes shift (210 nm) and the two well-resolved emission peaks separated by 140 nm. As a result, it is considered as a good candidate for high resolution hypochlorous acid imaging in live cells. The ratiometric fluorescent probe exhibited outstanding features of high sensitivity, high selectivity, rapid response time (within 50 s), and excellent mitochondria-targeting ability. Moreover, the probe can also be successfully applied to imaging endogenously hypochlorous acid in the mitochondria of living cells with low cytotoxicity, and high resolution.

  1. A carbon dot-based "off-on" fluorescent probe for highly selective and sensitive detection of phytic acid.

    PubMed

    Gao, Zhao; Wang, Libing; Su, Rongxin; Huang, Renliang; Qi, Wei; He, Zhimin

    2015-08-15

    We herein report a facile, one-step pyrolysis synthesis of photoluminescent carbon dots (CDs) using citric acid as the carbon source and lysine as the surface passivation reagent. The as-prepared CDs show narrow size distribution, excellent blue fluorescence and good photo-stability and water dispersivity. The fluorescence of the CDs was found to be effectively quenched by ferric (Fe(III)) ions with high selectivity via a photo-induced electron transfer (PET) process. Upon addition of phytic acid (PA) to the CDs/Fe(III) complex dispersion, the fluorescence of the CDs was significantly recovered, arising from the release of Fe(III) ions from the CDs/Fe(III) complex because PA has a higher affinity for Fe(III) ions compared to CDs. Furthermore, we developed an "off-on" fluorescence assay method for the detection of phytic acid using CDs/Fe(III) as a fluorescent probe. This probe enables the selective detection of PA with a linear range of 0.68-18.69 μM and a limit of detection (signal-to-noise ratio is 3) of 0.36 μM. The assay method demonstrates high selectivity, repeatability, stability and recovery ratio in the detection of the standard and real PA samples. We believe that the facile operation, low-cost, high sensitivity and selectivity render this CD-based "off-on" fluorescent probe an ideal sensing platform for the detection of PA.

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

    PubMed

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

    2014-08-01

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

  3. Diffusive behavior in LiMPO4 with M=Fe, Co, Ni probed by muon-spin relaxation

    NASA Astrophysics Data System (ADS)

    Sugiyama, Jun; Nozaki, Hiroshi; Harada, Masashi; Kamazawa, Kazuya; Ikedo, Yutaka; Miyake, Yasuhiro; Ofer, Oren; Månsson, Martin; Ansaldo, Eduardo J.; Chow, Kim H.; Kobayashi, Genki; Kanno, Ryoji

    2012-02-01

    In order to study the diffusive nature of lithium transition-metal phospho-olivines, we measured muon-spin relaxation (μ+SR) spectra for the polycrystalline LiMPO4 samples with M=Mn, Fe, Co, or Ni in the temperature range between 50 and 500 K. The μ+SR spectra under zero applied field are strongly affected by the magnetic moments of the 3d electrons in the M2+ ions so that, for LiMnPO4, it was difficult to detect the relaxation change caused by the diffusion due to the large Mn2+(S=5/2) moments. However, diffusive behavior was clearly observed via the relaxation due to nuclear dipolar fields above ˜150 K for LiFePO4, LiCoPO4, and LiNiPO4 as S decreased from 2 to 1. From the temperature dependence of the nuclear field fluctuation rate, self-diffusion coefficients of Li+ ions (DLi) at 300 K and its activation energy (Ea) were estimated, respectively, as ˜3.6(2)×10-10 cm2/s and Ea=0.10(2) eV for LiFePO4, ˜1.6(1)×10-10 cm2/s and Ea=0.10(1) eV for LiCoPO4, and ˜2.7(4)×10-10 cm2/s and Ea=0.17(2) eV for LiNiPO4, assuming that the diffusing Li+ ions jump between the regular site and interstitial sites.

  4. Distortional binding of transition state analogs to human purine nucleoside phosphorylase probed by magic angle spinning solid-state NMR

    PubMed Central

    Vetticatt, Mathew J.; Itin, Boris; Evans, Gary B.; Schramm, Vern L.

    2013-01-01

    Transition state analogs mimic the geometry and electronics of the transition state of enzymatic reactions. These molecules bind to the active site of the enzyme much tighter than substrate and are powerful noncovalent inhibitors. Immucillin-H (ImmH) and 4′-deaza-1′-aza-2′-deoxy-9-methylene Immucillin-H (DADMe-ImmH) are picomolar inhibitors of human purine nucleoside phosphorylase (hPNP). Although both molecules are electronically similar to the oxocarbenium-like dissociative hPNP transition state, DADMe-ImmH is more potent than ImmH. DADMe-ImmH captures more of the transition state binding energy by virtue of being a closer geometric match to the hPNP transition state than ImmH. A consequence of these similarities is that the active site of hPNP exerts greater distortional forces on ImmH than on DADMe-ImmH to “achieve” the hPNP transition state geometry. By using magic angle spinning solid-state NMR to investigate stable isotope-labeled ImmH and DADMe-ImmH, we have explored the difference in distortional binding of these two inhibitors to hPNP. High-precision determinations of internuclear distances from NMR recoupling techniques, rotational echo double resonance, and rotational resonance, have provided unprecedented atomistic insight into the geometric changes that occur upon binding of transition state analogs. We conclude that hPNP stabilizes conformations of these chemically distinct analogs having distances between the cation and leaving groups resembling those of the known transition state. PMID:24043827

  5. Structural transitions in full-length human prion protein detected by xenon as probe and spin labeling of the N-terminal domain

    PubMed Central

    Narayanan, Sunilkumar Puthenpurackal; Nair, Divya Gopalakrishnan; Schaal, Daniel; Barbosa de Aguiar, Marisa; Wenzel, Sabine; Kremer, Werner; Schwarzinger, Stephan; Kalbitzer, Hans Robert

    2016-01-01

    Fatal neurodegenerative disorders termed transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of fibrils of misfolded prion protein PrP. The noble gas xenon accommodates into four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23–230) as detected by [1H, 15N]-HSQC spectroscopy. In thermal equilibrium a fifth xenon binding site is formed transiently by amino acids A120 to L125 of the presumably disordered N-terminal domain and by amino acids K185 to T193 of the well-folded domain. Xenon bound PrP was modelled by restraint molecular dynamics. The individual microscopic and macroscopic dissociation constants could be derived by fitting the data to a model including a dynamic opening and closing of the cavities. As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain. This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn2+-binding to the octarepeat motif. PMID:27341298

  6. Structural transitions in full-length human prion protein detected by xenon as probe and spin labeling of the N-terminal domain.

    PubMed

    Narayanan, Sunilkumar Puthenpurackal; Nair, Divya Gopalakrishnan; Schaal, Daniel; Barbosa de Aguiar, Marisa; Wenzel, Sabine; Kremer, Werner; Schwarzinger, Stephan; Kalbitzer, Hans Robert

    2016-06-24

    Fatal neurodegenerative disorders termed transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of fibrils of misfolded prion protein PrP. The noble gas xenon accommodates into four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23-230) as detected by [(1)H, (15)N]-HSQC spectroscopy. In thermal equilibrium a fifth xenon binding site is formed transiently by amino acids A120 to L125 of the presumably disordered N-terminal domain and by amino acids K185 to T193 of the well-folded domain. Xenon bound PrP was modelled by restraint molecular dynamics. The individual microscopic and macroscopic dissociation constants could be derived by fitting the data to a model including a dynamic opening and closing of the cavities. As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain. This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn(2+)-binding to the octarepeat motif.

  7. Detection of chromosomal inversions using non-repetitive nucleic acid probes

    NASA Technical Reports Server (NTRS)

    Bailey, Susan M. (Inventor); Ray, F. Andrew (Inventor); Goodwin, Edwin H. (Inventor); Bedford, Joel S. (Inventor); Cornforth, Michael N. (Inventor)

    2012-01-01

    A method for the identification of chromosomal inversions is described. Single-stranded sister chromatids are generated, for example by CO-FISH. A plurality of non-repetitive, labeled probes of relatively small size are hybridized to portions of only one of a pair of single-stranded sister chromatids. If no inversion exists, all of the probes will hybridize to a first chromatid. If an inversion has occurred, these marker probes will be detected on the sister chromatid at the same location as the inversion on the first chromatid.

  8. Detection of Chromosomal Inversions Using Non-Repetitive Nucleic Acid Probes

    NASA Technical Reports Server (NTRS)

    Bailey, Susan M. (Inventor); Ray, F. Andrew (Inventor); Goodwin, Edwin H. (Inventor); Bedford, Joel S. (Inventor); Cornforth, Michael N. (Inventor)

    2014-01-01

    A method and a kit for the identification of chromosomal inversions are described. Single-stranded sister chromatids are generated, for example by CO-FISH. A plurality of non-repetitive, labeled probes of relatively small size are hybridized to portions of only one of a pair of single-stranded sister chromatids. If no inversion exists, all of the probes will hybridize to a first chromatid. If an inversion has occurred, these marker probes will be detected on the sister chromatid at the same location as the inversion on the first chromatid.

  9. Detection of Sialic Acid-Utilising Bacteria in a Caecal Community Batch Culture Using RNA-Based Stable Isotope Probing

    PubMed Central

    Young, Wayne; Egert, Markus; Bassett, Shalome A.; Bibiloni, Rodrigo

    2015-01-01

    Sialic acids are monosaccharides typically found on cell surfaces and attached to soluble proteins, or as essential components of ganglioside structures that play a critical role in brain development and neural transmission. Human milk also contains sialic acid conjugated to oligosaccharides, glycolipids, and glycoproteins. These nutrients can reach the large bowel where they may be metabolised by the microbiota. However, little is known about the members of the microbiota involved in this function. To identify intestinal bacteria that utilise sialic acid within a complex intestinal community, we cultured the caecal microbiota from piglets in the presence of 13C-labelled sialic acid. Using RNA-based stable isotope probing, we identified bacteria that consumed 13C-sialic acid by fractionating total RNA in isopycnic buoyant density gradients followed by 16S rRNA gene analysis. Addition of sialic acid caused significant microbial community changes. A relative rise in Prevotella and Lactobacillus species was accompanied by a corresponding reduction in the genera Escherichia/Shigella, Ruminococcus and Eubacterium. Inspection of isotopically labelled RNA sequences suggests that the labelled sialic acid was consumed by a wide range of bacteria. However, species affiliated with the genus Prevotella were clearly identified as the most prolific users, as solely their RNA showed significantly higher relative shares among the most labelled RNA species. Given the relevance of sialic acid in nutrition, this study contributes to a better understanding of their microbial transformation in the intestinal tract with potential implications for human health. PMID:25816158

  10. Electron spin resonance probe for the solvation of ionomer membranes and other microscopically heterogeneous systems. Cu[sup 2+] in nafion, sephadex and silica gel

    SciTech Connect

    Bednarek, J.; Schlick, S. )

    1992-01-01

    Cu[sup 2+] is a sensitive electron spin resonance (ESR) probe for the penetration of various polar solvents in membranes made of Nafion and as an indicator for the replacement of one solvent by another. The ESR parameters (g and [sup 63]Cu hyperfine tensors) can be translated into a structure of the solvent around the cation. The replacement of a solvent in the membrane by another depends on the polarity of the two solvents. The solvent with the largest dielectric constant, N-methylformamide (NMF), can be replaced by water but not by methanol or acetonitrile (dielectric constants 182, 78.5, 32.7, and 37.5, respectively). Preferential solvation of the cation by water in three water/acetonitrile mixtures (9:1, 1:1, and 1:9 by volume) in contact with silica gel, Sephadex, and Nafion has been observed in various degrees. Nafion is most selective, followed by Sephadex and by silica gel. The selectivity appears to be related to electrostatic interactions which are strongest in Nafion and weakest in silica gel. 43 refs., 6 figs., 1 tab.

  11. Pulsed EPR Determination of Water Accessibility to Spin-Labeled Amino Acid Residues in LHCIIb

    PubMed Central

    Volkov, A.; Dockter, C.; Bund, T.; Paulsen, H.; Jeschke, G.

    2009-01-01

    Membrane proteins reside in a structured environment in which some of their residues are accessible to water, some are in contact with alkyl chains of lipid molecules, and some are buried in the protein. Water accessibility of residues may change during folding or function-related structural dynamics. Several techniques based on the combination of pulsed electron paramagnetic resonance (EPR) with site-directed spin labeling can be used to quantify such water accessibility. Accessibility parameters for different residues in major plant light-harvesting complex IIb are determined by electron spin echo envelope modulation spectroscopy in the presence of deuterated water, deuterium contrast in transversal relaxation rates, analysis of longitudinal relaxation rates, and line shape analysis of electron-spin-echo-detected EPR spectra as well as by the conventional techniques of measuring the maximum hyperfine splitting and progressive saturation in continuous-wave EPR. Systematic comparison of these parameters allows for a more detailed characterization of the environment of the spin-labeled residues. These techniques are applicable independently of protein size and require ∼10–20 nmol of singly spin-labeled protein per sample. For a residue close to the N-terminus, in a domain unresolved in the existing x-ray structures of light-harvesting complex IIb, all methods indicate high water accessibility. PMID:19186148

  12. Hybridization probe for femtomolar quantification of selected nucleic acid sequences on a disposable electrode.

    PubMed

    Jenkins, Daniel M; Chami, Bilal; Kreuzer, Matthias; Presting, Gernot; Alvarez, Anne M; Liaw, Bor Yann

    2006-04-01

    Mixed monolayers of electroactive hybridization probes on gold surfaces of a disposable electrode were investigated as a technology for simple, sensitive, selective, and rapid gene identification. Hybridization to the ferrocene-labeled hairpin probes reproducibly diminished cyclic redox currents, presumably due to a displacement of the label from the electrode. Observed peak current densities were roughly 1000x greater than those observed in previous studies, such that results could easily be interpreted without the use of algorithms to correct for background polarization currents. Probes were sensitive to hybridization with a number of oligonucleotide sequences with varying homology, but target oligonucleotides could be distinguished from competing nontarget sequences based on unique "melting" profiles from the probe. Detection limits were demonstrated down to nearly 100 fM, which may be low enough to identify certain genetic conditions or infections without amplification. This technology has rich potential for use in field devices for gene identification as well as in gene microarrays.

  13. Human papillomavirus 35 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorincz, A.T.

    1989-07-18

    This patent describes an HPV 35 hybridization probe comprising a member selected from the group consisting of (i) HPV 35 DNA or fragments thereof labelled with a marker and (ii) HPV 35 RNA or fragments thereof labelled with a marker.

  14. Human papillomavirus 43 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorincz, A.T.

    1989-07-18

    This patent describes an HPV 43 hybridization probe comprising a member selected from the group consisting of (i) HPV 43 DNA or fragments thereof labelled with a marker and (ii) HPV 43 RNA or fragments thereof labelled with a marker.

  15. Human papillomavirus 56 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorinez, A.T.

    1990-03-13

    This patent describes an HPV 56 hybridization probe. It comprises: a member selected from the group consisting of HPV 56 DNA or fragments thereof labelled with a marker and HPV 56 RNA or fragments thereof labelled with a marker.

  16. Human papillomavirus 44 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorincz, A.T.

    1989-07-18

    This patent describes an HPV 44 hybridization probe comprising a member selected from the group consisting of (1) HPV 44 DNA or fragments thereof labelled with a marker and (ii) HPV 44 RNA or fragments thereof labelled with a marker.

  17. Y chromosome specific nucleic acid probe and method for identifying the Y chromosome in SITU

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich

    1999-01-01

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.

  18. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOEpatents

    Gray, J.W.; Weier, H.U.

    1998-11-24

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences. 9 figs.

  19. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich

    1998-01-01

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.

  20. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich

    2001-01-01

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.

  1. Y chromosome specific nucleic acid probe and method for identifying the Y chromosome in SITU

    DOEpatents

    Gray, J.W.; Weier, H.U.

    1999-03-30

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences. 9 figs.

  2. NanoCluster Beacon - A New Molecular Probe for Homogeneous Detection of Nucleic Acid Targets

    DTIC Science & Technology

    2011-02-01

    requires only a single preparation step (i.e. nanocluster formation on NC probes), but because there is no need to remove excess silver ions or...Oligonucleotide-templated nanoclusters consisting of a few atoms of silver (DNA/Ag NCs) have been made into a new molecular probe that “lights up...upon target DNA binding, termed a NanoCluster Beacon (NCB). We discovered that interactions between silver nanoclusters and a proximal, guanine- rich

  3. A universal strategy for visual chiral recognition of α-amino acids with L-tartaric acid-capped gold nanoparticles as colorimetric probes.

    PubMed

    Song, Guoxin; Zhou, Fulin; Xu, Chunli; Li, Baoxin

    2016-02-21

    The ability to recognize and quantify the chirality of alpha-amino acids constitutes the basis of many critical areas for specific targeting in drug development and metabolite probing. It is still challenging to conveniently distinguish the enantiomer of amino acids largely due to the lack of a universal and simple strategy. In this work, we report a strategy for the visual recognition of α-amino acids. It is based on the chirality of L-tartaric acid-capped gold nanoparticles (L-TA-capped AuNPs, ca. 13 nm in diameter). All of 19 right-handed α-amino acids can induce a red-to-blue color change of L-TA-capped AuNP solution, whereas all of the left-handed amino acids (except cysteine) cannot. The chiral recognition can be achieved by the naked eye and a simple spectrophotometer. This method does not require complicated chiral modification, and excels through its low-cost, good availability of materials and its simplicity. Another notable feature of this method is its high generality, and this method can discriminate almost all native α-amino acid enantiomers. This versatile method could be potentially used for high-throughput chiral recognition of amino acids.

  4. Probing the Substrate Specificity and Protein-Protein Interactions of the E. coli Fatty Acid Dehydratase, FabA

    PubMed Central

    Finzel, Kara; Nguyen, Chi; Jackson, David R.; Gupta, Aarushi; Tsai, Shiou-Chuan; Burkart, Michael D.

    2015-01-01

    Summary Microbial fatty acid biosynthetic enzymes are important targets for areas as diverse as antibiotic development to biofuel production. Elucidating the molecular basis of chain length control during fatty acid biosynthesis is crucial for the understanding of regulatory processes of this fundamental metabolic pathway. In Escherichia coli, the acyl carrier protein (AcpP) plays a central role by sequestering and shuttling the growing acyl chain between fatty acid biosynthetic enzymes. FabA, a β-hydroxylacyl-AcpP dehydratase, is an important enzyme in controlling fatty acid chain length and saturation levels. FabA-AcpP interactions are transient in nature and thus difficult to visualize. In this study, four mechanistic crosslinking probes mimicking varying acyl chain lengths were synthesized to systematically probe for modified chain length specificity of fourteen FabA mutants. These studies provide evidence for the AcpP interacting “positive patch,” FabA mutations that altered substrate specificity, and the roles that the FabA “gating residues” play in chain-length selection. PMID:26526101

  5. Fluorescent amino acid undergoing excited state intramolecular proton transfer for site-specific probing and imaging of peptide interactions.

    PubMed

    Sholokh, Marianna; Zamotaiev, Oleksandr M; Das, Ranjan; Postupalenko, Viktoriia Y; Richert, Ludovic; Dujardin, Denis; Zaporozhets, Olga A; Pivovarenko, Vasyl G; Klymchenko, Andrey S; Mély, Yves

    2015-02-12

    Fluorescent amino acids bearing environment-sensitive fluorophores are highly valuable tools for site-selective probing of peptide/ligand interactions. Herein, we synthesized a fluorescent l-amino acid bearing the 4'-methoxy-3-hydroxyflavone fluorophore (M3HFaa) that shows dual emission, as a result of an excited state intramolecular proton transfer (ESIPT). The dual emission of M3HFaa was found to be substantially more sensitive to hydration as compared to previous analogues. By replacing the Ala30 and Trp37 residues of a HIV-1 nucleocapsid peptide, M3HFaa was observed to preserve the peptide structure and functions. Interaction of the labeled peptides with nucleic acids and lipid vesicles produced a strong switch in their dual emission, favoring the emission of the ESIPT product. This switch was associated with the appearance of long-lived fluorescence lifetimes for the ESIPT product, as a consequence of the rigid environment in the complexes that restricted the relative motions of the M3HFaa aromatic moieties. The strongest restriction and thus the longest fluorescence lifetimes were observed at position 37 in complexes with nucleic acids, where the probe likely stacks with the nucleobases. Based on the dependence of the lifetime values on the nature of the ligand and the labeled position, two-photon fluorescence lifetime imaging was used to identify the binding partners of the labeled peptides microinjected into living cells. Thus, M3HFaa appears as a sensitive tool for monitoring site selectively peptide interactions in solution and living cells.

  6. Fluorescence In Situ Hybridization with Peptide Nucleic Acid Probes for Rapid Identification of Candida albicans Directly from Blood Culture Bottles

    PubMed Central

    Rigby, Susan; Procop, Gary W.; Haase, Gerhard; Wilson, Deborah; Hall, Geraldine; Kurtzman, Cletus; Oliveira, Kenneth; Von Oy, Sabina; Hyldig-Nielsen, Jens J.; Coull, James; Stender, Henrik

    2002-01-01

    A new fluorescence in situ hybridization (FISH) method that uses peptide nucleic acid (PNA) probes for identification of Candida albicans directly from positive-blood-culture bottles in which yeast was observed by Gram staining (herein referred to as yeast-positive blood culture bottles) is described. The test (the C. albicans PNA FISH method) is based on a fluorescein-labeled PNA probe that targets C. albicans 26S rRNA. The PNA probe is added to smears made directly from the contents of the blood culture bottle and hybridized for 90 min at 55°C. Unhybridized PNA probe is removed by washing of the mixture (30 min), and the smears are examined by fluorescence microscopy. The specificity of the method was confirmed with 23 reference strains representing phylogenetically related yeast species and 148 clinical isolates covering the clinically most significant yeast species, including C. albicans (n = 72), C. dubliniensis (n = 58), C. glabrata (n = 5), C. krusei (n = 2), C. parapsilosis (n = 4), and C. tropicalis (n = 3). The performance of the C. albicans PNA FISH method as a diagnostic test was evaluated with 33 routine and 25 simulated yeast-positive blood culture bottles and showed 100% sensitivity and 100% specificity. It is concluded that this 2.5-h method for the definitive identification of C. albicans directly from yeast-positive blood culture bottles provides important information for optimal antifungal therapy and patient management. PMID:12037084

  7. Real-time, in-situ analysis of silver ions using nucleic acid probes modified silica microfiber interferometry.

    PubMed

    Yu, Bo; Huang, Yunyun; Zhou, Jun; Guo, Tuan; Guan, Bai-Ou

    2017-04-01

    A sensitive Ag(+) sensor based on nucleic acid probes modified silica microfiber interferometry is designed and developed. The probes on microfiber surface plays the part on catching Ag(+) as tentacles, while their conformation change from random coils to hairpins. It induces the fiber surface refractive index change, which is captured by the optical fiber and translated into a significant wavelength shift in the interferometric fringe. Such a combination enables an improved concentration sensitivity of 0.22nm/log M and limit of detection of 1.36 × 10(-9)M, taking the advantage of real-time and in-situ analysis. It shows good selectivity in the present of many other metal ions and offers potential to analysis in real matrix, especially in the environmental samples must be analyzed in a short time. This may provide insights into the preparation of sensing platforms for optical quantification of other small molecular, supplementing the existing tools.

  8. Spin transition sensors based on β-amino-acid 1,2,4-triazole derivative.

    PubMed

    Dîrtu, Marinela M; Schmit, France; Naik, Anil D; Rotaru, Aurelian; Marchand-Brynaert, J; Garcia, Yann

    2011-01-01

    A β-aminoacid ester was successfully derivatized to yield to 4H-1,2-4-triazol-4-yl-propionate (βAlatrz) which served as a neutral bidentate ligand in the 1D coordination polymer [Fe(βAlatrz)(3)](CF(3)SO(3))(2)·0.5H(2)O (1·0.5H(2)O). The temperature dependence of the high-spin molar fraction derived from (57)Fe Mossbauer spectroscopy recorded on cooling below room temperature reveals an exceptionally abrupt single step transition between high-spin and low-spin states with a hysteresis loop of width 4 K (T(c) (↑) = 232 K and T(c) (↓) = 228 K) in agreement with magnetic susceptibility measurements. The material presents striking reversible thermochromism from white, at room temperature, to pink on quench cooling to liquid nitrogen, and acts as an alert towards temperature variations. The phase transition is of first order, as determined by differential scanning calorimetry, with transition temperatures matching the ones determined by SQUID and Mössbauer spectroscopy. The freshly prepared sample of 1·0.5H(2)O, dried in air, was subjected to annealing at 390 K, and the obtained white compound [Fe(βAlatrz)(3)](CF(3)SO(3))(2) (1) was found to exhibit a similar spin transition curve however much temperature was increased by (T(c) (↑) = 252 K and T(c) (↓) = 248 K). The removal of lattice water molecules from 1·0.5H(2)O is not accompanied by a change of the morphology and of the space group, and the chain character is preserved. However, an internal pressure effect stabilizing the low-spin state is evidenced.

  9. Focused upon hybridization: rapid and high sensitivity detection of DNA using isotachophoresis and peptide nucleic acid probes.

    PubMed

    Ostromohov, Nadya; Schwartz, Ortal; Bercovici, Moran

    2015-09-15

    We present a novel assay for rapid and high sensitivity detection of nucleic acids without amplification. Utilizing the neutral backbone of peptide nucleic acids (PNA), our method is based on the design of low electrophoretic mobility PNA probes, which do not focus under isotachophoresis (ITP) unless bound to their target sequence. Thus, background noise associated with free probes is entirely eliminated, significantly improving the signal-to-noise ratio while maintaining a simple single-step assay requiring no amplification steps. We provide a detailed analytical model and experimentally demonstrate the ability to detect targets as short as 17 nucleotides (nt) and a limit of detection of 100 fM with a dynamic range of 5 decades. We also demonstrate that the assay can be successfully implemented for detection of DNA in human serum without loss of signal. The assay requires 15 min to complete, and it could potentially be used in applications where rapid and highly sensitive amplification-free detection of nucleic acids is desired.

  10. Fast Li ion dynamics in the solid electrolyte Li7 P3 S11 as probed by (6,7) Li NMR spin-lattice relaxation.

    PubMed

    Wohlmuth, Dominik; Epp, Viktor; Wilkening, Martin

    2015-08-24

    The development of safe and long-lasting all-solid-state batteries with high energy density requires a thorough characterization of ion dynamics in solid electrolytes. Commonly, conductivity spectroscopy is used to study ion transport; much less frequently, however, atomic-scale methods such as nuclear magnetic resonance (NMR) are employed. Here, we studied long-range as well as short-range Li ion dynamics in the glass-ceramic Li7 P3 S11 . Li(+) diffusivity was probed by using a combination of different NMR techniques; the results are compared with those obtained from electrical conductivity measurements. Our NMR relaxometry data clearly reveal a very high Li(+) diffusivity, which is reflected in a so-called diffusion-induced (6) Li NMR spin-lattice relaxation peak showing up at temperatures as low as 313 K. At this temperature, the mean residence time between two successful Li jumps is in the order of 3×10(8) s(-1) , which corresponds to a Li(+) ion conductivity in the order of 10(-4) to 10(-3) S cm(-1) . Such a value is in perfect agreement with expectations for the crystalline but metastable glass ceramic Li7 P3 S11 . In contrast to conductivity measurements, NMR analysis reveals a range of activation energies with values ranging from 0.17 to 0.26 eV, characterizing Li diffusivity in the bulk. In our case, through-going Li ion transport, when probed by using macroscopic conductivity spectroscopy, however, seems to be influenced by blocking grain boundaries including, for example, amorphous regions surrounding the Li7 P3 S11 crystallites. As a result of this, long-range ion transport as seen by impedance spectroscopy is governed by an activation energy of approximately 0.38 eV. The findings emphasize how surface and grain boundary effects can drastically affect long-range ionic conduction. If we are to succeed in solid-state battery technology, such effects have to be brought under control by, for example, sophisticated densification or through the preparation

  11. Real-Time PCR Genotyping using Taqman Probes to Detect High Oleic Acid Peanuts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Oleic acid, a monounsaturated, omega-9 fatty acid is an important agronomic trait in peanut cultivars because it provides increased shelf life, improved flavor, enhanced fatty acid composition, and a beneficial effect on human health. Currently, most high oleic peanuts confer limited resistance to ...

  12. Probing the acidity of carboxylic acids in protic ionic liquids, water, and their binary mixtures: activation energy of proton transfer.

    PubMed

    Shukla, Shashi Kant; Kumar, Anil

    2013-02-28

    Acidity functions were used to express the ability of a solvent/solution to donate/accept a proton to a solute. The present work accounts for the acidity determination of HCOOH, CH3COOH, and CH3CH2COOH in the alkylimidazolium-based protic ionic liquids (PILs), incorporated with carboxylate anion, water, and in a binary mixture of PIL and water using the Hammett acidity function, H0. A reversal in the acidity trend was observed, when organic acids were transferred from water to PIL. It was emphasized that an increased stabilization offered by PIL cation toward the more basic conjugate anion of organic acid was responsible for this anomalous change in acidity order in PILs, which was absent in water. The greater stabilization of a basic organic anion by PIL cation is discussed in terms of the stable hard–soft acid base (HSAB) pairing. A change in the H0 values of these acids was observed with a change in temperature, and a linear correlation between the ln H0 and 1/T was noted. This relationship points toward the activation energy of proton transfer (E(a,H+)), a barrier provided by the medium during the proton transfer from Brønsted acid to indicator. The H0 function in binary mixtures points to the involvement of pseudosolvent, the behavior of which changes with the nature and concentration of acid. The presence of the maxima/minima in the H0 function is discussed in terms of the synergetic behavior of the pseudosolvent composed of the mixtures of aqueous PILs.

  13. Modelling of retention of pesticides in reversed-phase high-performance liquid chromatography: quantitative structure-retention relationships based on solute quantum-chemical descriptors and experimental (solvatochromic and spin-probe) mobile phase descriptors.

    PubMed

    D'Archivio, Angelo Antonio; Ruggieri, Fabrizio; Mazzeo, Pietro; Tettamanti, Enzo

    2007-06-19

    A quantitative structure-retention relationship (QSRR) analysis based on multilinear regression (MLR) and artificial neural networks (ANNs) is carried out to model the combined effect of solute structure and eluent composition on the retention behaviour of pesticides in isocratic reversed-phase high-performance liquid chromatography (RP-HPLC). The octanol-water partition coefficient and four quantum chemical descriptors (the total dipole moment, the mean polarizability, the anisotropy of the polarizability and a descriptor of hydrogen-bonding based on the atomic charges on acidic and basic chemical functionalities) are considered as solute descriptors. In order to identify suitable mobile phase descriptors, encoding composition-dependent properties of both methanol- and acetonitrile-containing mobile phases, the Kamlet-Taft solvatochromic parameters (polarity-dipolarity, hydrogen-bond acidity and hydrogen-bond basicity, pi*, alpha and beta, respectively) and the 14N hyperfine-splitting constant (aN) of a spin-probe dissolved in the eluent are examined. A satisfactory description of mobile phase properties influencing the solute retention is provided by aN and beta or alternatively pi* and beta. The two seven-parameter models resulting from combination of aN and beta, or pi* and beta, with the solute descriptors were tested on a set of 26 pesticides representative of 10 different chemical classes in a wide range of mobile phase composition (30-60% (v/v) water-methanol and 30-70% (v/v) water-acetonitrile). Within the explored experimental range, the acidity of the eluent, as quantified by alpha, is almost constant, and this parameter is in fact irrelevant. The results reveal that aN and pi*, that can be considered as interchangeable mobile phase descriptors, are the most influent variables in the respective models. The predictive ability of the proposed models, as tested on an external data set, is quite good (Q2 close to 0.94) when a MLR approach is used, but the

  14. Proteomic-based stable isotope probing reveals taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton

    DOE PAGES

    Bryson, Samuel; Li, Zhou; Pett-Ridge, Jennifer; ...

    2016-04-26

    Heterotrophic marine bacterioplankton are a critical component of the carbon cycle, processing nearly a quarter of annual global primary production, yet defining how substrate utilization preferences and resource partitioning structure these microbial communities remains a challenge. In this study, we utilized proteomics-based stable isotope probing (proteomic SIP) to characterize the assimilation of amino acids by coastal marine bacterioplankton populations. We incubated microcosms of seawater collected from Newport, OR and Monterey Bay, CA with 1 M 13C-amino acids for 15 and 32 hours. Subsequent analysis of 13C incorporation into protein biomass quantified the frequency and extent of isotope enrichment for identifiedmore » proteins. Using these metrics we tested whether amino acid assimilation patterns were different for specific bacterioplankton populations. Proteins associated with Rhodobacterales and Alteromonadales tended to have a significantly high number of tandem mass spectra from 13C-enriched peptides, while Flavobacteriales and SAR11 proteins generally had significantly low numbers of 13C-enriched spectra. Rhodobacterales proteins associated with amino acid transport and metabolism had an increased frequency of 13C-enriched spectra at time-point 2, while Alteromonadales ribosomal proteins were 13C- enriched across time-points. Overall, proteomic SIP facilitated quantitative comparisons of dissolved free amino acids assimilation by specific taxa, both between sympatric populations and between protein functional groups within discrete populations, allowing an unprecedented examination of population-level metabolic responses to resource acquisition in complex microbial communities.« less

  15. Hybridization-based detection of Helicobacter pylori at human body temperature using advanced locked nucleic acid (LNA) probes.

    PubMed

    Fontenete, Sílvia; Guimarães, Nuno; Leite, Marina; Figueiredo, Céu; Wengel, Jesper; Filipe Azevedo, Nuno

    2013-01-01

    The understanding of the human microbiome and its influence upon human life has long been a subject of study. Hence, methods that allow the direct detection and visualization of microorganisms and microbial consortia (e.g. biofilms) within the human body would be invaluable. In here, we assessed the possibility of developing a variant of fluorescence in situ hybridization (FISH), named fluorescence in vivo hybridization (FIVH), for the detection of Helicobacter pylori. Using oligonucleotide variations comprising locked nucleic acids (LNA) and 2'-O-methyl RNAs (2'OMe) with two types of backbone linkages (phosphate or phosphorothioate), we were able to successfully identify two probes that hybridize at 37 °C with high specificity and sensitivity for H. pylori, both in pure cultures and in gastric biopsies. Furthermore, the use of this type of probes implied that toxic compounds typically used in FISH were either found to be unnecessary or could be replaced by a non-toxic substitute. We show here for the first time that the use of advanced LNA probes in FIVH conditions provides an accurate, simple and fast method for H. pylori detection and location, which could be used in the future for potential in vivo applications either for this microorganism or for others.

  16. Spectroscopic quantification of 5-hydroxymethylcytosine in genomic DNA using boric acid-functionalized nano-microsphere fluorescent probes.

    PubMed

    Chen, Hua-Yan; Wei, Jing-Ru; Pan, Jiong-Xiu; Zhang, Wei; Dang, Fu-Quan; Zhang, Zhi-Qi; Zhang, Jing

    2017-05-15

    5-hydroxymethylcytosine (5hmC) is the sixth base of DNA. It is involved in active DNA demethylation and can be a marker of diseases such as cancer. In this study, we developed a simple and sensitive 2-(4-boronophenyl)quinoline-4-carboxylic acid modified poly (glycidyl methacrylate (PBAQA-PGMA) fluorescent probe to detect the 5hmC content of genomic DNA based on T4 β-glucosyltransferase-catalyzed glucosylation of 5hmC. The fluorescence-enhanced intensity recorded from the DNA sample was proportional to its 5-hydroxymethylcytosine content and could be quantified by fluorescence spectrophotometry. The developed probe showed good detection sensitivity and selectivity and a good linear relationship between the fluorescence intensity and the concentration of 5 hmC within a 0-100nM range. Compared with other fluorescence detection methods, this method not only could determine trace amounts of 5 hmC from genomic DNA but also could eliminate the interference of fluorescent dyes and the need for purification. It also could avoid multiple labeling. Because the PBAQA-PGMA probe could enrich the content of glycosyl-5-hydroxymethyl-2-deoxycytidine from a complex ground substance, it will broaden the linear detection range and improve sensitivity. The limit of detection was calculated to be 0.167nM after enrichment. Furthermore, the method was successfully used to detect 5-hydroxymethylcytosine from mouse tissues.

  17. Mercaptopropionic acid-capped CdTe quantum dots as fluorescence probe for the determination of salicylic acid in pharmaceutical products.

    PubMed

    Bunkoed, Opas; Kanatharana, Proespichaya

    2015-11-01

    Mercaptopropionic acid (MPA)-capped cadmium telluride (CdTe) quantum dot (QDs) fluorescent probes were synthesized in aqueous solution and used for the determination of salicylic acid. The interaction between the MPA-capped CdTe QDs and salicylic acid was studied using fluorescence spectroscopy and some parameters that could modify the fluorescence were investigated to optimize the measurements. Under optimum conditions, the quenched fluorescence intensity of MPA-capped CdTe QDs was linearly proportional to the concentration of salicylic acid in the range of 0.5-40 µg mL(-1) with a coefficient of determination of 0.998, and the limit of detection was 0.15 µg mL(-1). The method was successfully applied to the determination of salicylic acid in pharmaceutical products, and satisfactory results were obtained that were in agreement with both the high pressure liquid chromatography (HPLC) method and the claimed values. The recovery of the method was in the range 99 ± 3% to 105 ± 9%. The proposed method is simple, rapid, cost effective, highly sensitivity and eminently suitable for the quality control of pharmaceutical preparation. The possible mechanisms for the observed quenching reaction was also discussed.

  18. A confocal study on the visualization of chromaffin cell secretory vesicles with fluorescent targeted probes and acidic dyes.

    PubMed

    Moreno, Alfredo; SantoDomingo, Jaime; Fonteriz, Rosalba I; Lobatón, Carmen D; Montero, Mayte; Alvarez, Javier

    2010-12-01

    Secretory vesicles have low pH and have been classically identified as those labelled by a series of acidic fluorescent dyes such as acridine orange or neutral red, which accumulate into the vesicles according to the pH gradient. More recently, several fusion proteins containing enhanced green fluorescent protein (EGFP) and targeted to the secretory vesicles have been engineered. Both targeted fluorescent proteins and acidic dyes have been used, separately or combined, to monitor the dynamics of secretory vesicle movements and their fusion with the plasma membrane. We have now investigated in detail the degree of colocalization of both types of probes using several fusion proteins targeted to the vesicles (synaptobrevin2-EGFP, Cromogranin A-EGFP and neuropeptide Y-EGFP) and several acidic dyes (acridine orange, neutral red and lysotracker red) in chromaffin cells, PC12 cells and GH(3) cells. We find that all the acidic dyes labelled the same population of vesicles. However, that population was largely different from the one labelled by the targeted proteins, with very little colocalization among them, in all the cell types studied. Our data show that the vesicles containing the proteins more characteristic of the secretory vesicles are not labelled by the acidic dyes, and vice versa. Peptide glycyl-L-phenylalanine 2-naphthylamide (GPN) produced a rapid and selective disruption of the vesicles labelled by acidic dyes, suggesting that they could be mainly lysosomes. Therefore, these labelling techniques distinguish two clearly different sets of acidic vesicles in neuroendocrine cells. This finding should be taken into account whenever vesicle dynamics is studied using these techniques.

  19. Carboxylic Acid Ionophores as Probes of the Role of Calcium in Biological Systems

    NASA Technical Reports Server (NTRS)

    Reed, P. W.

    1983-01-01

    The biological effects of calcium ionophores are described, focusing on arachidonic acid oxygenation, and the formation of a number of oxygenated metabolites of arachidonic acid. These metabolites are involved in a number of bodily functions, and their production may be regulated by calcium.

  20. Spin pumping and inverse spin Hall effects—Insights for future spin-orbitronics (invited)

    SciTech Connect

    Zhang, Wei Jungfleisch, Matthias B.; Jiang, Wanjun; Fradin, Frank Y.; Pearson, John E.; Hoffmann, Axel; Sklenar, Joseph; Ketterson, John B.

    2015-05-07

    Quantification of spin-charge interconversion has become increasingly important in the fast-developing field of spin-orbitronics. Pure spin current generated by spin pumping acts as a sensitive probe for many bulk and interface spin-orbit effects, which has been indispensable for the discovery of many promising new spin-orbit materials. We apply spin pumping and inverse spin Hall effect experiments, as a useful metrology, and study spin-orbit effects in a variety of metals and metal interfaces. We quantify the spin Hall effects in Ir and W using the conventional bilayer structures and discuss the self-induced voltage in a single layer of ferromagnetic permalloy. Finally, we extend our discussions to multilayer structures and quantitatively reveal the spin current flow in two consecutive normal metal layers.

  1. Spin pumping and inverse spin Hall effects—Insights for future spin-orbitronics (invited)

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Jungfleisch, Matthias B.; Jiang, Wanjun; Sklenar, Joseph; Fradin, Frank Y.; Pearson, John E.; Ketterson, John B.; Hoffmann, Axel

    2015-05-01

    Quantification of spin-charge interconversion has become increasingly important in the fast-developing field of spin-orbitronics. Pure spin current generated by spin pumping acts as a sensitive probe for many bulk and interface spin-orbit effects, which has been indispensable for the discovery of many promising new spin-orbit materials. We apply spin pumping and inverse spin Hall effect experiments, as a useful metrology, and study spin-orbit effects in a variety of metals and metal interfaces. We quantify the spin Hall effects in Ir and W using the conventional bilayer structures and discuss the self-induced voltage in a single layer of ferromagnetic permalloy. Finally, we extend our discussions to multilayer structures and quantitatively reveal the spin current flow in two consecutive normal metal layers.

  2. Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-05-01

    Benzene carboxylic acids and benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by 1H, 13C and 15N NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations.

  3. Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis Using ᴅ-Amino Acids

    PubMed Central

    Reichau, Sebastian; Blackmore, Nicola J.; Jiao, Wanting; Parker, Emily J.

    2016-01-01

    Chirality plays a major role in recognition and interaction of biologically important molecules. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) is the first enzyme of the shikimate pathway, which is responsible for the synthesis of aromatic amino acids in bacteria and plants, and a potential target for the development of antibiotics and herbicides. DAH7PS from Mycobacterium tuberculosis (MtuDAH7PS) displays an unprecedented complexity of allosteric regulation, with three interdependent allosteric binding sites and a ternary allosteric response to combinations of the aromatic amino acids l-Trp, l-Phe and l-Tyr. In order to further investigate the intricacies of this system and identify key residues in the allosteric network of MtuDAH7PS, we studied the interaction of MtuDAH7PS with aromatic amino acids that bear the non-natural d-configuration, and showed that the d-amino acids do not elicit an allosteric response. We investigated the binding mode of d-amino acids using X-ray crystallography, site directed mutagenesis and isothermal titration calorimetry. Key differences in the binding mode were identified: in the Phe site, a hydrogen bond between the amino group of the allosteric ligands to the side chain of Asn175 is not established due to the inverted configuration of the ligands. In the Trp site, d-Trp forms no interaction with the main chain carbonyl group of Thr240 and less favourable interactions with Asn237 when compared to the l-Trp binding mode. Investigation of the MtuDAH7PSN175A variant further supports the hypothesis that the lack of key interactions in the binding mode of the aromatic d-amino acids are responsible for the absence of an allosteric response, which gives further insight into which residues of MtuDAH7PS play a key role in the transduction of the allosteric signal. PMID:27128682

  4. Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis Using ᴅ-Amino Acids.

    PubMed

    Reichau, Sebastian; Blackmore, Nicola J; Jiao, Wanting; Parker, Emily J

    2016-01-01

    Chirality plays a major role in recognition and interaction of biologically important molecules. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) is the first enzyme of the shikimate pathway, which is responsible for the synthesis of aromatic amino acids in bacteria and plants, and a potential target for the development of antibiotics and herbicides. DAH7PS from Mycobacterium tuberculosis (MtuDAH7PS) displays an unprecedented complexity of allosteric regulation, with three interdependent allosteric binding sites and a ternary allosteric response to combinations of the aromatic amino acids l-Trp, l-Phe and l-Tyr. In order to further investigate the intricacies of this system and identify key residues in the allosteric network of MtuDAH7PS, we studied the interaction of MtuDAH7PS with aromatic amino acids that bear the non-natural d-configuration, and showed that the d-amino acids do not elicit an allosteric response. We investigated the binding mode of d-amino acids using X-ray crystallography, site directed mutagenesis and isothermal titration calorimetry. Key differences in the binding mode were identified: in the Phe site, a hydrogen bond between the amino group of the allosteric ligands to the side chain of Asn175 is not established due to the inverted configuration of the ligands. In the Trp site, d-Trp forms no interaction with the main chain carbonyl group of Thr240 and less favourable interactions with Asn237 when compared to the l-Trp binding mode. Investigation of the MtuDAH7PSN175A variant further supports the hypothesis that the lack of key interactions in the binding mode of the aromatic d-amino acids are responsible for the absence of an allosteric response, which gives further insight into which residues of MtuDAH7PS play a key role in the transduction of the allosteric signal.

  5. Kinetics of rapid covalent bond formation of aniline with humic acid: ESR investigations with nitroxide spin labels

    NASA Astrophysics Data System (ADS)

    Glinka, Kevin; Matthies, Michael; Theiling, Marius; Hideg, Kalman; Steinhoff, Heinz-Jürgen

    2016-04-01

    Sulfonamide antibiotics used in livestock farming are distributed to farmland by application of slurry as fertilizer. Previous work suggests rapid covalent binding of the aniline moiety to humic acids found in soil. In the current work, kinetics of this binding were measured in X-band EPR spectroscopy by incubating Leonardite humic acid (LHA) with a paramagnetic aniline spin label (anilino-NO (2,5,5-Trimethyl-2-(3-aminophenyl)pyrrolidin-1-oxyl)). Binding was detected by a pronounced broadening of the spectral lines after incubation of LHA with anilino-NO. The time evolution of the amplitude of this feature was used for determining the reaction kinetics. Single- and double-exponential models were fitted to the data obtained for modelling one or two first-order reactions. Reaction rates of 0.16 min-1 and 0.012 min-1, were found respectively. Addition of laccase peroxidase did not change the kinetics but significantly enhanced the reacting fraction of anilino-NO. This EPR-based method provides a technically simple and effective method for following rapid binding processes of a xenobiotic substance to humic acids.

  6. Probing Protein Structure by Amino Acid-Specific Covalent Labeling and Mass Spectrometry

    PubMed Central

    Mendoza, Vanessa Leah; Vachet, Richard W.

    2009-01-01

    For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies. PMID:19016300

  7. Orbital elementary excitations as probes of entanglement and quantum phase transitions of collective spins in an entangled Bose-Einstein condensate

    NASA Astrophysics Data System (ADS)

    Wu, Rukuan; Shi, Yu

    2011-02-01

    A mixture of two species of pseudospin-(1)/(2) Bose gases exhibits interesting interplay between spin and orbital degrees of freedom. Expectation values of various quantities of the collective spins of the two species play crucial roles in the Gross-Pitaevskii-like equations governing the four orbital wave functions in which Bose-Einstein condensation occurs. Consequently, the elementary excitations of these orbital wave functions reflect properties of the collective spins. When the coupling between the two collective spins is isotropic, the energy gap of the gapped orbital excitation peaks. There is a quantum phase transition in the ground state of the effective Hamiltonian of the two collective spins, which have previously been found to be maximally entangled.

  8. Probing Phosphorus Efficient Low Phytic Acid Content Soybean Genotypes with Phosphorus Starvation in Hydroponics Growth System.

    PubMed

    Kumar, Varun; Singh, Tiratha Raj; Hada, Alkesh; Jolly, Monica; Ganapathi, Andy; Sachdev, Archana

    2015-10-01

    Phosphorus is an essential nutrient required for soybean growth but is bound in phytic acid which causes negative effects on both the environment as well as the animal nutrition. Lowering of phytic acid levels is associated with reduced agronomic characteristics, and relatively little information is available on the response of soybean plants to phosphorus (P) starvation. In this study, we evaluated the effects of different P starvation concentrations on the phytic acid content, growth, and yield of seven mutant genotypes along with the unirradiated control, JS-335, in a hydroponics growth system. The low phytic acid containing mutant genotypes, IR-JS-101, IR-DS-118, and IR-V-101, showed a relatively high growth rate in low P concentration containing nutrient solution (2 μM), whereas the high P concentration (50 μM) favored the growth of IR-DS-111 and IR-DS-115 mutant genotypes containing moderate phytate levels. The mutant genotypes with high phytic acid content, IR-DS-122, IR-DS-114, and JS-335, responded well under P starvation and did not have any significant effect on the growth and yield of plants. Moreover, the reduction of P concentration in nutrient solution from 50 to 2 μM also reduced the phytic acid content in the seeds of all the soybean genotypes under study. The desirable agronomic performance of low phytic acid containing mutant genotype IR-DS-118 reported in this study suggested it to be a P-efficient genotype which could be considered for agricultural practices under P limiting soils.

  9. Boronic acids as probes for investigation of allosteric modulation of the chemokine receptor CXCR3.

    PubMed

    Bernat, Viachaslau; Admas, Tizita Haimanot; Brox, Regine; Heinemann, Frank W; Tschammer, Nuska

    2014-11-21

    The chemokine receptor CXCR3 is a G protein-coupled receptor, which conveys extracellular signals into cells by changing its conformation upon agonist binding. To facilitate the mechanistic understanding of allosteric modulation of CXCR3, we combined computational modeling with the synthesis of novel chemical tools containing boronic acid moiety, site-directed mutagenesis, and detailed functional characterization. The design of boronic acid derivatives was based on the predictions from homology modeling and docking. The choice of the boronic acid moiety was dictated by its unique ability to interact with proteins in a reversible covalent way, thereby influencing conformational dynamics of target biomolecules. During the synthesis of the library we have developed a novel approach for the purification of drug-like boronic acids. To validate the predicted binding mode and to identify amino acid residues responsible for the transduction of signal through CXCR3, we conducted a site-directed mutagenesis study. With the use of allosteric radioligand RAMX3 we were able to establish the existence of a second allosteric binding pocket in CXCR3, which enables different binding modes of structurally closely related allosteric modulators of CXCR3. We have also identified residues Trp109(2.60) and Lys300(7.35) inside the transmembrane bundle of the receptor as crucial for the regulation of the G protein activation. Furthermore, we report the boronic acid 14 as the first biased negative allosteric modulator of the receptor. Overall, our data demonstrate that boronic acid derivatives represent an outstanding tool for determination of key receptor-ligand interactions and induction of ligand-biased signaling.

  10. Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same

    DOEpatents

    Chee, Mark; Gingeras, Thomas R.; Fodor, Stephen P. A.; Hubble, Earl A.; Morris, MacDonald S.

    1999-01-19

    The invention provides an array of oligonucleotide probes immobilized on a solid support for analysis of a target sequence from a human immunodeficiency virus. The array comprises at least four sets of oligonucleotide probes 9 to 21 nucleotides in length. A first probe set has a probe corresponding to each nucleotide in a reference sequence from a human immunodeficiency virus. A probe is related to its corresponding nucleotide by being exactly complementary to a subsequence of the reference sequence that includes the corresponding nucleotide. Thus, each probe has a position, designated an interrogation position, that is occupied by a complementary nucleotide to the corresponding nucleotide. The three additional probe sets each have a corresponding probe for each probe in the first probe set. Thus, for each nucleotide in the reference sequence, there are four corresponding probes, one from each of the probe sets. The three corresponding probes in the three additional probe sets are identical to the corresponding probe from the first probe or a subsequence thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the four corresponding probes.

  11. Probing the Influence of Amino Acids on Photoluminescence from Carbon Nanotubes Suspended with DNA.

    PubMed

    Kurnosov, N V; Leontiev, V S; Karachevtsev, V A

    2016-11-01

    The quantitative analysis of amino acid levels in the human organism is required for the early clinical diagnosis of a variety of diseases. In this work the influence of 13 amino acid doping on the photoluminescence (PL) from the semiconducting single-walled carbon nanotubes (SWNTs) suspended with single-stranded DNA (ssDNA) in water has been studied. Amino acid doping leads to the PL enhancement and the strongest increase was found after cysteine doping of the nanotube suspension while addition of other amino acids yielded the significantly smaller effect. The emphasis of cysteine molecules is attributed to presence of the reactive thiol group that turns cysteine into reducing agent that passivates the p-defects on the nanotube sidewall and increases the PL intensity. The reasons of PL enhancement after doping with other amino acids are discussed. The response of nanotube PL to cysteine addition depends on the nanotube aqueous suspension preparation with tip or bath sonication treatment. The enhancement of the emission from different nanotube species after cysteine doping was analyzed too. It was shown that the increase of the carbon nanotube PL at addition of cysteine allows successful monitoring of the cysteine concentration in aqueous solution in the range of 50-1000 μM.

  12. d-Amino Acid Probes for Penicillin Binding Protein-based Bacterial Surface Labeling*

    PubMed Central

    Fura, Jonathan M.; Kearns, Daniel; Pires, Marcos M.

    2015-01-01

    Peptidoglycan is an essential and highly conserved mesh structure that surrounds bacterial cells. It plays a critical role in retaining a defined cell shape, and, in the case of pathogenic Gram-positive bacteria, it lies at the interface between bacterial cells and the host organism. Intriguingly, bacteria can metabolically incorporate unnatural d-amino acids into the peptidoglycan stem peptide directly from the surrounding medium, a process mediated by penicillin binding proteins (PBPs). Metabolic peptidoglycan remodeling via unnatural d-amino acids has provided unique insights into peptidoglycan biosynthesis of live bacteria and has also served as the basis of a synthetic immunology strategy with potential therapeutic implications. A striking feature of this process is the vast promiscuity displayed by PBPs in tolerating entirely unnatural side chains. However, the chemical space and physical features of this side chain promiscuity have not been determined systematically. In this report, we designed and synthesized a library of variants displaying diverse side chains to comprehensively establish the tolerability of unnatural d-amino acids by PBPs in both Gram-positive and Gram-negative organisms. In addition, nine Bacillus subtilis PBP-null mutants were evaluated with the goal of identifying a potential primary PBP responsible for unnatural d-amino acid incorporation and gaining insights into the temporal control of PBP activity. We empirically established the scope of physical parameters that govern the metabolic incorporation of unnatural d-amino acids into bacterial peptidoglycan. PMID:26499795

  13. Ninhydrin-sodium molybdate chromogenic analytical probe for the assay of amino acids and proteins.

    PubMed

    Anantharaman, Shivakumar; Padmarajaiah, Nagaraja; Al-Tayar, Naef Ghllab Saeed; Shrestha, Ashwinee Kumar

    2017-02-15

    A sensitive method has been proposed for the quantification of amino acids and proteins using ninhydrin and sodium molybdate as chromogenic substrates in citrate buffer of pH5.6. A weak molybdate-hydrindantin complex plays the role in the formation of Ruhemann's purple. The linear response for the amino acid, amino acid mixture and Bovine serum albumin is between 0.999 and 66.80μM, 1.52 and 38μM and 5 and 100μg/L, respectively. The molar absorptivity of the individual amino acid by the proposed reaction extends from 0.58×10(4) to 2.86×10(4)M(-1)cm(-1). The linearity equations for the proposed ninhydrin-molybdate for amino acid mixture is Abs=0.021×Conc (μM)-0.002. The applicability of the proposed method has been justified in food and biological samples in conjunction with Kjeldahl method.

  14. Ninhydrin-sodium molybdate chromogenic analytical probe for the assay of amino acids and proteins

    NASA Astrophysics Data System (ADS)

    Anantharaman, Shivakumar; Padmarajaiah, Nagaraja; Al-Tayar, Naef Ghllab Saeed; Shrestha, Ashwinee Kumar

    2017-02-01

    A sensitive method has been proposed for the quantification of amino acids and proteins using ninhydrin and sodium molybdate as chromogenic substrates in citrate buffer of pH 5.6. A weak molybdate-hydrindantin complex plays the role in the formation of Ruhemann's purple. The linear response for the amino acid, amino acid mixture and Bovine serum albumin is between 0.999 and 66.80 μM, 1.52 and 38 μM and 5 and 100 μg/L, respectively. The molar absorptivity of the individual amino acid by the proposed reaction extends from 0.58 × 104 to 2.86 × 104 M- 1 cm- 1. The linearity equations for the proposed ninhydrin-molybdate for amino acid mixture is Abs = 0.021 × Conc (μM) - 0.002. The applicability of the proposed method has been justified in food and biological samples in conjunction with Kjeldahl method.

  15. Spin crossover in [ MnIII (pyrol)3 tren] probed by high-pressure and low-temperature x-ray diffraction

    NASA Astrophysics Data System (ADS)

    Guionneau, Philippe; Marchivie, Mathieu; Garcia, Yann; Howard, Judith A. K.; Chasseau, Daniel

    2005-12-01

    The interplay between the solid-state spin-crossover features and the structural properties is analyzed for the [MnIII(pyrol)3tren] complex on the basis of high-pressure and low-temperature single-crystal x-ray-diffraction experiments. In particular, the low-temperature ( 30K , 105Pa ) low spin crystal structure is compared to the low-temperature ( 60K , 105Pa ) high spin and to the high-pressure ( 293K , 1.00GPa ) high spin crystal structures. The low-temperature structural properties show the structural modifications due to the spin crossover in a Mn(III) complex. Comparison of these structural modifications to those described for mononuclear Fe(II) spin-crossover compounds emphasizes significant differences, such as in bond length variation and polyhedron distortion, for example. Elsewhere, analysis of the high-pressure data shows that the internal stress on the metal ion is not the cause of the occurrence of the thermal spin crossover, contrary to a general belief.

  16. Fabrication and characterization of polylactic acid and polylactic acid/multi-walled carbon nanotube nanofibers through centrifugal spinning

    NASA Astrophysics Data System (ADS)

    Patlan, Richard

    Biocompatible polymer nanofibers hold great potential in the biomedical engineering field. Their biodegradable nature and enhanced properties could help solve a wide array of health related problems, particularly in the areas of tissue regeneration, drug delivery, and biosensor design. The novel Forcespinning™ method allows the production of submicron fibers without many of the drawbacks found in electrospinning, while also providing a substantial increase in fiber production. The aim of the study was to utilize this method to fabricate non-woven nanofibrous mats composed of polylactic acid (PLA) and polylactic acid/multi-walled carbon nanotube composite fibers. The morphology, thermal properties, and crystalline structure of the resulting nanofibers were then characterized using Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), Thermogravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC), and X-Ray Diffraction (XRD).

  17. Proteomic-based stable isotope probing reveals taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton

    SciTech Connect

    Bryson, Samuel; Li, Zhou; Pett-Ridge, Jennifer; Robert L. Hettich; Mayali, Xavier; Pan, Chongle; Mueller, Ryan S.

    2016-04-26

    Heterotrophic marine bacterioplankton are a critical component of the carbon cycle, processing nearly a quarter of annual global primary production, yet defining how substrate utilization preferences and resource partitioning structure these microbial communities remains a challenge. In this study, we utilized proteomics-based stable isotope probing (proteomic SIP) to characterize the assimilation of amino acids by coastal marine bacterioplankton populations. We incubated microcosms of seawater collected from Newport, OR and Monterey Bay, CA with 1 M 13C-amino acids for 15 and 32 hours. Subsequent analysis of 13C incorporation into protein biomass quantified the frequency and extent of isotope enrichment for identified proteins. Using these metrics we tested whether amino acid assimilation patterns were different for specific bacterioplankton populations. Proteins associated with Rhodobacterales and Alteromonadales tended to have a significantly high number of tandem mass spectra from 13C-enriched peptides, while Flavobacteriales and SAR11 proteins generally had significantly low numbers of 13C-enriched spectra. Rhodobacterales proteins associated with amino acid transport and metabolism had an increased frequency of 13C-enriched spectra at time-point 2, while Alteromonadales ribosomal proteins were 13C- enriched across time-points. Overall, proteomic SIP facilitated quantitative comparisons of dissolved free amino acids assimilation by specific taxa, both between sympatric populations and between protein functional groups within discrete populations, allowing an unprecedented examination of population-level metabolic responses to resource acquisition in complex microbial communities.

  18. Label-free electronic probing of nucleic acids and proteins at the nanoscale using the nanoneedle biosensor

    PubMed Central

    Esfandyarpour, Rahim; Javanmard, Mehdi; Koochak, Zahra; Esfandyarpour, Hesaam; Harris, James S.; Davis, Ronald W.

    2013-01-01

    Detection of proteins and nucleic acids is dominantly performed using optical fluorescence based techniques, which are more costly and timely than electrical detection due to the need for expensive and bulky optical equipment and the process of fluorescent tagging. In this paper, we discuss our study of the electrical properties of nucleic acids and proteins at the nanoscale using a nanoelectronic probe we have developed, which we refer to as the Nanoneedle biosensor. The nanoneedle consists of four thin film layers: a conductive layer at the bottom acting as an electrode, an oxide layer on top, and another conductive layer on top of that, with a protective oxide above. The presence of proteins and nucleic acids near the tip results in a decrease in impedance across the sensing electrodes. There are three basic mechanisms behind the electrical response of DNA and protein molecules in solution under an applied alternating electrical field. The first change stems from modulation of the relative permittivity at the interface. The second mechanism is the formation and relaxation of the induced dipole moment. The third mechanism is the tunneling of electrons through the biomolecules. The results presented in this paper can be extended to develop low cost point-of-care diagnostic assays for the clinical setting. PMID:24404047

  19. Site-specific insertion of nitroxide-spin labels into DNA probes by click chemistry for structural analyses by ELDOR spectroscopy.

    PubMed

    Flaender, M; Sicoli, G; Fontecave, Th; Mathis, G; Saint-Pierre, C; Boulard, Y; Gambarelli, S; Gasparutto, D

    2008-01-01

    A new approach is described for the insertion of nitroxide spin-labels at specific positions within DNA oligomers. The latter bioconjugaison strategy is based on a click chemistry 1,3-dipolar cycloaddition between a spin-labeling reagent, namely the 4-azido-TEMPO, and alkyne modified uridine-containing oligonucleotides. This highly efficient labeling method was applied for site-specific incorporation of two TEMPO units within a set of double-stranded DNA constructs. Then the determination of the inter-nitroxide distances was achieved by using a four-pulses DEER technique that successfully validates the new site-directed spin labeling strategy.

  20. Novel emissive bio-inspired non-proteinogenic coumarin-alanine amino acid: fluorescent probe for polyfunctional systems.

    PubMed

    Oliveira, Elisabete; Capelo, José Luis; Lima, João Carlos; Lodeiro, Carlos

    2012-10-01

    Two new bio-inspired non-proteinogenic compounds L1 and L2, containing coumarin and/or acridine chromophores and bearing as spacer an alanine amino acid were successfully synthesized and fully characterized by elemental analysis, (1)H and (13)C NMR, infrared spectroscopy (KBr discs), melting point, ESI-TOF (electrospray ionization-time of flight-mass), UV-vis absorption and emission spectroscopy, fluorescence quantum yields and lifetime measurements. A relative fluorescence quantum yield of 0.02 was determined for both compounds. In L2 the presence of an intramolecular energy transfer from the coumarin to the acridine unit was observed. L1 and L2 are quite sensitive to the basicity of the environment. At alkaline values both compounds show a strong quenching in the fluorescence emission, attributed to the photoinduced electron transfer (PET). However, both deprotonated forms recover the emission with the addition of Zn(2+), Cd(2+) and Al(3+) metal ions. As multifunctional emissive probes, the titration of L1 and L2 with lanthanides (III), Eu(3+) and Tb(3+) was also explored as new visible bio-probes in the absence and in the presence of liposomes. In a liposomal environment a lower energy transfer was observed.

  1. Identification and quantification of acetic acid bacteria in wine and vinegar by TaqMan-MGB probes.

    PubMed

    Torija, M J; Mateo, E; Guillamón, J M; Mas, A

    2010-04-01

    A Real-Time PCR (RT-PCR) assay was developed using TaqMan minor groove binder (MGB) probes for the specific detection and quantification of five acetic acid bacteria (AAB) species (Acetobacter pasteurianus, Acetobacter aceti, Gluconacetobacter hansenii, Gluconacetobacter europaeus and Gluconobacter oxydans) in wine and vinegar. The primers and probes, designed from the 16S rRNA gene, showed good specificity with the target AAB species. The technique was tested on AAB grown in glucose medium (GY) and inoculated samples of red wine and wine vinegar. Standard curves were constructed with the five target species in all these matrices. Quantification was linear over at least 5 log units using both serial dilution of purified DNA and cells. When this technique was tested in GY medium and inoculated matrices, at least 10(2)-10(3) cells/ml were detected. To quantify low populations of AAB in microbiologically complex samples, a PCR enrichment including part of the 16S-23S rRNA gene ITS region was needed to increase the amount of target DNA compared to non-target DNA. The RT-PCR assay used in this study is a reliable, specific and fast method for quantifying these five AAB species in wine and vinegar.

  2. Phenylboronic acid-based (19)F MRI probe for the detection and imaging of hydrogen peroxide utilizing its large chemical-shift change.

    PubMed

    Nonaka, Hiroshi; An, Qi; Sugihara, Fuminori; Doura, Tomohiro; Tsuchiya, Akira; Yoshioka, Yoshichika; Sando, Shinsuke

    2015-01-01

    Herein, we report on a new (19)F MRI probe for the detection and imaging of H2O2. Our designed 2-fluorophenylboronic acid-based (19)F probe promptly reacted with H2O2 to produce 2-fluorophenol via boronic acid oxidation. The accompanying (19)F chemical-shift change reached 31 ppm under our experimental conditions. Such a large chemical-shift change allowed for the imaging of H2O2 by (19)F chemical-shift-selective MRI.

  3. Technique paper for wet-spinning poly(L-lactic acid) and poly(DL-lactide-co-glycolide) monofilament fibers.

    PubMed

    Nelson, Kevin D; Romero, Andres; Waggoner, Paula; Crow, Brent; Borneman, Angela; Smith, George M

    2003-12-01

    A simple and repeatable method is described for wet-spinning poly(L-lactic acid) (PLLA) and poly(DL-lactic-co-glycolic acid) (PLGA) monofilament fibers. These fibers are strong, elastic, and suitable for many applications, including use as tissue-engineering scaffolds. The PLLA wet-extruded fibers do not show additional strain-induced crystallization as a result of drawing the fibers during fabrication; however, there is an apparent increase in crystallinity late in the degradation process in saline at 37 degrees C. We have measured the molecular weight degradation in saline at 37 degrees C for fibers of both PLLA and PLGA. Changing solvent systems, polymer blends, and winding rates alters mechanical and morphological properties of these fibers for specific applications. The authors discuss a possible theoretical explanation for these observed changes due to changes in polymer concentration, solvent system, and coagulation bath properties. This wet-extrusion process is simple and inexpensive enough to be carried out in almost any laboratory interested in tissue engineering.

  4. Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids.

    PubMed

    Öjemalm, Karin; Higuchi, Takashi; Lara, Patricia; Lindahl, Erik; Suga, Hiroaki; von Heijne, Gunnar

    2016-09-20

    Cotranslational translocon-mediated insertion of membrane proteins into the endoplasmic reticulum is a key process in membrane protein biogenesis. Although the mechanism is understood in outline, quantitative data on the energetics of the process is scarce. Here, we have measured the effect on membrane integration efficiency of nonproteinogenic analogs of the positively charged amino acids arginine and lysine incorporated into model transmembrane segments. We provide estimates of the influence on the apparent free energy of membrane integration (ΔGapp) of "snorkeling" of charged amino acids toward the lipid-water interface, and of charge neutralization. We further determine the effect of fluorine atoms and backbone hydrogen bonds (H-bonds) on ΔGapp These results help establish a quantitative basis for our understanding of membrane protein assembly in eukaryotic cells.

  5. Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids

    PubMed Central

    Öjemalm, Karin; Higuchi, Takashi; Lara, Patricia; Lindahl, Erik; Suga, Hiroaki

    2016-01-01

    Cotranslational translocon-mediated insertion of membrane proteins into the endoplasmic reticulum is a key process in membrane protein biogenesis. Although the mechanism is understood in outline, quantitative data on the energetics of the process is scarce. Here, we have measured the effect on membrane integration efficiency of nonproteinogenic analogs of the positively charged amino acids arginine and lysine incorporated into model transmembrane segments. We provide estimates of the influence on the apparent free energy of membrane integration (ΔGapp) of “snorkeling” of charged amino acids toward the lipid–water interface, and of charge neutralization. We further determine the effect of fluorine atoms and backbone hydrogen bonds (H-bonds) on ΔGapp. These results help establish a quantitative basis for our understanding of membrane protein assembly in eukaryotic cells. PMID:27601675

  6. Near-infrared spectroscopy (NIRS) with a fibre-optic probe for the prediction of the amino acid composition in animal feeds.

    PubMed

    González-Martín, Inmaculada; Alvarez-García, Noelia; González-Cabrera, José Miguel

    2006-05-15

    The amino acids alanine, aspartic acid, glutamic acid, glycine, phenylalanine, valine, lysine, proline, and tyrosine present in feeds with different textures (blocks, tablets, granules and flour (meal) and used in different stages of animal feeding regimes (lactation, growth, maintenance, etc.) were analysed using near-infrared reflectance spectroscopy (NIRS) technology together with a remote reflectance fibre-optic probe. The method allows immediate control of the animal feeds without prior sample treatment or destruction through direct application of the fibre-optic probe on the sample. The regression method used was Modified Partial Least Squares (MPLS). The equations developed to determine the amino acid contents of the feeds afforded high values for the RSQ coefficient (0.814-0.963) in all the amino acids with the exception of lysine (0.687). The statistical prediction descriptors SEP, SEP(C) (with values between 0.134 for valine and 0.015 for aspartic acid) and bias indicated that the amino acid values in feeds predicted with NIRS with a fibre optic probe are comparable to those obtained with the chemical ion-exchange HPLC method.

  7. Amino acid-based ionic liquids: using XPS to probe the electronic environment via binding energies.

    PubMed

    Hurisso, Bitu Birru; Lovelock, Kevin R J; Licence, Peter

    2011-10-21

    Here we report the synthesis and characterisation by X-ray photoelectron spectroscopy (XPS) of eight high purity amino acid-based ionic liquids (AAILs), each containing the 1-octyl-3-methylimidazolium, [C(8)C(1)Im](+), as a standard reference cation. All expected elements were observed and the electronic environments of these elements identified. A fitting model for the carbon 1s region of the AAILs is reported; the C aliphatic component of the cation was used as an internal reference to obtain a series of accurate and reproducible binding energies. Comparisons are made between XP spectra of the eight AAILs and selected non-functionalised ionic liquids. 1-octyl-3-methylimidazolium acetate was also studied as a model of the carboxyl containing amino acid anion. The influence of anionic substituent groups on the measured binding energies of all elements is presented, and communication between anion and cation is investigated. This data is interpreted in terms of hard and soft anions and compared to the Kamlet-Taft hydrogen bond acceptor ability, β, for the ionic liquids. A linear correlation is presented which suggests that the functional side chain, or R group, of the amino acid has little impact upon the electronic environment of the charge-bearing moieties within the anions and cations studied.

  8. Re-engineering of CYP2C9 to probe acid-base substrate selectivity.

    PubMed

    Tai, Guoying; Dickmann, Leslie J; Matovic, Nicholas; DeVoss, James J; Gillam, Elizabeth M J; Rettie, Allan E

    2008-10-01

    A common feature of many CYP2C9 ligands is their weak acidity. As revealed by crystallography, the structural basis for this behavior involves a charge-pairing interaction between an anionic moiety on the substrate and an active site R108 residue. In the present study we attempted to re-engineer CYP2C9 to better accept basic ligands by charge reversal at this key residue. We expressed and purified the R108E and R108E/D293N mutants and compared their ability with that of native CYP2C9 to interact with (S)-warfarin, diclofenac, pyrene, propranolol, and ibuprofen amine. As expected, the R108E mutant maintained all the native enzyme's pyrene 1-hydroxylation activity, but catalytic activity toward diclofenac and (S)-warfarin was abrogated. In contrast, the double mutant displayed much less selectivity in its behavior toward these control ligands. Neither of the mutants displayed significant enhancement of propranolol metabolism, and all three preparations exhibited a type II (inhibitor) rather than type I (substrate) spectrum with ibuprofen amine, although binding became progressively weaker with the single and double mutants. Collectively, these data underscore the importance of the amino acid at position 108 in the acid substrate selectivity of CYP2C9, highlight the accommodating nature of the CYP2C9 active site, and provide a cautionary note regarding facile re-engineering of these complex cytochrome P450 active sites.

  9. Using modern tools to probe the structure-function relationship of fatty acid synthases

    PubMed Central

    Burkart, Michael D.

    2015-01-01

    Fatty acid biosynthesis is essential to life and represents one of the most conserved pathways in Nature, preserving the same handful of chemical reactions over all species. Recent interest in the molecular details of the de novo fatty acid synthase (FAS) has been heightened by demand for renewable fuels and the emergence of multidrug resistant bacterial strains. Central to FAS is the acyl carrier protein (ACP), a protein chaperone that shuttles the growing acyl chain between catalytic enzymes within the FAS. Human efforts to alter fatty acid biosynthesis for oil production, chemical feedstock or antimicrobial purposes has been met with limited success in part due to a lack of detailed molecular information behind the ACP-partner protein interactions inherent to the pathway. This review will focus on recently developed tools for the modification of ACP and analysis of protein-protein interactions, such as mechanism-based crosslinking, and the studies exploiting them. Discussion specific to each enzymatic domain focuses first on mechanism and known inhibitors, followed by available structures and known interactions with ACP. While significant unknowns remain, new understandings into the intricacies of FAS point to future advances in manipulating this complex molecular factory. PMID:25676190

  10. Spin-current emission governed by nonlinear spin dynamics

    PubMed Central

    Tashiro, Takaharu; Matsuura, Saki; Nomura, Akiyo; Watanabe, Shun; Kang, Keehoon; Sirringhaus, Henning; Ando, Kazuya

    2015-01-01

    Coupling between conduction electrons and localized magnetization is responsible for a variety of phenomena in spintronic devices. This coupling enables to generate spin currents from dynamical magnetization. Due to the nonlinearity of magnetization dynamics, the spin-current emission through the dynamical spin-exchange coupling offers a route for nonlinear generation of spin currents. Here, we demonstrate spin-current emission governed by nonlinear magnetization dynamics in a metal/magnetic insulator bilayer. The spin-current emission from the magnetic insulator is probed by the inverse spin Hall effect, which demonstrates nontrivial temperature and excitation power dependences of the voltage generation. The experimental results reveal that nonlinear magnetization dynamics and enhanced spin-current emission due to magnon scatterings are triggered by decreasing temperature. This result illustrates the crucial role of the nonlinear magnon interactions in the spin-current emission driven by dynamical magnetization, or nonequilibrium magnons, from magnetic insulators. PMID:26472712

  11. Picosecond Spin Caloritronics

    NASA Astrophysics Data System (ADS)

    Cahill, David G.

    The coupling of spin and heat, i.e., spin caloritronics, gives rise to new physical phenomena in nanoscale spin devices and new ways to manipulate local magnetization. Our work in this field takes advantage of recent advances in the measurement and understanding of heat transport at the nanoscale using ultrafast lasers. We use a picosecond duration pump laser pulses as a source of heat and picosecond duration probe laser pulses to detect changes in temperature, spin accumulation, and spin transfer torque using a combination of time-domain thermoreflectance and time-resolved magneto-optic Kerr effect Our pump-probe optical methods enable us to change the temperature of ferromagnetic layers on a picosecond time-scale and generate enormous heat fluxes on the order of 100 GW m-2 that persist for ~ 30 ps. Thermally-driven ultrafast demagnetization of a perpendicular ferromagnet leads to spin accumulation in a normal metal and spin transfer torque in an in-plane ferromagnet. The data are well described by models of spin generation and transport based on differences and gradients of thermodynamic parameters. The spin-dependent Seebeck effect of a perpendicular ferromagnetic layer converts a heat current into spin current, which in turn can be used to exert a spin transfer torque (STT) on a second ferromagnetic layer with in-plane magnetization. Using a [Co,Ni] multilayer as the source of spin, an energy fluence of ~ 4 J m-2 creates thermal STT sufficient to induce ~ 1 % tilting of the magnetization of a 2 nm-thick CoFeB layer.

  12. Locked Nucleic Acid Probe-Based Real-Time PCR Assay for the Rapid Detection of Rifampin-Resistant Mycobacterium tuberculosis.

    PubMed

    Zhao, Yong; Li, Guilian; Sun, Chongyun; Li, Chao; Wang, Xiaochen; Liu, Haican; Zhang, Pingping; Zhao, Xiuqin; Wang, Xinrui; Jiang, Yi; Yang, Ruifu; Wan, Kanglin; Zhou, Lei

    2015-01-01

    Drug-resistant Mycobacterium tuberculosis can be rapidly diagnosed through nucleic acid amplification techniques by analyzing the variations in the associated gene sequences. In the present study, a locked nucleic acid (LNA) probe-based real-time PCR assay was developed to identify the mutations in the rpoB gene associated with rifampin (RFP) resistance in M. tuberculosis. Six LNA probes with the discrimination capability of one-base mismatch were designed to monitor the 23 most frequent rpoB mutations. The target mutations were identified using the probes in a "probe dropout" manner (quantification cycle = 0); thus, the proposed technique exhibited superiority in mutation detection. The LNA probe-based real-time PCR assay was developed in a two-tube format with three LNA probes and one internal amplification control probe in each tube. The assay showed excellent specificity to M. tuberculosis with or without RFP resistance by evaluating 12 strains of common non-tuberculosis mycobacteria. The limit of detection of M. tuberculosis was 10 genomic equivalents (GE)/reaction by further introducing a nested PCR method. In a blind validation of 154 clinical mycobacterium isolates, 142/142 (100%) were correctly detected through the assay. Of these isolates, 88/88 (100%) were determined as RFP susceptible and 52/54 (96.3%) were characterized as RFP resistant. Two unrecognized RFP-resistant strains were sequenced and were found to contain mutations outside the range of the 23 mutation targets. In conclusion, this study established a sensitive, accurate, and low-cost LNA probe-based assay suitable for a four-multiplexing real-time PCR instrument. The proposed method can be used to diagnose RFP-resistant tuberculosis in clinical laboratories.

  13. Probing the transition state for nucleic acid hybridization using phi-value analysis.

    PubMed

    Kim, Jandi; Shin, Jong-Shik

    2010-04-27

    Genetic regulation by noncoding RNA elements such as microRNA and small interfering RNA (siRNA) involves hybridization of a short single-stranded RNA with a complementary segment in a target mRNA. The physical basis of the hybridization process between the structured nucleic acids is not well understood primarily because of the lack of information about the transition-state structure. Here we use transition-state theory, inspired by phi-value analysis in protein folding studies, to provide quantitative analysis of the relationship between changes in the secondary structure stability and the activation free energy. Time course monitoring of the hybridization reaction was performed under pseudo-steady-state conditions using a single fluorophore. The phi-value analysis indicates that the native secondary structure remains intact in the transition state. The nativelike transition state was confirmed via examination of the salt dependence of the hybridization kinetics, indicating that the number of sodium ions associated with the transition state was not substantially affected by changes in the native secondary structure. These results propose that hybridization between structured nucleic acids undergoes a transition state leading to formation of a nucleation complex and then is followed by sequential displacement of preexisting base pairings involving successive small energy barriers. The proposed mechanism might provide new insight into physical processes during small RNA-mediated gene silencing, which is essential to selection of a target mRNA segment for siRNA design.

  14. Probing Hydronium Ion Histidine NH Exchange Rate Constants in the M2 Channel via Indirect Observation of Dipolar-Dephased (15)N Signals in Magic-Angle-Spinning NMR.

    PubMed

    Fu, Riqiang; Miao, Yimin; Qin, Huajun; Cross, Timothy A

    2016-12-14

    Water-protein chemical exchange in membrane-bound proteins is an important parameter for understanding how proteins interact with their aqueous environment, but has been difficult to observe in membrane-bound biological systems. Here, we demonstrate the feasibility of probing specific water-protein chemical exchange in membrane-bound proteins in solid-state MAS NMR. By spin-locking the (1)H magnetization along the magic angle, the (1)H spin diffusion is suppressed such that a water-protein chemical exchange process can be monitored indirectly by dipolar-dephased (15)N signals through polarization transfer from (1)H. In the example of the Influenza A full length M2 protein, the buildup of dipolar-dephased (15)N signals from the tetrad of His37 side chains have been observed as a function of spin-lock time. This confirms that hydronium ions are in exchange with protons in the His37 NH bonds at the heart of the M2 proton conduction mechanism, with an exchange rate constant of ∼1750 s(-1) for pH 6.2 at -10 °C.

  15. Adaptation and validation of E-probe diagnostic nucleic acid analysis for detection of Escherichia coli O157:H7 in metagenomic data of complex food matrices

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Foodborne pathogens are an increasing problem threatening the US food supply. The need for rapid sensitive diagnostic tools that can address multiple types and taxonomic classes of foodbourne pathogens is growing. This paper describes the adaptation of E-probe Diagnostic Nucleic acid Analysis (EDNA)...

  16. ESTIMATION OF BACTERIAL CELL NUMBERS IN HUMIC ACID-RICH SALT MARSH SEDIMENTS WITH PROBES DIRECTED TO 16S RIBOSOMAL DNA

    EPA Science Inventory

    The feasibility of using probes directed towards ribosomal DNAs (rDNAs) as a quantitative approach to estimating cell numbers was examined and applied to study the structure of a bacterial community in humic acid-rich salt marsh sediments. Hybridizations were performed with membr...

  17. Association of a cucumber mosaic virus strain with mosaic disease of banana, Musa paradisiaca--an evidence using immuno/nucleic acid probe.

    PubMed

    Srivastava, A; Raj, S K; Haq, Q M; Srivastava, K M; Singh, B P; Sane, P V

    1995-12-01

    Virus causing severe chlorosis/mosaic disease of banana was identified as a strain of cucumber mosaic virus (CMV). Association of CMV with the disease was established by Western immunoblot using polyclonal antibodies to CMV-T and slot blot hybridization with nucleic acid probe of CMV-P genome.

  18. New Real-Time PCR Assay Using Locked Nucleic Acid Probes To Assess Prevalence of ParC Mutations in Fluoroquinolone-Susceptible Streptococcus pneumoniae Isolates from France

    PubMed Central

    Decousser, Jean-Winoc; Methlouthi, Imen; Pina, Patrick; Collignon, Anne; Allouch, Pierre

    2006-01-01

    A real-time PCR assay with locked nucleic acid probes was developed to screen mutations at codons 79 and 83 of the Streptococcus pneumoniae parC gene. Only silent mutations were detected among 236 French invasive fluoroquinolone-susceptible strains. This test could be useful for some high-risk patients or in national surveys. PMID:16569894

  19. Microscopic studies of nonlocal spin dynamics and spin transport (invited)

    SciTech Connect

    Adur, Rohan; Du, Chunhui; Cardellino, Jeremy; Scozzaro, Nicolas; Wolfe, Christopher S.; Wang, Hailong; Herman, Michael; Bhallamudi, Vidya P.; Pelekhov, Denis V.; Yang, Fengyuan; Hammel, P. Chris

    2015-05-07

    Understanding the behavior of spins coupling across interfaces in the study of spin current generation and transport is a fundamental challenge that is important for spintronics applications. The transfer of spin angular momentum from a ferromagnet into an adjacent normal material as a consequence of the precession of the magnetization of the ferromagnet is a process known as spin pumping. We find that, in certain circumstances, the insertion of an intervening normal metal can enhance spin pumping between an excited ferromagnetic magnetization and a normal metal layer as a consequence of improved spin conductance matching. We have studied this using inverse spin Hall effect and enhanced damping measurements. Scanned probe magnetic resonance techniques are a complementary tool in this context offering high resolution magnetic resonance imaging, localized spin excitation, and direct measurement of spin lifetimes or damping. Localized magnetic resonance studies of size-dependent spin dynamics in the absence of lithographic confinement in both ferromagnets and paramagnets reveal the close relationship between spin transport and spin lifetime at microscopic length scales. Finally, detection of ferromagnetic resonance of a ferromagnetic film using the photoluminescence of nitrogen vacancy spins in neighboring nanodiamonds demonstrates long-range spin transport between insulating materials, indicating the complexity and generality of spin transport in diverse, spatially separated, material systems.

  20. Microscopic studies of nonlocal spin dynamics and spin transport (invited)

    NASA Astrophysics Data System (ADS)

    Adur, Rohan; Du, Chunhui; Cardellino, Jeremy; Scozzaro, Nicolas; Wolfe, Christopher S.; Wang, Hailong; Herman, Michael; Bhallamudi, Vidya P.; Pelekhov, Denis V.; Yang, Fengyuan; Hammel, P. Chris

    2015-05-01

    Understanding the behavior of spins coupling across interfaces in the study of spin current generation and transport is a fundamental challenge that is important for spintronics applications. The transfer of spin angular momentum from a ferromagnet into an adjacent normal material as a consequence of the precession of the magnetization of the ferromagnet is a process known as spin pumping. We find that, in certain circumstances, the insertion of an intervening normal metal can enhance spin pumping between an excited ferromagnetic magnetization and a normal metal layer as a consequence of improved spin conductance matching. We have studied this using inverse spin Hall effect and enhanced damping measurements. Scanned probe magnetic resonance techniques are a complementary tool in this context offering high resolution magnetic resonance imaging, localized spin excitation, and direct measurement of spin lifetimes or damping. Localized magnetic resonance studies of size-dependent spin dynamics in the absence of lithographic confinement in both ferromagnets and paramagnets reveal the close relationship between spin transport and spin lifetime at microscopic length scales. Finally, detection of ferromagnetic resonance of a ferromagnetic film using the photoluminescence of nitrogen vacancy spins in neighboring nanodiamonds demonstrates long-range spin transport between insulating materials, indicating the complexity and generality of spin transport in diverse, spatially separated, material systems.

  1. Duality of two pairs of double-walled nanotubes consisting of S=1 and S=3/2 spins probed by means of a quantum simulation approach

    NASA Astrophysics Data System (ADS)

    Liu, Zhaosen; Ian, Hou

    2017-01-01

    Using a quantum simulation approach, we investigate in the present work the spontaneous magnetic properties of two pairs of double-walled cylindrical nanotubes consisting of different spins. Our simulated magnetic and thermodynamic properties for each pair of them are precisely identical, exhibiting a fascinating property of the nature world and demonstrating the correctness of our simulation approach. The second pair of nanotubes are frustrated, two magnetic phases of distinct spin configurations appear in the low temperature region, but only the inner layer consisting of small spins is frustrated evidently, its magnetization is considerably suppressed in the high temperature phase. Moreover, the nanosystems exhibit typical Ising-like behavior due to the uniaxial anisotropy along the z-direction, and evident finite-size effects as well.

  2. ESA mission ROSETTA will probe for chirality of cometary amino acids.

    PubMed

    Thiemann, W H; Meierhenrich, U

    2001-01-01

    New crucial theoretical investigations on the origin of biomolecular chirality are reviewed briefly. With the goal to investigate these theories our team is going to perform the 'chirality-experiment' in the near future with cometary matter. In 2012 the robotical lander RoLand will detach from the orbiter of the ROSETTA spacecraft and set down on the surface of comet 46P/Wirtanen in order to separate and identify cometary organic compounds via GC-MS in situ. Chiral organics will be separated into their enantiomers by application of 3 capillary columns coated with different kinds of stationary phases. Non-volatile compounds like amino acids will be derivatized in especially developed gas phase alkylation steps avoiding reactions in the liquid phase. The results of these preliminary gas phase reactions are presented in this article.

  3. A chromo- and fluorogenic sensor for probing the cancer biomarker lysophosphatidic acid.

    PubMed

    Zhao, Wenwen; Liu, Weimin; Zhang, Wenjun; Zeng, Lintao; Fan, Zhiyuan; Wu, Jiasheng; Wang, Pengfei

    2012-04-21

    A novel chromo- and fluorogenic sensor, 4-(4-dimethylaminostyryl)-1-hexadecylpyridinium (DSHP) for lysophosphatidic acid (LPA) was successfully developed by incorporating a long alkyl chain into the cyanine molecule. DSHP shows excellent selectivity and high sensitivity towards LPA with a detection limit of about 7.09 × 10(-7) M based on electrostatic and hydrophobic interactions between the sensor and LPA. Upon addition of LPA ranging from 0 to 7.5 × 10(-4) M, DSHP displays an 'on-off-on' fluorescence response and obvious colour change. Good linear relationships between the fluorescence intensity and LPA concentrations were achieved in the fluorescence quenching ranges of 0-28 μM and 34-52 μM, which could be attributed to the combined effects of the photoinduced electron transfer and LPA-induced aggregation of the sensor molecules.

  4. Pharmacophore-based database mining for probing fragmental drug-likeness of diketo acid analogues.

    PubMed

    Bak, A; Magdziarz, T; Polanski, J

    2012-01-01

    A number of the structurally diverse chemical compounds with functional diketo acid (DKA) subunit(s) have been revealed by combined online and MoStBiodat 3D pharmacophore-guided ZINC and PubChem database screening. We used the structural data available from such screening to analyse the similarities of the compounds containing the DKA fragment. Generally, the analysis by principal component analysis and self-organizing neural network approaches reveals four families of compounds complying with the chemical constitution (aromatic, aliphatic) of the compounds. From a practical point of view, similar studies may reveal potential bioisosteres of known drugs, e.g. raltegravir/elvitegravir. In this context, it seems that mono-halogenated aryl substructures with para group show the closest similarity to these compounds, in contrast to structures where the aromatic ring is halogenated in both ortho- and para-locations.

  5. In vivo quantitative visualization of hypochlorous acid in the liver using a novel selective two-photon fluorescent probe

    NASA Astrophysics Data System (ADS)

    Wang, Haolu; Jayachandran, Aparna; Gravot, Germain; Liang, Xiaowen; Thorling, Camilla A.; Zhang, Run; Liu, Xin; Roberts, Michael S.

    2016-11-01

    Hypochlorous acid (HOCl) plays a vital role in physiological events and diseases. During hepatic ischemia-reperfusion (I/R) injury, HOCl is generated by neutrophils and diffuses into hepatocytes, causing oxidant stress-mediated injury. Although many probes have been developed to detect HOCl, most were difficult to be distinguished from endogenous fluorophores in intravital imaging and only can be employed under one-photon microscopy. A novel iridium(III) complex-based ferrocene dual-signaling chemosensor (Ir-Fc) was designed and synthesized. Ir-Fc exhibited a strong positive fluorescent response only in the presence of HOCl, whereas negligible fluorescent signals were observed upon the additions of other reactive oxygen/nitrogen species and metal ions. There was a good linear relationship between probe responsive fluorescent intensity and HOCl concentration. Ir-Fc was then intravenously injected into BALB/c mice at the final concentration of 50 μM and the mouse livers were imaged using multiphoton microscopy (MPM). In the I/R liver, reduced autofluorescence was detected by MPM, indicating the hepatocyte necrosis. Remarkable enhancement of red fluorescence was observed in hepatocytes with decreased autofluorescence, indicating the reaction of Ir-Fc with endogenous HOCl molecules. The cellular concentration of HOCl was first calculated based on the intensity of MPM images. No obvious toxic effects were observed in histological examination of major organs after Ir-Fc injection. In summary, Ir-Fc has low cytotoxicity, high specificity to HOCl, and rapid "off-on" fluorescence. It is suitable for dynamic quantitatively monitoring HOCl generation using MPM at the cellular level. This technique can be readily extended to examination of liver diseases and injury.

  6. A new method for ABO genotyping using fluorescence melting curve analysis based on peptide nucleic acid probes.

    PubMed

    Lee, Kyungmyung; Park, Hyun-Chul; An, Sanghyun; Ahn, Eu-Ree; Lee, Yang-Han; Kim, Mi-Jung; Lee, Eun-Jung; Park, Jae Sin; Jung, Jin Wook; Lim, Sikeun

    2015-09-01

    ABO genotyping has been routinely used to identify suspects or unknown remains in crime investigations. Probe-based fluorescence melting curve analysis (FMCA) is a powerful tool for mutation detection and is based on melting temperature shifts due to thermal denaturation. In the present study, we developed a new method for ABO genotyping using peptide nucleic acid (PNA) probe-based FMCA. This method allowed for the simultaneous detection of three single nucleotide polymorphism (SNP) sites in the ABO gene (nucleotide positions 261, 526, and 803) and the determination of 14 ABO genotypes (A/A, A/O01 or A/O02, A/O03, B/B, B/O01 or B/O02, B/O03, O01/O01 or O01/O02 or O02/O02, O01/O03 or O02/O03, O03/O03, A/B, cis-AB01/A, cis-AB01/B, cis-AB01/O01 or cis-AB01/O02, and cis-AB01/cis-AB01). Using this method, we analyzed 80 samples and successfully identified ABO genotypes (A/A [n=5], A/O01 or A/O02 [n=23], B/B [n=3], B/O01 or B/O02 [n=18], A/B [n=9], O01/O01 or O01/O02 or O02/O02 [n=20], cis-AB01/A [n=1], and cis-AB01/O01 or cis-AB01/O02 [n=1]). In addition, all steps in the method, including polymerase chain reaction, PNA probe hybridization, and FMCA, could be performed in one single closed tube in less than 3h. Since no processing or separation steps were required during analysis, this method was more convenient and rapid than traditional methods and reduced the risk of contamination. Thus, this method may be an effective and helpful tool in forensic investigations.

  7. A Focker-Planck description of the spin Seebeck effect

    NASA Astrophysics Data System (ADS)

    Reyes, Guillermo; Reyes, Juan Adrian

    Thermally driven spin-wave spin current in a ferromagnetic material FM and the resulting electric signal in a metal probe placed on the FM are theoretically investigated by considering a thermally fluctuating spin at the interface of a FM-metal junction. We develop an analytical formulation to establish a Focker Plank equation for the probability distribution as a function of magnetization components of the material, for calculating the spin Seebeck signal detected by the metal probe, which converts spin current to charge current by the inverse spin Hall effect. The spin current is induced in the metal probe via an exchange interaction when the metal senses the temperature gradient.

  8. On the cellular metabolism of the click chemistry probe 19-alkyne arachidonic acid.

    PubMed

    Robichaud, Philippe Pierre; Poirier, Samuel J; Boudreau, Luc H; Doiron, Jérémie A; Barnett, David A; Boilard, Eric; Surette, Marc E

    2016-10-01

    Alkyne and azide analogs of natural compounds that can be coupled to sensitive tags by click chemistry are powerful tools to study biological processes. Arachidonic acid (AA) is a FA precursor to biologically active compounds. 19-Alkyne-AA (AA-alk) is a sensitive clickable AA analog; however, its use as a surrogate to study AA metabolism requires further evaluation. In this study, AA-alk metabolism was compared with that of AA in human cells. Jurkat cell uptake of AA was 2-fold greater than that of AA-alk, but significantly more AA-Alk was elongated to 22:4. AA and AA-alk incorporation into and remodeling between phospholipid (PL) classes was identical indicating equivalent CoA-independent AA-PL remodeling. Platelets stimulated in the pre-sence of AA-alk synthesized significantly less 12-lipoxygenase (12-LOX) and cyclooxygenase products than in the presence of AA. Ionophore-stimulated neutrophils produced significantly more 5-LOX products in the presence of AA-alk than AA. Neutrophils stimulated with only exogenous AA-alk produced significantly less 5-LOX products compared with AA, and leukotriene B4 (LTB4)-alk was 12-fold less potent at stimulating neutrophil migration than LTB4, collectively indicative of weaker leukotriene B4 receptor 1 agonist activity of LTB4-alk. Overall, these results suggest that the use of AA-alk as a surrogate for the study of AA metabolism should be carried out with caution.

  9. Probing Gαi1 Protein Activation at Single Amino Acid Resolution

    PubMed Central

    Sun, Dawei; Maeda, Shoji; Matkovic, Milos; Mendieta, Sandro; Mayer, Daniel; Dawson, Roger; Schertler, Gebhard F.X.; Madan Babu, M.; Veprintsev, Dmitry B.

    2016-01-01

    We present comprehensive single amino acid resolution maps of the residues stabilising the human Gαi1 subunit in nucleotide- and receptor-bound states. We generated these maps by measuring the effects of alanine mutations on the stability of Gαi1 and of the rhodopsin-Gαi1 complex. We identified stabilization clusters in the GTPase and helical domains responsible for structural integrity and the conformational changes associated with activation. In activation cluster I, helices α1 and α5 pack against strands β1-3 to stabilize the nucleotide-bound states. In the receptor-bound state, these interactions are replaced by interactions between α5 and strands β4-6. Key residues in this cluster are Y320, crucial for the stabilization of the receptor-bound state, and F336, which stabilizes nucleotide-bound states. Destabilization of helix α1, caused by rearrangement of this activation cluster, leads to the weakening of the inter-domain interface and release of GDP. PMID:26258638

  10. Probing the interaction of the amino acid alanine with the surface of ZnO(1010).

    PubMed

    Gao, Y K; Traeger, F; Shekhah, O; Idriss, H; Wöll, C

    2009-10-01

    The adsorption modes and stability of the amino acid alanine (NH(2)-CH(CH(3))-COOH) have been studied on the nonpolar single crystal surface of zinc oxide, ZnO(1010), experimentally by X-ray photoelectron spectroscopy (XPS) and computationally using density functional theory (DFT). Deposition at 200 K was found to lead to the formation of multilayers identified by an XPS N1s peak at 401.7 eV assigned to the NH(3)(+) group, a fingerprint of the zwitterionic structure of alanine in the solid state. Heating to 300 K resulted in the removal of most of the multilayers with the remaining surface coverage estimated to 0.4 with respect to Zn cations. At this temperature most of the alanine molecules are found to be deprotonated (dissociated), yielding a carboxylate species (NH(2)-CH(CH(3))-COO(-) (a) + OH (s); where O is surface oxygen, (a) for adsorbed and (s) for surface species). Further heating of the surface resulted in a gradual decrease of the surface coverage and by 500 K a large fraction of adsorbed alanine molecules have desorbed from the surface. Total energy DFT computations of different adsorbate species identified two stable dissociative adsorption modes: bidentate and monodentate. The bidentate species with adsorption energy of 1.75 eV was found to be more stable than the monodentate species by about 0.7 eV.

  11. Probing the interaction of caffeic acid with ZnO nanoparticles.

    PubMed

    Belay, Abebe; Kim, Hyung Kook; Hwang, Yoon-Hwae

    2016-05-01

    The binding of ZnO nanoparticles (NPs) and caffeic acid (CFA) was investigated using fluorescence quenching, UV/vis absorption spectrscopy, Fourier transform infrared (FTIR) spectroscopy, transmission electron microscopy (TEM) and dynamic light scattering (DLS) at different temperatures. The study results indicated fluorescence quenching between ZnO NPs and CFA rationalized in terms of a static quenching mechanism or the formation of non-fluorescent CFA-ZnO. From fluorescence quenching spectral analysis, the binding constant (K(a)), number of binding sites (n) and thermodynamic properties were determined. Values of the quenching (K(SV)) and binding (K(a)) constants decrease with increasing temperature and the number of binding sites n = 2. The thermodynamic parameters determined using Van't Hoff equation indicated that binding occurs spontaneously involving the hydrogen bond, and van der Waal's forces played a major role in the reaction of ZnO NPs with CFA. The FTIR, TEM and DLS measurements also indicated differences in the structure, morphology and size of CFA, ZnO NPs and their corresponding CFA-ZnO.

  12. Estimation of Bacterial Cell Numbers in Humic Acid-Rich Salt Marsh Sediments with Probes Directed to 16S Ribosomal DNA

    PubMed Central

    Edgcomb, Virginia P.; McDonald, John H.; Devereux, Richard; Smith, David W.

    1999-01-01

    The feasibility of using probes directed towards ribosomal DNAs (rDNAs) as a quantitative approach to estimating cell numbers was examined and applied to study the structure of a bacterial community in humic acid-rich salt marsh sediments. Hybridizations were performed with membrane-bound nucleic acids by using seven group-specific DNA oligonucleotide probes complementary to 16S rRNA coding regions. These included a general eubacterial probe and probes encompassing most members of the gram-negative, mesophilic sulfate-reducing bacteria (SRB). DNA was extracted from sediment samples, and contaminating materials were removed by a series of steps. Efficiency of DNA extraction was 48% based on the recovery of tritiated plasmid DNA added to samples prior to extraction. Reproducibility of the extraction procedure was demonstrated by hybridizations to replicate samples. Numbers of target cells in samples were estimated by comparing the amount of hybridization to extracted DNA obtained with each probe to that obtained with a standard curve of genomic DNA for reference strains included on the same membrane. In June, numbers of SRB detected with an SRB-specific probe ranged from 6.0 × 107 to 2.5 × 109 (average, 1.1 × 109 ± 5.2 × 108) cells g of sediment−1. In September, numbers of SRB detected ranged from 5.4 × 108 to 7.3 × 109 (average, 2.5 × 109 ± 1.5 × 109) cells g of sediment−1. The capability of using rDNA probes to estimate cell numbers by hybridization to DNA extracted from complex matrices permits initiation of detailed studies on community composition and changes in communities based on cell numbers in formerly intractable environments. PMID:10103245

  13. Chromatographic analysis of the effects of fatty acids and glycation on binding by probes for Sudlow sites I and II to human serum albumin.

    PubMed

    Anguizola, Jeanethe; Debolt, Erin; Suresh, D; Hage, David S

    2016-05-15

    The primary endogenous ligands of human serum albumin (HSA) are non-esterified fatty acids, with 0.1-2mol of fatty acids normally being bound to HSA. In type II diabetes, fatty acid levels in serum are often elevated, and the presence of high glucose results in an increase in the non-enzymatic glycation of HSA. High-performance affinity chromatography (HPAC) was used to examine the combined effects of glycation and the presence of long chain fatty acids on the binding of HSA with R-warfarin and l-tryptophan (i.e., probes for Sudlow sites I and II, the major sites for drugs on this protein). Zonal elution competition studies were used to examine the interactions of myristic acid, palmitic acid and stearic acid with these probes on HSA. It was found that all these fatty acids had direct competition with R-warfarin at Sudlow site I of normal HSA and glycated HSA, with the glycated HSA typically having stronger binding for the fatty acids at this site. At Sudlow site II, direct competition was observed for all the fatty acids with l-tryptophan when using normal HSA, while glycated HSA gave no competition or positive allosteric interactions between these fatty acids and l-tryptophan. These data indicated that glycation can alter the interactions of drugs and fatty acids at specific binding sites on HSA. The results of this study should lead to a better understanding of how these interactions may change during diabetes and demonstrate how HPAC can be used to examine drug/solute-protein interactions in complex systems.

  14. Spin foams without spins

    NASA Astrophysics Data System (ADS)

    Hnybida, Jeff

    2016-10-01

    We formulate the spin foam representation of discrete SU(2) gauge theory as a product of vertex amplitudes each of which is the spin network generating function of the boundary graph dual to the vertex. In doing so the sums over spins have been carried out. The boundary data of each n-valent node is explicitly reduced with respect to the local gauge invariance and has a manifest geometrical interpretation as a framed polyhedron of fixed total area. Ultimately, sums over spins are traded for contour integrals over simple poles and recoupling theory is avoided using generating functions.

  15. Preparation and application of cysteine-capped ZnS nanoparticles as fluorescence probe in the determination of nucleic acids

    NASA Astrophysics Data System (ADS)

    Li, Yongxin; Chen, Jinlong; Zhu, Changqin; Wang, Lun; Zhao, Danhua; Zhuo, Shujuan; Wu, Yuqin

    2004-07-01

    Cysteine-capped ZnS nanometer-sized fluorescent particles were produced by a colloidal aqueous synthesis. The functionalized nanoparticles are water-soluble and suitable for biological application. A synchronous fluorescence method has been developed for the rapid determination of DNA with functionalized nano-ZnS as a fluorescence probe, based on the synchronous fluorescence enhancement of cysteine-capped nano-ZnS in the presence of DNA. When Δ λ=190 nm, maximum synchronous fluorescence is produced at 267 nm at pH 5.12. Under optimum conditions, the synchronous fluorescence intensity is proportional to the concentration of nucleic acids in the range 0.1-1.2 μg ml -1 for calf thymus DNA, 0.1-0.6 μg ml -1 for fish sperm DNA. The corresponding detection limit is 32.9 ng ml -1 for calf thymus DNA and 24.6 ng ml -1 for fish sperm DNA. This method is simple, inexpensive, rapid and sensitive. The recovery and relative standard deviation are satisfactory.

  16. Counterion distribution surrounding spherical nucleic acid-Au nanoparticle conjugates probed by small-angle x-ray scattering.

    PubMed

    Kewalramani, Sumit; Zwanikken, Jos W; Macfarlane, Robert J; Leung, Cheuk-Yui; Olvera de la Cruz, Monica; Mirkin, Chad A; Bedzyk, Michael J

    2013-12-23

    The radial distribution of monovalent cations surrounding spherical nucleic acid-Au nanoparticle conjugates (SNA-AuNPs) is determined by in situ small-angle x-ray scattering (SAXS) and classical density functional theory (DFT) calculations. Small differences in SAXS intensity profiles from SNA-AuNPs dispersed in a series of solutions containing different monovalent ions (Na(+), K(+), Rb(+), or Cs(+)) are measured. Using the "heavy ion replacement" SAXS (HIRSAXS) approach, we extract the cation-distribution-dependent contribution to the SAXS intensity and show that it agrees with DFT predictions. The experiment-theory comparisons reveal the radial distribution of cations as well as the conformation of the DNA in the SNA shell. The analysis shows an enhancement to the average cation concentration in the SNA shell that can be up to 15-fold, depending on the bulk solution ionic concentration. The study demonstrates the feasibility of HIRSAXS in probing the distribution of monovalent cations surrounding nanoparticles with an electron dense core (e.g., metals).

  17. Synthesis of fluorescent D-amino acids (FDAAs) and their use for probing peptidoglycan synthesis and bacterial growth in situ

    PubMed Central

    Kuru, Erkin; Tekkam, Srinivas; Hall, Edward

    2015-01-01

    Fluorescent D-amino acids (FDAAs) are efficiently incorporated into the peptidoglycan of diverse bacterial species at the sites of active peptidoglycan biosynthesis, allowing specific and covalent probing of bacterial growth with minimal perturbation. Here, we provide a protocol for the synthesis of four FDAAs emitting light in blue, green or red and for their use in peptidoglycan labeling of live bacteria. Our modular synthesis protocol gives easy access to a library of different FDAAs made with commercially available fluorophores. FDAAs can be synthesized in a typical chemistry laboratory in 2–3 days. The simple labeling procedure involves addition of the FDAAs to the bacterial sample for the desired labeling duration and stopping further label incorporation by fixation or by washing away excess dye. We discuss several scenarios for the use of these labels including short or long labeling durations, and the combination of different labels in pure culture or complex environmental samples. Depending on the experiment, FDAA labeling can take as little as 30 s for a rapidly growing species such as Escherichia coli. PMID:25474031

  18. Conformers of β-aminoisobutyric acid probed by jet-cooled microwave and matrix isolation infrared spectroscopic techniques.

    PubMed

    Kuş, N; Sharma, A; Peña, I; Bermúdez, M C; Cabezas, C; Alonso, J L; Fausto, R

    2013-04-14

    β-aminoisobutyric acid (BAIBA) has been studied in isolation conditions: in the gas phase and trapped into a cryogenic N2 matrix. A solid sample of the compound was vaporized by laser ablation and investigated through their rotational spectra in a supersonic expansion using two different spectroscopic techniques: broadband chirped pulse Fourier transform microwave spectroscopy and conventional molecular beam Fourier transform microwave spectroscopy. Four conformers with structures of two types could be successfully identified by comparison of the experimental rotational and (14)N nuclear quadruple coupling constants with those predicted theoretically: type A, bearing an OH⋯N intramolecular hydrogen bond and its carboxylic group in the trans geometry (H-O-C=O dihedral ∼180°), and type B, having an NH⋯O bond and the cis arrangement of the carboxylic group. These two types of conformers could also be trapped from the gas phase into a cryogenic N2 matrix and probed by Fourier transform infrared (IR) spectroscopy. In situ irradiation of BAIBA isolated in N2 matrix of type B conformers using near-IR radiation tuned at the frequency of the O-H stretching 1st overtone (∼6930 cm(-1)) of these forms allowed to selectively convert them into type A conformers and into a new type of conformers of higher energy (type D) bearing an NH⋯O=C bond and a O-H "free" trans carboxylic group.

  19. Conformers of β-aminoisobutyric acid probed by jet-cooled microwave and matrix isolation infrared spectroscopic techniques

    NASA Astrophysics Data System (ADS)

    Kuş, N.; Sharma, A.; Peña, I.; Bermúdez, M. C.; Cabezas, C.; Alonso, J. L.; Fausto, R.

    2013-04-01

    β-aminoisobutyric acid (BAIBA) has been studied in isolation conditions: in the gas phase and trapped into a cryogenic N2 matrix. A solid sample of the compound was vaporized by laser ablation and investigated through their rotational spectra in a supersonic expansion using two different spectroscopic techniques: broadband chirped pulse Fourier transform microwave spectroscopy and conventional molecular beam Fourier transform microwave spectroscopy. Four conformers with structures of two types could be successfully identified by comparison of the experimental rotational and 14N nuclear quadruple coupling constants with those predicted theoretically: type A, bearing an OH⋯N intramolecular hydrogen bond and its carboxylic group in the trans geometry (H-O-C=O dihedral ˜180°), and type B, having an NH⋯O bond and the cis arrangement of the carboxylic group. These two types of conformers could also be trapped from the gas phase into a cryogenic N2 matrix and probed by Fourier transform infrared (IR) spectroscopy. In situ irradiation of BAIBA isolated in N2 matrix of type B conformers using near-IR radiation tuned at the frequency of the O-H stretching 1st overtone (˜6930 cm-1) of these forms allowed to selectively convert them into type A conformers and into a new type of conformers of higher energy (type D) bearing an NH⋯O=C bond and a O-H "free" trans carboxylic group.

  20. Tensor spin observables and spin stucture at low Q2

    SciTech Connect

    Slifer, Karl J.

    2015-04-01

    We discuss recent spin structure results from Jefferson Lab, and outline an emerging program to study tensor spin observables using solid deuteron targets. These new experiments open the potential to study hidden color, the tensor nature of short range correlations, and to probe for exotic gluonic states.

  1. Influence of a thermochromic anion on the spin crossover of iron(II) trinuclear complexes probed by Mössbauer spectroscopy

    NASA Astrophysics Data System (ADS)

    Robert, François; Naik, Anil D.; Garcia, Yann

    2010-03-01

    The insertion of thermochromic anions (1 and 2) into triazole based iron(II) trinuclear spin crossover complexes [FeII3(hyetrz)6(H2O)6](1 or 2)4Cl2 paves the way to a large panel of multifunctional materials. In addition to a gradual thermo-induced spin conversion of the central metal ion on cooling below room temperature, an unexpected split of the Mössbauer signal of the external iron(II) ions as well as pronounced relaxation phenomenon for the central HS iron(II) ion was discovered. This phenomenon is suggested to be induced by the tautomeric equilibrium between enol and keto forms of the anion.

  2. A genetically encoded probe for the identification of proteins that form sulfenic acid in response to H2O2 in Saccharomyces cerevisiae.

    PubMed

    Takanishi, Christina L; Wood, Matthew J

    2011-06-03

    It is widely known that reactive oxygen species (ROS), such as hydrogen peroxide, play important roles in cellular signaling and initiation of oxidative stress responses via thiol modifications. Identification of the targets of these modifications will provide a better understanding of the relationship between ROS and human diseases, such as cancer and atherosclerosis. Sulfenic acid is the principle product of a reaction between hydrogen peroxide and a reactive protein cysteine. This reversible post-translational modification plays an important role in enzyme active sites, signaling transduction via disulfide bond formation, as well as an intermediate to overoxidation products during oxidative stress. By re-engineering the C-terminal cysteine rich domain (cCRD) of the Yap1 transcription factor, we were able to create a genetically encoded probe for the general detection and identification of proteins that form sulfenic acid in vivo. The Yap1-cCRD probe has been used previously in the identification of proteins that form sulfenic acid in Escherichia coli. Here we demonstrate the successful use of the Yap1-cCRD probe in the identification of proteins that form sulfenic acid in response to hydrogen peroxide in Saccharomyces cerevisiae.

  3. Unravelling the Bacterial Vaginosis-Associated Biofilm: A Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes.

    PubMed

    Hardy, Liselotte; Jespers, Vicky; Dahchour, Nassira; Mwambarangwe, Lambert; Musengamana, Viateur; Vaneechoutte, Mario; Crucitti, Tania

    2015-01-01

    Bacterial vaginosis (BV), a condition defined by increased vaginal discharge without significant inflammation, is characterized by a change in the bacterial composition of the vagina. Lactobacillus spp., associated with a healthy vaginal microbiome, are outnumbered by BV-associated organisms. These bacteria could form a polymicrobial biofilm which allows them to persist in spite of antibiotic treatment. In this study, we examined the presence of Gardnerella vaginalis and Atopobium vaginae in vaginal biofilms using Peptide Nucleic Acid (PNA) probes targeting these bacteria. For this purpose, we developed three new PNA probes for A. vaginae. The most specific A. vaginae probe, AtoITM1, was selected and then used in an assay with two existing probes, Gard162 and BacUni-1, to evaluate multiplex FISH on clinical samples. Using quantitative polymerase chain reaction (qPCR) as the gold standard, we demonstrated a sensitivity of 66.7% (95% confidence interval: 54.5% - 77.1%) and a specificity of 89.4% (95% confidence interval: 76.1% - 96%) of the new AtoITM1 probe. FISH enabled us to show the presence of a polymicrobial biofilm in bacterial vaginosis, in which Atopobium vaginae is part of a Gardnerella vaginalis-dominated biofilm. We showed that the presence of this biofilm is associated with high bacterial loads of A. vaginae and G. vaginalis.

  4. Unravelling the Bacterial Vaginosis-Associated Biofilm: A Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes

    PubMed Central

    Hardy, Liselotte; Jespers, Vicky; Dahchour, Nassira; Mwambarangwe, Lambert; Musengamana, Viateur; Vaneechoutte, Mario; Crucitti, Tania

    2015-01-01

    Bacterial vaginosis (BV), a condition defined by increased vaginal discharge without significant inflammation, is characterized by a change in the bacterial composition of the vagina. Lactobacillus spp., associated with a healthy vaginal microbiome, are outnumbered by BV-associated organisms. These bacteria could form a polymicrobial biofilm which allows them to persist in spite of antibiotic treatment. In this study, we examined the presence of Gardnerella vaginalis and Atopobium vaginae in vaginal biofilms using Peptide Nucleic Acid (PNA) probes targeting these bacteria. For this purpose, we developed three new PNA probes for A. vaginae. The most specific A. vaginae probe, AtoITM1, was selected and then used in an assay with two existing probes, Gard162 and BacUni-1, to evaluate multiplex FISH on clinical samples. Using quantitative polymerase chain reaction (qPCR) as the gold standard, we demonstrated a sensitivity of 66.7% (95% confidence interval: 54.5% - 77.1%) and a specificity of 89.4% (95% confidence interval: 76.1% - 96%) of the new AtoITM1 probe. FISH enabled us to show the presence of a polymicrobial biofilm in bacterial vaginosis, in which Atopobium vaginae is part of a Gardnerella vaginalis-dominated biofilm. We showed that the presence of this biofilm is associated with high bacterial loads of A. vaginae and G. vaginalis. PMID:26305575

  5. The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

    PubMed Central

    Naccache, Samia N.; Greninger, Alexander L.; Lee, Deanna; Coffey, Lark L.; Phan, Tung; Rein-Weston, Annie; Aronsohn, Andrew; Hackett, John; Delwart, Eric L.

    2013-01-01

    Next-generation sequencing was used for discovery and de novo assembly of a novel, highly divergent DNA virus at the interface between the Parvoviridae and Circoviridae. The virus, provisionally named parvovirus-like hybrid virus (PHV), is nearly identical by sequence to another DNA virus, NIH-CQV, previously detected in Chinese patients with seronegative (non-A-E) hepatitis. Although we initially detected PHV in a wide range of clinical samples, with all strains sharing ∼99% nucleotide and amino acid identity with each other and with NIH-CQV, the exact origin of the virus was eventually traced to contaminated silica-binding spin columns used for nucleic acid extraction. Definitive confirmation of the origin of PHV, and presumably NIH-CQV, was obtained by in-depth analyses of water eluted through contaminated spin columns. Analysis of environmental metagenome libraries detected PHV sequences in coastal marine waters of North America, suggesting that a potential association between PHV and diatoms (algae) that generate the silica matrix used in the spin columns may have resulted in inadvertent viral contamination during manufacture. The confirmation of PHV/NIH-CQV as laboratory reagent contaminants and not bona fide infectious agents of humans underscores the rigorous approach needed to establish the validity of new viral genomes discovered by next-generation sequencing. PMID:24027301

  6. The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns.

    PubMed

    Naccache, Samia N; Greninger, Alexander L; Lee, Deanna; Coffey, Lark L; Phan, Tung; Rein-Weston, Annie; Aronsohn, Andrew; Hackett, John; Delwart, Eric L; Chiu, Charles Y

    2013-11-01

    Next-generation sequencing was used for discovery and de novo assembly of a novel, highly divergent DNA virus at the interface between the Parvoviridae and Circoviridae. The virus, provisionally named parvovirus-like hybrid virus (PHV), is nearly identical by sequence to another DNA virus, NIH-CQV, previously detected in Chinese patients with seronegative (non-A-E) hepatitis. Although we initially detected PHV in a wide range of clinical samples, with all strains sharing ∼99% nucleotide and amino acid identity with each other and with NIH-CQV, the exact origin of the virus was eventually traced to contaminated silica-binding spin columns used for nucleic acid extraction. Definitive confirmation of the origin of PHV, and presumably NIH-CQV, was obtained by in-depth analyses of water eluted through contaminated spin columns. Analysis of environmental metagenome libraries detected PHV sequences in coastal marine waters of North America, suggesting that a potential association between PHV and diatoms (algae) that generate the silica matrix used in the spin columns may have resulted in inadvertent viral contamination during manufacture. The confirmation of PHV/NIH-CQV as laboratory reagent contaminants and not bona fide infectious agents of humans underscores the rigorous approach needed to establish the validity of new viral genomes discovered by next-generation sequencing.

  7. Use of dimedone-based chemical probes for sulfenic acid detection evaluation of conditions affecting probe incorporation into redox-sensitive proteins.

    PubMed

    Klomsiri, Chananat; Nelson, Kimberly J; Bechtold, Erika; Soito, Laura; Johnson, Lynnette C; Lowther, W Todd; Ryu, Seong-Eon; King, S Bruce; Furdui, Cristina M; Poole, Leslie B

    2010-01-01

    Sulfenic acids, formed as transient intermediates during the reaction of cysteine residues with peroxides, play significant roles in enzyme catalysis and regulation, and are also involved in the redox regulation of transcription factors and other signaling proteins. Therefore, interest in the identification of protein sulfenic acids has grown substantially in the past few years. Dimedone, which specifically traps sulfenic acids, has provided the basis for the synthesis of a novel group of compounds that derivatize 1,3-cyclohexadione, a dimedone analogue, with reporter tags such as biotin for affinity capture and fluorescent labels for visual detection. These reagents allow identification of the cysteine sites and proteins that are sensitive to oxidation and permit identification of the cellular conditions under which such oxidations occur. We have shown that these compounds are reactive and specific toward sulfenic acids and that the labeled proteins can be detected at high sensitivity using gel analysis or mass spectrometry. Here, we further characterize these reagents, showing that the DCP-Bio1 incorporation rates into three sulfenic acid containing proteins, papaya papain, Escherichia coli fRMsr, and the Salmonella typhimurium peroxiredoxin AhpC, are significantly different and, in the case of fRMsr, are unaffected by changes in buffer pH from 5.5 and 8.0. We also provide protocols to label protein sulfenic acids in cellular proteins, either by in situ labeling of intact cells or by labeling at the time of lysis. We show that the addition of alkylating reagents and catalase to the lysis buffer is critical in preventing the formation of sulfenic acid subsequent to cell lysis. Data presented herein also indicate that the need to standardize, as much as possible, the protein and reagent concentrations during labeling. Finally, we introduce several new test or control proteins that can be used to evaluate labeling procedures and efficiencies.

  8. Development and Evaluation of Novel Real-Time Reverse Transcription-PCR Assays with Locked Nucleic Acid Probes Targeting Leader Sequences of Human-Pathogenic Coronaviruses.

    PubMed

    Chan, Jasper Fuk-Woo; Choi, Garnet Kwan-Yue; Tsang, Alan Ka-Lun; Tee, Kah-Meng; Lam, Ho-Yin; Yip, Cyril Chik-Yan; To, Kelvin Kai-Wang; Cheng, Vincent Chi-Chung; Yeung, Man-Lung; Lau, Susanna Kar-Pui; Woo, Patrick Chiu-Yat; Chan, Kwok-Hung; Tang, Bone Siu-Fai; Yuen, Kwok-Yung

    2015-08-01

    Based on findings in small RNA-sequencing (Seq) data analysis, we developed highly sensitive and specific real-time reverse transcription (RT)-PCR assays with locked nucleic acid probes targeting the abundantly expressed leader sequences of Middle East respiratory syndrome coronavirus (MERS-CoV) and other human coronaviruses. Analytical and clinical evaluations showed their noninferiority to a commercial multiplex PCR test for the detection of these coronaviruses.

  9. Fluorescence determination of DNA with 1-pyrenebutyric acid nanoparticles coated with β-cyclodextrin as a fluorescence probe

    NASA Astrophysics Data System (ADS)

    Wang, Lun; Bian, Guirong; Wang, Leyu; Dong, Ling; Chen, Hongqi; Xia, Tingting

    2005-04-01

    A novel ultrasonication method has been successfully developed for the preparation of 1-pyrenebutyric acid (PBAC)/β-cyclodextrin(β-CD) complex nanoparticles. The as-prepared nanoparticles are characterized by transmission electron microscopy (TEM), fluorescence excitation and emission spectroscopy. Complex nanoparticles prepared with ultrasonication are smaller and better dispersed than single PBAC nanoparticles. At pH 3.0, the relative fluorescence intensity of complex nanoparticles of PBAC/β-CD can be quenched by the concentration of DNA. Based on this, a novel fluorimetric method has been developed for rapid determination of DNA. In comparison with single organic fluorophores, these nanoparticle probes are better water-solubility, more stable and do not suffer from blinking. Under optimum conditions, the calibration graphs are linear over the range 0.2-15 μg mL -1 for calf thymus DNA (ct-DNA) and 0.3-12 μg mL -1 for fish sperm DNA (fs-DNA). The corresponding detection limit is 0.01 μg mL -1 for ct-DNA and 0.02 μg mL -1 for fs-DNA. The relative standard deviation of seven replicate measurements is 1.2% for 2.0 μg mL -1 ct-DNA and 1.4% for 2.0 μg mL -1 fs-DNA, respectively. The method is simple and sensitive. The recovery and relative standard deviation are very satisfactory. A mechanism proposed to explain the process also has been studied.

  10. Hydrothermal synthetic mercaptopropionic acid stabled CdTe quantum dots as fluorescent probes for detection of Ag⁺.

    PubMed

    Gan, Ting-Ting; Zhang, Yu-Jun; Zhao, Nan-Jing; Xiao, Xue; Yin, Gao-Fang; Yu, Shao-Hui; Wang, Huan-Bo; Duan, Jing-Bo; Shi, Chao-Yi; Liu, Wen-Qing

    2012-12-01

    Mercaptopropionic acid (MPA) capped CdTe quantum dots (QDs) with particle size 3 nm have been successfully synthesized in aqueous medium by hydrothermal synthesis method. And the effects of different metal ions on MPA capped CdTe QDs fluorescence were studied using fluorescence spectrometry. The results demonstrated that at the same concentration level, Ag(+) could strongly quench CdTe QDs fluorescence, and the other metal ions had little effect on CdTe QDs fluorescence except Cu(2+). On the basis of this fact, a rapid, simple, highly sensitive and selective method based on fluorescence quenching principle for Ag(+) detection in aqueous solution was proposed. Under optimal conditions, the quenched fluorescence intensity (F(0)-F) increased linearly with the concentration of Ag(+) ranging from 4 × 10(-7) to 32 × 10(-7)mol L(-1). The limit of detection for Ag(+) was 4.106 × 10(-8)mol L(-1). The obtained plot of F(0)/F versus [Ag(+)] was an upward curvature, concave towards the y-axis, rather than a straight line. The modified form of the Stern-Volmer equation was third order in Ag(+) concentration. According to the modified Stern-Volmer equation, it can be inferred that dynamic quenching and static quenching simultaneously occurred when Ag(+) interacted with MPA capped CdTe QDs. At the same time other factors might also influence the quenching process. Based on this study, hydrothermal synthesized MPA capped CdTe QDs with particle size 3 nm may be used as a novel fluorescence probe to quantificationally and selectively detect Ag(+).

  11. Electron Spin Density on the N-Donor Atoms of Cu(II)-(Bis)oxamidato Complexes As Probed by a Pulse ELDOR Detected NMR.

    PubMed

    Aliabadi, Azar; Zaripov, Ruslan; Salikhov, Kev; Voronkova, Violeta; Vavilova, Evgeniya; Abdulmalic, Mohammad A; Rüffer, Tobias; Büchner, Bernd; Kataev, Vladislav

    2015-10-29

    We have applied the pulse ELDOR detected NMR (EDNMR) technique to determine the tensors of the transferred Cu (S = 1/2) - (14)N (I = 1) hyperfine (HF) interaction in single crystals of diamagnetically diluted mononuclear o-phenylenebis(N(R)-oxamide) complexes of [(n)Bu4N]2[Cu(opboR2)] (R = Et 1, (n)Pr 2) (1%) in a host lattice of [(n)Bu4N]2[Ni(opboR2)] (R = Et 3, (n)Pr 4) (99%) (1@3 and 2@4)). To facilitate the analysis of our EDNMR data and to analyze possible manifestations of the nuclear quadrupole interaction in the EDNMR spectra, we have treated a model electron-nuclear system of the coupled S = 1/2 and I = 1 spins using the spin density matrix formalism. It appears that this interaction yields a peculiar asymmetry of the EDMR spectra that manifests not only in the shift of the positions of the EDNMR lines that correspond to the forbidden EPR transitions, as expected, but also in the intensities of the EDNMR lines. The symmetric shape of the experimental spectra suggests the conclusion that, in the studied complexes, the quadrupole interaction is negligible. This has simplified the analysis of the spectra. The HF tensors of all four N donor atoms could be accurately determined. On the basis of the HF tensors, an estimate of the spin density transferred from the central paramagnetic Cu(II) ion to the N donor atoms reveals its unequal distribution. We discuss possible implications of our estimates for the magnetic exchange paths and interaction strengths in respective trinuclear complexes [Cu3(opboR2) (pmdta)2](NO3)2 (R = Et 6, (n)Pr 7).

  12. Probing Framework-Restricted Metal Axial Ligation and Spin State Patterns in a Post-Synthetically Reduced Iron-Porphyrin-Based Metal-Organic Framework.

    PubMed

    Kucheryavy, Pavel; Lahanas, Nicole; Velasco, Ever; Sun, Cheng-Jun; Lockard, Jenny V

    2016-04-07

    An iron-porphyrin-based metal organic framework PCN-222(Fe) is investigated upon postsynthetic reduction with piperidine. Fe K-edge X-ray absorption and Kβ mainline emission spectroscopy measurements reveal the local coordination geometry, oxidation, and spin state changes experienced by the Fe sites upon reaction with this axially coordinating reducing agent. Analysis and fitting of these data confirm the binding pattern predicted by a space-filling model of the structurally constrained pore environments. These results are further supported by UV-vis diffuse reflectance, IR, and resonance Raman spectroscopy data.

  13. Spin-phonon and magnetostriction phenomena in CaMn{sub 7}O{sub 12} helimagnet probed by Raman spectroscopy

    SciTech Connect

    Nonato, A.; Araujo, B. S.; Ayala, A. P.; Maciel, A. P.; Yanez-Vilar, S.; Sanchez-Andujar, M.; Senaris-Rodriguez, M. A.; Paschoal, C. W. A.

    2014-12-01

    In this letter, we investigated the temperature-dependent Raman spectra of CaMn{sub 7}O{sub 12} helimagnet from room temperature down to 10 K. The temperature dependence of the Raman mode parameters shows remarkable anomalies for both antiferromagnetic and incommensurate transitions that this compound undergoes at low temperatures. The anomalies observed at the magnetic ordering transition indicate a spin-phonon coupling at higher-temperature magnetic transition in this material, while a magnetostriction effect at the lower-temperature magnetic transition.

  14. Positively charged polymer brush-functionalized filter paper for DNA sequence determination following Dot blot hybridization employing a pyrrolidinyl peptide nucleic acid probe.

    PubMed

    Laopa, Praethong S; Vilaivan, Tirayut; Hoven, Voravee P

    2013-01-07

    As inspired by the Dot blot analysis, a well known technique in molecular biology and genetics for detecting biomolecules, a new paper-based platform for colorimetric detection of specific DNA sequences employing peptide nucleic acid (PNA) as a probe has been developed. In this particular study, a pyrrolidinyl PNA bearing a conformationally rigid d-prolyl-2-aminocyclopentanecarboxylic acid backbone (acpcPNA) was used as a probe. The filter paper was modified to be positively charged with grafted polymer brushes of quaternized poly(dimethylamino)ethyl methacrylate (QPDMAEMA) prepared by surface-initiated polymerization of 2-(dimethylamino)ethyl methacrylate from the filter paper via ARGET ATRP followed by quaternization with methyl iodide. Following the Dot blot format, a DNA target was first immobilized via electrostatic interactions between the positive charges of the QPDMAEMA brushes and negative charges of the phosphate backbone of DNA. Upon hybridization with the biotinylated pyrrolidinyl peptide nucleic acid (b-PNA) probe, the immobilized DNA can be detected by naked eye observation of the yellow product generated by the enzymatic reaction employing HRP-labeled streptavidin. It has been demonstrated that this newly developed assay was capable of discriminating between complementary and single base mismatch targets at a detection limit of at least 10 fmol. In addition, the QPDMAEMA-grafted filter paper exhibited a superior performance to the commercial membranes, namely Nylon 66 and nitrocellulose.

  15. Analysis of Protein–Protein Interactions in MCF-7 and MDA-MB-231 Cell Lines Using Phthalic Acid Chemical Probes

    PubMed Central

    Liang, Shih-Shin; Wang, Tsu-Nai; Tsai, Eing-Mei

    2014-01-01

    Phthalates are a class of plasticizers that have been characterized as endocrine disrupters, and are associated with genital diseases, cardiotoxicity, hepatotoxicity, and nephrotoxicity in the GeneOntology gene/protein database. In this study, we synthesized phthalic acid chemical probes and demonstrated differing protein–protein interactions between MCF-7 cells and MDA-MB-231 breast cancer cell lines. Phthalic acid chemical probes were synthesized using silicon dioxide particle carriers, which were modified using the silanized linker 3-aminopropyl triethoxyslane (APTES). Incubation with cell lysates from breast cancer cell lines revealed interactions between phthalic acid and cellular proteins in MCF-7 and MDA-MB-231 cells. Subsequent proteomics analyses indicated 22 phthalic acid-binding proteins in both cell types, including heat shock cognate 71-kDa protein, ATP synthase subunit beta, and heat shock protein HSP 90-beta. In addition, 21 MCF-7-specific and 32 MDA-MB-231 specific phthalic acid-binding proteins were identified, including related proteasome proteins, heat shock 70-kDa protein, and NADPH dehydrogenase and ribosomal correlated proteins, ras-related proteins, and members of the heat shock protein family, respectively. PMID:25402641

  16. Probing the photoexcited states of rhodium corroles by time-resolved Q-band EPR. Observation of strong spin-orbit coupling effects.

    PubMed

    Rozenshtein, V; Wagnert, L; Berg, A; Stavitski, E; Berthold, T; Kothe, G; Saltsman, I; Gross, Z; Levanon, H

    2008-06-19

    The photoexcited states of two 5,10,15-tris(pentafluorophenyl)corroles (tpfc), hosting Rh(III) in their core, namely Rh(pyr)(PPh 3)(tpfc) and Rh(PPh 3)(tpfc), have been studied by time-resolved electron paramagnetic resonance (TREPR) combined with pulsed laser excitation. Using the transient nutation technique, the spin polarized spectra are assigned to photoexcited triplet states. The spectral widths observed for the two Rh(III) corroles crucially depend on the axial ligands at the Rh(III) metal ion. In case of Rh(PPh 3)(tpfc), the TREPR spectra are found to extend over 200 mT, which exceeds the spectral width of non-transition-metal corroles by more than a factor of 3. Moreover, the EPR lines of the Rh(III) corroles are less symmetric than those of the non-transition-metal corrroles. The peculiarities in the TREPR spectra of the Rh(III) corroles can be rationalized in terms of strong spin-orbit coupling (SOC) associated with the transition-metal character of the Rh(III) ion. It is assumed that SOC in the photoexcited Rh(III) corroles effectively admixes metal centered (3)dd-states to the corrole centered (3)pipi*-states detected in the TREPR experiments. This admixture leads to an increased zero-field splitting and a large g-tensor anisotropy as manifested by the excited Rh(III) corroles.

  17. Probing Supermassive Black Hole Spins in MCG--6-30-15 and NGC 1365 with XMM-Newton and NuSTAR

    NASA Astrophysics Data System (ADS)

    Brenneman, Laura; Walton, Dom; Marinucci, Andrea; Matt, Giorgio; Risaliti, Guido; Harrison, Fiona; Stern, Daniel

    2014-08-01

    We report on detailed spectral modeling of the Seyfert 1 AGNs NGC 1365 and MCG--6-30-15 using simultaneous, broadband X-ray spectra from XMM-Newton and NuSTAR. Both of these galaxies show evidence for relativistic reflection from the inner accretion disk in addition to complex, variable absorption. The high signal-to-noise across the 0.3-79 keV energy band enabled by these observations allows us to definitively disentangle the spectral signatures of the continuum, warm and cold absorption, and reflection from the torus and the inner disk in both sources. These deep pointings also enable the use of time-resolved spectral fitting in order to assess the role of each component in driving the spectral and temporal variability of the AGNs. This type of analysis allows us to isolate the relativistic reflection signatures in each object, facilitating the most accurate, precise constrains ever obtained on the spins of their supermassive black holes. We present our spin measurements, as well as a discussion of sources of systematic error. Finally, we place our results in the context of relativistic light-bending models in an effort to characterize the structure of the innermost regions of these AGNs.

  18. Development of a novel europium complex-based luminescent probe for time-gated luminescence imaging of hypochlorous acid in living samples

    NASA Astrophysics Data System (ADS)

    Liu, Xiangli; Guo, Lianying; Song, Bo; Tang, Zhixin; Yuan, Jingli

    2017-03-01

    Luminescent lanthanide complexes are key reagents used in the time-gated luminescence bioassay technique, but functional lanthanide complexes that can act as luminescent probes for specifically responding to analytes are very limited. In this work, we designed and synthesized a novel Eu3+ complex-based luminescence probe for hypochlorous acid (HOCl), NPPTTA-Eu3+, by using terpyridine polyacid-Eu3+, dinitrophenyl, and hydrazine as luminophore, quencher and HOCl-recognizer moieties, respectively. In the absence of HOCl, the probe is non-luminescent due to the strong luminescence quenching of the dinitrophenyl group in the complex. However, upon reaction with HOCl, the dinitrophenyl moiety is rapidly cleaved from the probe, which affords a strongly luminescent Eu3+ complex CPTTA-Eu3+, accompanied by a ∼900-fold luminescence enhancement with a long luminescence lifetime of 1.41 ms. This unique luminescence response of NPPTTA-Eu3+ to HOCl allowed NPPTTA-Eu3+ to be conveniently used as a probe for highly selective and sensitive detection of HOCl under the time-gated luminescence mode. In addition, by loading NPPTTA-Eu3+ into RAW 264.7 macrophage cells and Daphnia magna, the generation of endogenous HOCl in RAW 264.7 cells and the uptake of exogenous HOCl by Daphnia magna were successfully imaged on a true-color time-gated luminescence microscope. The results demonstrated the practical applicability of NPPTTA-Eu3+ as an efficient probe for time-gated luminescence imaging of HOCl in living cells and organisms.

  19. Synthesis of a new Ni-phenanthroline complex and its application as an electrochemical probe for detection of nucleic acid.

    PubMed

    Qiu, Bin; Guo, Longhua; Guo, Chunhua; Guo, Zhiyong; Lin, Zhenyu; Chen, Guonan

    2011-01-15

    A new DNA sensor using a nickel(II) phenanthroline complex ([Ni(phen)(2)PHPIP]·2ClO(4)) as the electrochemical probe was developed. The sensor is very sensitive and selective for calf thymus DNA (ctDNA) detection in aqueous medium. The Ni-phenanthroline probe was synthesized by a two-step preparation using p-hydroxy-phenylimidazo-1,10-phenanthroline (PHPIP) as the ligand and characterized with IR, UV and MS. Some interesting electrochemical properties of the Ni-complex and the interactions of the complex with ctDNA were reported. The calculated dynamics parameters of the electrode process indicate that there are obvious interactions between the probe and the ctDNA in aqueous solution. Under constant potential conditions, the redox current peak of the probe (Ni-complex) decreases obviously as the probe interacts/binds with ctDNAs. This unexpected electrochemical behavior may suggest that a new adduct through the binding of Ni-phenanthroline complex with ctDNA is formed electrochemically. By estimation, the binding ratio of the probe and ctDNA was found to be 1:1 with a binding constant β=4.29×10(5) mol L(-1) in aqueous solution at room temperature.

  20. Surface spin-valve effect.

    PubMed

    Yanson, I K; Naidyuk, Yu G; Fisun, V V; Konovalenko, A; Balkashin, O P; Triputen, L Yu; Korenivski, V

    2007-04-01

    We report an observation of spin-valve-like hysteresis within a few atomic layers at a ferromagnetic interface. We use phonon spectroscopy of nanometer-sized point contacts as an in situ probe to study the mechanism of the effect. Distinctive energy phonon peaks for contacts with dissimilar nonmagnetic outer electrodes allow localizing the observed spin switching to the top or bottom interfaces for nanometer thin ferromagnetic layers. The mechanism consistent with our data is energetically distinct atomically thin surface spin layers that can form current- or field-driven surface spin-valves within a single ferromagnetic film.

  1. A peptide nucleic acid-functionalized carbon nitride nanosheet as a probe for in situ monitoring of intracellular microRNA.

    PubMed

    Liao, Xianjiu; Wang, Quanbo; Ju, Huangxian

    2015-06-21

    A novel probe for recognition of both cancer cells and intracellular microRNA (miRNA) is designed by functionalizing a carbon nitride nanosheet (f-CNNS) with a Cy5-labeled peptide nucleic acid (Cy5-PNA) and folate. The interaction between Cy5-PNA and CNNS quenches the fluorescence of Cy5, and the presence of folate endows the probe with good specificity to folate acceptor overexpressed cells. The probe can be specifically taken up by cancer cells with an incubation step. Upon the recognition of the PNA to complementary miRNA, the hybridization product is released from the CNNS surface, which leads to the fluorescence recovery and provides a specific method for sensing of miRNA. Thus, this probe can be used for cell-specific intracellular miRNA sensing with a confocal microscope. Using miRNA-18a as a target model, the dynamic changes of its expression level inside living cells can be monitored with the proposed method. This method possesses promising applications in the study of miRNA related bioprocesses and biomedicine.

  2. Effect of solvent on the physical and morphological properties of poly(lactic acid) nanofibers obtained by solution blow spinning

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Solution blow spinning (SBS) is a simple, safe, and inexpensive alternative to electrospinning for making nanofibers from polymer solutions. However, since SBS is a relatively new technique, there is a general lack of information on polymer solutions and properties that affect fiber morphology and i...

  3. Assessing the acidity of high silica chabazite H-SSZ-13 by FTIR using CO as molecular probe: Comparison with H-SAPO-34.

    PubMed

    Bordiga, Silvia; Regli, Laura; Cocina, Donato; Lamberti, Carlo; Bjørgen, Morten; Lillerud, Karl Petter

    2005-02-24

    Zeolitic materials based on the chabazite topology, such as H-SAPO-34, possess unique shape-selectivity properties for converting methanol into light olefins. In addition to the topology, zeolite acidity is inherently linked to catalyst activity and selectivity. The acidic properties of high silica chabazite (H-SSZ-13) have attracted much attention in the past decade because the material represents an idealized model system having one acidic site per cage. Conclusions drawn so far have essentially been founded on quantum chemical methods. An experimentally based benchmark of the acidity of H-SSZ-13 has hitherto not been available. In this work, transmission FTIR spectroscopy provides a description of the different acidic sites of H-SSZ-13 by using CO as molecular probe at 70 K. The results demonstrate that H-SSZ-13 is a strongly Brønsted acidic material, essentially having two distinct families of acidic sites. In contrast to numerous preceding reports, we find it fundamental to consider proton distributions among all four possible sites, and do not delimit the interpretations to only two sites. The present data consistently suggest the most abundant family of protons to have three members being located on different crystalline positions on the eight-membered-ring window giving access to the chabazite cage. Consequently, these protons are exposed to two neighboring cages. The second, and less abundant family, is constituted by only one site that is situated on the six-membered ring defining the top/bottom of the barrel-shaped chabazite cage. This proton is therefore only exposed to one cage and requires a higher CO pressure to form adducts. Toward CO, both families of sites possess the same acidity. Parallel experiments were also carried out for the isostructural and commercially important H-SAPO-34 having an equal density of acidic sites. This is the first attempt to directly compare, on an experimental basis, the acidity of these two materials.

  4. Identification of PCR-amplified genetically modified organisms (GMOs) DNA by peptide nucleic acid (PNA) probes in anion-exchange chromatographic analysis.

    PubMed

    Rossi, Stefano; Lesignoli, Francesca; Germini, Andrea; Faccini, Andrea; Sforza, Stefano; Corradini, Roberto; Marchelli, Rosangela

    2007-04-04

    PCR products obtained by selective amplification of transgenic DNA derived from food samples containing Roundup Ready soybean or Bt-176 maize have been analyzed by anion-exchange HPLC. Peptide nucleic acids (PNAs), oligonucleotide analogues known to bind to complementary single-stranded DNA with high affinity and specificity, have been used as specific probes in order to assess the identity of the peaks observed. Two different protocols were adopted in order to obtain single-stranded DNA: amplification with an excess of one primer or digestion of one DNA strand. The single-stranded DNA was mixed with the PNA probe, and the presence of a specific sequence was revealed through detection of the corresponding PNA:DNA peak with significantly different retention time. Advantages and limits of this approach are discussed. The method was tested with reference materials and subsequently applied to commercial samples.

  5. Probing molecular dynamics in chromatographic systems using high-resolution 1H magic-angle-spinning NMR spectroscopy: interaction between p-Xylene and C18-bonded silica.

    PubMed

    Coen, Muireann; Wilson, Ian D; Nicholson, Jeremy K; Tang, Huiru; Lindon, John C

    2004-06-01

    The exact nature of the interaction between small molecules and chromatographic solid phases has been the subject of much research, but detailed understanding of the molecular dynamics in such systems remains elusive. High-resolution (1)H magic-angle-spinning (MAS) NMR spectroscopy has been applied to the investigation of C18-bonded silica material as used in chromatographic separation techniques together with an adsorbed model analyte, p-xylene. Two distinct p-xylene and water environments were identified within the C18-bonded silica through the measurement of (1)H NMR chemical shifts, T(1) and T(2) relaxation times and diffusion coefficients, including their temperature dependence. The results have been analyzed in terms of two environments, p-xylene within the C18 chains, in slow exchange on the NMR time scale with p-xylene in a more mobile state adsorbed as a layer in close proximity to the C18 particles, but which is distinct from free liquid p-xylene. The techniques used here could have more general applications, including the study of drug molecules bound into phospholipid membranes in micelles or vesicles.

  6. Structural dynamics of the actomyosin complex probed by a bifunctional spin label that cross-links SH1 and SH2.

    PubMed

    Thompson, Andrew R; Naber, Nariman; Wilson, Clyde; Cooke, Roger; Thomas, David D

    2008-12-01

    We have used a bifunctional spin label (BSL) to cross-link Cys(707) (SH1) and Cys(697) (SH2) in the catalytic domain of myosin subfragment 1 (S1). BSL induces the same weakened ATPase activity and actin-binding affinity that is observed when SH1 and SH2 are cross-linked with pPDM, which traps an analog of the post-hydrolysis state A.M.ADP.P. Electron paramagnetic resonance showed that BSL reports the global orientation and dynamics of S1. When bound to actin in oriented muscle fibers in the absence of ATP, BSL-S1 showed almost complete orientational disorder, as reported previously for the weakly bound A.M.ADP. In contrast, helical order is observed for the strongly bound state A.M. Saturation transfer electron paramagnetic resonance showed that the disorder of cross-linked S1 on actin is nearly static on the microsecond timescale, at least 30 times slower than that of A.M.ADP. We conclude that cross-linked S1 exhibits rotational disorder comparable to that of A.M.ADP, slow rotational mobility comparable to that of A.M, and intermediate actin affinity. These results support the hypothesis that the catalytic domain of myosin is orientationally disordered on actin in a post-hydrolysis state in the early stages of force generation.

  7. Long-range Li+ dynamics in the lithium argyrodite Li7PSe6 as probed by rotating-frame spin-lattice relaxation NMR.

    PubMed

    Epp, V; Gün, O; Deiseroth, H-J; Wilkening, M

    2013-05-21

    Lithium-rich argyrodites belong to a relatively new group of fast ion conducting solids. They might serve as powerful electrolytes in all-solid-state lithium-ion batteries being, from a medium-term point of view, the key technology when safe energy storage systems have to be developed. Spin-lattice relaxation (SLR) nuclear magnetic resonance (NMR) measurements carried out in the rotating frame of reference turned out to be the method of choice to study Li dynamics in argyrodites. When plotted as a function of the inverse temperature, the SLR rates log10(R1ρ) reveal an asymmetric diffusion-induced rate peak. The rate peak contains information on the Li jump rate, the activation energy of the hopping process as well as correlation effects. In particular, considering the high-temperature flank of the SLR NMR rate peak recorded in the rotating frame of reference, an activation energy of approximately 0.49 eV is found. This value represents long-range lithium jump diffusion in crystalline Li7PSe6. As an example, at 325 K the Li jump rate determined from SLR NMR is in the order of 1.4 × 10(5) s(-1). The pronounced asymmetry of the rate peak R1ρ(1/T) points to correlated Li motion. It is comparable to that which is typically found for structurally disordered materials showing a broad range of correlation times.

  8. Cellular delivery of quantum dot-bound hybridization probe for detection of intracellular pre-microRNA using chitosan/poly(γ-glutamic acid) complex as a carrier.

    PubMed

    Geng, Yao; Lin, Dajie; Shao, Lijia; Yan, Feng; Ju, Huangxian

    2013-01-01

    A quantum dot (QD)-bound hybridization probe was designed for detection of intracellular pre-miRNA using chitosan (CS)/poly(γ-glutamic acid) (γ-PGA) complex as a gene vector. The probe was prepared by assembling thiolated RNA to gold nanoparticle (Au NP) via Au-S bond and then binding 3'-end amine of the RNA to the carboxy group capped on quantum dot surface. The QD-RNA-Au NP probe was assembled on the vector by mixing with aqueous γ-PGA solution and then CS solution to construct a gene delivery system for highly effective cellular uptake and delivery. After the probe was released from CS/γ-PGA complex to the cytoplasm by electrostatic repulsion at intracellular pH, it hybridized with pre-miRNA precursor as target. The formed product was then cleaved by RNase III Dicer, leading to the separation of QDs from Au NPs and fluorescence emission of QDs, which could be detected by confocal microscopic imaging to monitor the amount of the intracellular pre-miRNA precursor. The in vitro assays revealed that the QD-RNA-Au NP was a robust, sensitive and selective probe for quantitative detection of target pre-miRNA. Using MDA-MB231 and MCF-7 breast cancer cells as models, the relative amount of pre-miRNA let-7a could be successfully compared. Since the amount of miRNA is related to the progress and prognosis of cancer, this strategy could be expected to hold promising application potential in medical research and clinical diagnostics.

  9. Fragmentation of spinning branes

    NASA Astrophysics Data System (ADS)

    Yamada, D.

    2008-07-01

    The near-horizon geometries of spinning D3-, M2- and M5-branes are examined by the probes immersed in a co-rotating frame. It is found that the geometries become unstable at critical values of the spin angular velocity by emitting the branes. We show that this instability corresponds to the metastability of the black hole systems and different from the known (local) thermodynamic instability. For the D3 case, the instability found here is in complete agreement with the known metastability of the \\mathcal{N}=4 super-Yang Mills theory with R-symmetry chemical potentials.

  10. Electrically-induced Spin Coherence by Ultrafast Electrical Spin Injection.

    NASA Astrophysics Data System (ADS)

    Beschoten, B.; Schreiber, L.; Moritz, J.; Schwark, C.; Guentherodt, G.; Lou, X.; Crowell, P.; Adelmann, C.; Palmstrom, C.

    2008-03-01

    Efficient electrical spin injection from a ferromagnet into a semiconductor has been demonstrated for various material systems by steady-state experiments. We introduce a novel time-resolved technique based on electrical pumping and optical probing. As a pump we apply ultrafast current pulses (˜200ps) to electrically inject spin packets from an iron layer through a reverse biased Schottky barrier into a n-GaAs layer. Spin coherence in the semiconductor is probed by subsequent spin precession in a transverse magnetic field using time-resolved Faraday rotation. We observe spin precession for current pulse widths down to 200 ps. The spin polarization of the spin packets is directly measured by Faraday rotation and is found to increase linearly with the current pulse width for pulses shorter than 3 ns at small magnetic fields. This finding together with independent measurements of the samples' high frequency bandwidth indicate that even shorter than 200 ps pulses might be used for generating coherent spin currents in our devices. Work supported by BMBF, DFG and HGF.

  11. Spin noise in the anisotropic central spin model

    NASA Astrophysics Data System (ADS)

    Hackmann, Johannes; Anders, Frithjof B.

    2014-01-01

    Spin-noise measurements can serve as a direct probe for the microscopic decoherence mechanism of an electronic spin in semiconductor quantum dots (QDs). We have calculated the spin-noise spectrum in the anisotropic central spin model using a Chebyshev expansion technique which exactly accounts for the dynamics up to an arbitrary long but fixed time in a finite-size system. In the isotropic case, describing QD charge with a single electron, the short-time dynamics is in good agreement with quasistatic approximations for the thermodynamic limit. The spin-noise spectrum, however, shows strong deviations at low frequencies with a power-law behavior of ω-3/4 corresponding to a t-1/4 decay at intermediate and long times. In the Ising limit, applicable to QDs with heavy-hole spins, the spin-noise spectrum exhibits a threshold behavior of (ω-ωL)-1/2 above the Larmor frequency ωL=gμBB. In the generic anisotropic central spin model we have found a crossover from a Gaussian type of spin-noise spectrum to a more Ising-type spectrum with increasing anisotropy in a finite magnetic field. In order to make contact with experiments, we present ensemble averaged spin-noise spectra for QD ensembles charged with single electrons or holes. The Gaussian-type noise spectrum evolves to a more Lorentzian shape spectrum with increasing spread of characteristic time scales and g factors of the individual QDs.

  12. Spin decoherence of magnetic atoms on surfaces

    NASA Astrophysics Data System (ADS)

    Delgado, F.; Fernández-Rossier, J.

    2017-02-01

    We review the problem of spin decoherence of magnetic atoms deposited on a surface. Recent breakthroughs in scanning tunnelling microscopy (STM) make it possible to probe the spin dynamics of individual atoms, either isolated or integrated in nanoengineered spin structures. Transport pump and probe techniques with spin polarized tips permit measuring the spin relaxation time T1 , while novel demonstration of electrically driven STM single spin resonance has provided a direct measurement of the spin coherence time T2 of an individual magnetic adatom. Here we address the problem of spin decoherence from the theoretical point of view. First we provide a short general overview of decoherence in open quantum systems and we discuss with some detail ambiguities that arise in the case of degenerate spectra, relevant for magnetic atoms. Second, we address the physical mechanisms that allows probing the spin coherence of magnetic atoms on surfaces. Third, we discuss the main spin decoherence mechanisms at work on a surface, most notably, Kondo interaction, but also spin-phonon coupling and dephasing by Johnson noise. Finally, we briefly discuss the implications in the broader context of quantum technologies.

  13. Current-induced spin-wave Doppler shift.

    PubMed

    Vlaminck, Vincent; Bailleul, Matthieu

    2008-10-17

    Spin transfer appears to be a promising tool for improving spintronics devices. Experiments that quantitatively access the magnitude of the spin transfer are required for a fundamental understanding of this phenomenon. By inductively measuring spin waves propagating along a permalloy strip subjected to a large electrical current, we observed a current-induced spin wave Doppler shift that we relate to the adiabatic spin transfer torque. Because spin waves provide a well-defined system for performing spin transfer, we anticipate that they could be used as an accurate probe of spin-polarized transport in various itinerant ferromagnets.

  14. Optical manipulation of a multilevel nuclear spin in ZnO: Master equation and experiment

    NASA Astrophysics Data System (ADS)

    Buß, J. H.; Rudolph, J.; Wassner, T. A.; Eickhoff, M.; Hägele, D.

    2016-04-01

    We demonstrate the dynamics and optical control of a large quantum mechanical solid state spin system consisting of a donor electron spin strongly coupled to the 9/2 nuclear spin of 115In in the semiconductor ZnO. Comparison of electron spin dynamics observed by time-resolved pump-probe spectroscopy with density matrix theory reveals nuclear spin pumping via optically oriented electron spins, coherent spin-spin interaction, and quantization effects of the ten nuclear spin levels. Modulation of the optical electron spin orientation at frequencies above 1 MHz gives evidence for fast optical manipulation of the nuclear spin state.

  15. Observation of an organic acid mediated spin state transition in a Co(II)-Schiff base complex: an EPR, HYSCORE, and DFT study.

    PubMed

    Vinck, Evi; Carter, Emma; Murphy, Damien M; Van Doorslaer, Sabine

    2012-08-06

    The interactions of a weak organic acid (acetic acid, HOAc) with a toluene solution of the Co(II)-Schiff base type complex, (R,R')-N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexane-diamino Co(II) (labeled [Co(1)]), was investigated using EPR, HYSCORE, and DFT computations. This activated [Co(II)(1)] system is extremely important within the context of asymmetric catalysts (notably the hydrolytic kinetic resolution of epoxides) despite the lack of detailed structural information about the nature of the paramagnetic species present. Under anaerobic conditions, the LS [Co(II)(1)] complex with a |yz, (2)A(2)〉 ground state is converted into a low-spin (LS) and a high-spin (HS) complex in the presence of the acid. The newly formed LS state is assigned to the coordinated [Co(II)(1)]-(HOAc) complex, possessing a |z(2), (2)A(1)〉 ground state (species A; g(x) = 2.42, g(y) = 2.28, g(z) = 2.02, A(x) = 100, A(y) = 120, A(z) = 310 MHz). The newly formed HS state is assigned to an acetate coordinated [Co(II)(1)]-(OAc(-)) complex, possessing an S = 3/2 spin ground state (species B, responsible for a broad EPR signal with g ≈ 4.6). These spin ground states were confirmed with DFT calculations using the hybrid BP86 and B3LYP functionals. Under aerobic conditions, the LS and HS complexes (species A and B) are not observed; instead, a new HS complex (species C) is formed. This complex is tentatively assigned to a paramagnetic superoxo bridged dimer (AcO(-))[Co(II)(1)···O(2)(-)Co(III)(1)](HOAc), as distinct from the more common diamagnetic peroxo bridged dimers. Species C is characterized by a very broad HS EPR signal (g(x) = 5.1, g(y) = 3.9, g(z) = 2.1) and is reversibly formed by oxygenation of the LS [Co(II)(1)]-(HOAc) complex to the superoxo complex [Co(III)(1)O(2)(-)](HOAc), which subsequently forms the association complex C by interaction with the HS [Co(II)(1)](OAc(-)) species. The LS and HS complexes were also identified using other organic acids (benzoic and

  16. Sensitive, Efficient Quantitation of 13C-Enriched Nucleic Acids via Ultrahigh-Performance Liquid Chromatography-Tandem Mass Spectrometry for Applications in Stable Isotope Probing.

    PubMed

    Wilhelm, Roland; Szeitz, András; Klassen, Tara L; Mohn, William W

    2014-12-01

    Stable isotope probing (SIP) of nucleic acids is a powerful tool for studying the functional traits of microbial populations within complex communities, but SIP involves a number of technical challenges. Many of the difficulties in DNA-SIP and RNA-SIP experiments can be effectively overcome with an efficient, sensitive method for quantitating the isotopic enrichment of nucleic acids. Here, we present a sensitive method for quantitating (13)C enrichment of nucleic acids, requiring a few nanograms of sample, and we demonstrate its utility in typical DNA-SIP and RNA-SIP experiments. All five nucleobases (adenine, guanine, cytosine, thymine, and uracil) were separated and detected by using ultrahigh-performance liquid chromatography-tandem mass spectrometry. We detected all isotopic species in samples with as low as 1.5 atom% (13)C above natural abundance, using 1-ng loadings. Quantitation was used to characterize the isotopic enrichment kinetics of cellulose- and lignin-based microcosm experiments and to optimize the recovery of enriched nucleic acids. Application of our method will minimize the quantity of expensive isotopically labeled substrates required and reduce the risk of failed experiments due to insufficient recovery of labeled nucleic acids for sequencing library preparation.

  17. Sensitive, Efficient Quantitation of 13C-Enriched Nucleic Acids via Ultrahigh-Performance Liquid Chromatography–Tandem Mass Spectrometry for Applications in Stable Isotope Probing

    PubMed Central

    Wilhelm, Roland; Szeitz, András; Klassen, Tara L.

    2014-01-01

    Stable isotope probing (SIP) of nucleic acids is a powerful tool for studying the functional traits of microbial populations within complex communities, but SIP involves a number of technical challenges. Many of the difficulties in DNA-SIP and RNA-SIP experiments can be effectively overcome with an efficient, sensitive method for quantitating the isotopic enrichment of nucleic acids. Here, we present a sensitive method for quantitating 13C enrichment of nucleic acids, requiring a few nanograms of sample, and we demonstrate its utility in typical DNA-SIP and RNA-SIP experiments. All five nucleobases (adenine, guanine, cytosine, thymine, and uracil) were separated and detected by using ultrahigh-performance liquid chromatography–tandem mass spectrometry. We detected all isotopic species in samples with as low as 1.5 atom% 13C above natural abundance, using 1-ng loadings. Quantitation was used to characterize the isotopic enrichment kinetics of cellulose- and lignin-based microcosm experiments and to optimize the recovery of enriched nucleic acids. Application of our method will minimize the quantity of expensive isotopically labeled substrates required and reduce the risk of failed experiments due to insufficient recovery of labeled nucleic acids for sequencing library preparation. PMID:25217022

  18. Design of Selenium-Based Chiral Chemical Probes for Simultaneous Enantio- and Chemosensing of Chiral Carboxylic Acids with Remote Stereogenic Centers by NMR Spectroscopy.

    PubMed

    Shyshkanov, Sergey A; Orlov, Nikolai V

    2016-10-17

    Selenium-based enantiopure chiral chemical probes have been designed in a modular way starting from available amino alcohols. The probes developed were found to be efficient in chemoselective interaction with carboxylic functions of chiral substrates leading to diastereomeric amide formation and in sensing α-, β-, and remote (up to seven bonds away from the carboxylic group) chiral centers by using (77) Se NMR spectroscopy. As a result, it was possible to determine the enantiomeric ratio of structurally diverse individual chiral acids including polyfunctional compounds and drugs with high accuracy. An approach to analyzing the crude reaction mixtures has been successfully developed by using bifunctional selenium- and fluorine-containing chiral probes. More importantly, it was revealed that, based on the (77) Se NMR data obtained, it is possible to obtain primary information about the location and nature of the substituents at the chiral center (chemo- and enantiosensing), which can simplify the structural elucidation of complex compounds. The derivatization procedure takes as little as 5 min and can be performed directly in an NMR tube followed by NMR measurements without any isolation and purification steps.

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

    PubMed

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

    1988-12-01

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

  20. Incorporation of extra amino acids in peptide recognition probe to improve specificity and selectivity of an electrochemical peptide-based sensor.

    PubMed

    Zaitouna, Anita J; Maben, Alex J; Lai, Rebecca Y

    2015-07-30

    We investigated the effect of incorporating extra amino acids (AA) at the n-terminus of the thiolated and methylene blue-modified peptide probe on both specificity and selectivity of an electrochemical peptide-based (E-PB) HIV sensor. The addition of a flexible (SG)3 hexapeptide is, in particular, useful in improving sensor selectivity, whereas the addition of a highly hydrophilic (EK)3 hexapeptide has shown to be effective in enhancing sensor specificity. Overall, both E-PB sensors fabricated using peptide probes with the added AA (SG-EAA and EK-EAA) showed better specificity and selectivity, especially when compared to the sensor fabricated using a peptide probe without the extra AA (EAA). For example, the selectivity factor recorded in the 50% saliva was ∼2.5 for the EAA sensor, whereas the selectivity factor was 7.8 for both the SG-EAA and EK-EAA sensors. Other sensor properties such as the limit of detection and dynamic range were minimally affected by the addition of the six AA sequence. The limit of detection was 0.5 nM for the EAA sensor and 1 nM for both SG-EAA and EK-EAA sensors. The saturation target concentration was ∼200 nM for all three sensors. Unlike previously reported E-PB HIV sensors, the peptide probe functions as both the recognition element and antifouling passivating agent; this modification eliminates the need to include an additional antifouling diluent, which simplifies the sensor design and fabrication protocol.

  1. Fluorescence sensing of phosdrin pesticide by the luminescent Eu(III)- and Tb(III)-bis(coumarin-3-carboxylic acid) probes

    NASA Astrophysics Data System (ADS)

    Hussein, Belal H. M.; Khairy, Gasser M.; Kamel, Rasha M.

    2016-04-01

    Luminescence quenching of the Eu(III)- and Tb(III)-bis (coumarin-3-carboxylic acid) (Ln(III)-(CCA)2) probes has been studied in the presence of organophosphorus or organochlorine pesticides; Phosdrin (P1), Malathion (P2), Profenofos (P3), Formothion (P4), Heptachlor (P5), and Endosulfan (P6). The luminescence intensity of lanthanide complex probes Ln(III)-(CCA)2 decreases as the concentration of the Phosdrin pesticide increases, while the other investigated pesticides have no significant influence on the lanthanide fluorescent intensities. It is observed that the quenching of Eu(III) and Tb(III)-coumarin-3-carboxylic acid by Phosdrin proceeds via static quenching processes according to Stern-Volmer plot. The binding constants (K) and the thermodynamic parameters of the interaction of Ln(III)-(CCA)2 with Phosdrin have been determined. A direct method for the determination of the Phosdrin in ethanol has been developed based on the luminescence changes of the Ln(III)-(CCA)2-phosdrin ternary complexes. The detection limits of P1 were 6.28 and 1.07 μM in case of Eu(III) and Tb(III)-complex, respectively. The influence of various interfering species on the detection of P1 has been investigated to assess the analytical applicability of the method. The new method was applied to determine the Phosdrin pesticide in different types of water samples.

  2. Muon spin rotation in solids

    NASA Technical Reports Server (NTRS)

    Stronach, C. E.

    1983-01-01

    The muon spin rotation (MuSR) technique is used to probe the microscopic electron density in materials. High temperature MuSR and magnetization measurements in nickel are in progress to allow an unambiguous determination of the muon impurity interaction and the impurity induced change in local spin density. The first results on uniaxial stress induced frequency shifts in an Fe single crystal are also reported.

  3. Probing the General Time Scale Question of Boronic Acid Binding with Sugars in Aqueous Solution at Physiological pH

    PubMed Central

    Ni, Nanting; Laughlin, Sarah; Wang, Yingji; Feng, You; Zheng, Yujun

    2012-01-01

    The boronic acid group is widely used in chemosensor design due to its ability to reversibly bind diol-containing compounds. The thermodynamic properties of the boronic acid-diol binding process have been investigated extensively. However, there are few studies of the kinetic properties of such binding processes. In this report, stopped-flow method was used for the first time to study the kinetic properties of the binding between three model arylboronic acids, 4-, 5-, and 8-isoquinolinylboronic acids, and various sugars. With all the boronic acid-diol pair sexamined, reactions were complete within seconds. The kon values with various sugars follow the order of D-fructose >D-tagatose>D-mannose >D-glucose. This trend tracks the thermodynamic binding affinities for these sugars and demonstrates that the “on” rate is the key factor determining the binding constant. PMID:22464680

  4. Probing the origin of acetyl-CoA and oxaloacetate entering the citric acid cycle from the 13C labeling of citrate released by perfused rat hearts.

    PubMed

    Comte, B; Vincent, G; Bouchard, B; Des Rosiers, C

    1997-10-17

    We present a strategy for simultaneous assessment of the relative contributions of anaplerotic pyruvate carboxylation, pyruvate decarboxylation, and fatty acid oxidation to citrate formation in the perfused rat heart. This requires perfusing with a mix of 13C-substrates and determining the 13C labeling pattern of a single metabolite, citrate, by gas chromatography-mass spectrometry. The mass isotopomer distributions of the oxaloacetate and acetyl moieties of citrate allow calculation of the flux ratios: (pyruvate carboxylation)/(pyruvate decarboxylation), (pyruvate carboxylation)/(citrate synthesis), (pyruvate decarboxylation)/(citrate synthesis) (pyruvate carboxylation)/(fatty acid oxidation), and (pyruvate decarboxylation)/(fatty acid oxidation). Calculations, based on precursor-product relationship, are independent of pool size. The utility of our method was demonstrated for hearts perfused under normoxia with [U-13C3](lactate + pyruvate) and [1-13C]octanoate under steady-state conditions. Under these conditions, effluent and tissue citrate were similarly enriched in all 13C mass isotopomers. The use of effluent citrate instead of tissue citrate allows probing substrate fluxes through the various reactions non-invasively in the intact heart. The methodology should also be applicable to hearts perfused with other 13C-substrates, such as 1-13C-labeled long chain fatty acid, and under various conditions, provided that assumptions on which equations are developed are valid.

  5. Acid-base equilibrium dynamics in methanol and dimethyl sulfoxide probed by two-dimensional infrared spectroscopy.

    PubMed

    Lee, Chiho; Son, Hyewon; Park, Sungnam

    2015-07-21

    Two-dimensional infrared (2DIR) spectroscopy, which has been proven to be an excellent experimental method for studying thermally-driven chemical processes, was successfully used to investigate the acid dissociation equilibrium of HN3 in methanol (CH3OH) and dimethyl sulfoxide (DMSO) for the first time. Our 2DIR experimental results indicate that the acid-base equilibrium occurs on picosecond timescales in CH3OH but that it occurs on much longer timescales in DMSO. Our results imply that the different timescales of the acid-base equilibrium originate from different proton transfer mechanisms between the acidic (HN3) and basic (N3(-)) species in CH3OH and DMSO. In CH3OH, the acid-base equilibrium is assisted by the surrounding CH3OH molecules which can directly donate H(+) to N3(-) and accept H(+) from HN3 and the proton migrates through the hydrogen-bonded chain of CH3OH. On the other hand, the acid-base equilibrium in DMSO occurs through the mutual diffusion of HN3 and N3(-) or direct proton transfer. Our 2DIR experimental results corroborate different proton transfer mechanisms in the acid-base equilibrium in protic (CH3OH) and aprotic (DMSO) solvents.

  6. Single spin relaxometry of spin noise from a ferromagnet

    NASA Astrophysics Data System (ADS)

    Casola, Francesco; van der Sar, Toeno; Walsworth, Ronald; Yacoby, Amir

    2015-03-01

    The introduction of new schemes for the measurement of spatially resolved dynamic magnetic properties of strongly correlated electrons is essential for the study of condensed matter magnetism and the development of novel spintronic devices. Here we show the possibility to detect the magnetic spin noise produced by a thin (~ 30 nm) layer of a patterned micro-sized ferromagnet (Ni81Fe19) by optical initialization and read-out of the single spin state of a nearby nitrogen vacancy center (NV) in diamond. For the interpretation of our results, we develop a general framework describing single-spin stray field detection in terms of a filter function sensitive mostly to spin fluctuations with wavevector ~ 1 / d , where d is the NV-ferromagnet distance. Our results pave the way towards quantitative and non-perturbative detection of spectral properties in nanomagnets, establishing NV center magnetometry as an emergent probe of collective spin dynamics in condensed matter.

  7. [Study of erythrocyte dehydration using spin labels].

    PubMed

    Moiseev, V A; Mezhidov, S Kh; Nardid, O A

    1989-01-01

    Possibility of studying erythrocyte dehydration by ESR-spin probe is substantiated. Dehydration of erythrocytes in relation to osmolarity of sodium chloride solutions is investigated. The results are shown to agree with the data obtained by radioisotope method.

  8. A Rapid Approach for Fabricating Boronic Acid-Functionalized Plates for On-Probe Detection of Glycoprotein and Glycopeptide

    PubMed Central

    Liu, Yu-Ching; Chen, Chao-Jung

    2017-01-01

    We developed a rapid and simple approach without using complex mechanical or chemical protocols to fabricate boronic acid-functionalized plates for glycoprotein or glycopeptide enrichment and mass spectrometry (MS) analysis. By coating the boronic acid-functionalized silica particles on a polydimethylsiloxane (PDMS)-coated matrix-assisted laser desorption/ionization (MALDI) plate, these particles can form a firmly monolayer of particles on PDMS membrane for sample handling without peeling off. The boronic acid particles-coated PDMS plate (BP plate) was successfully applied to the enrichment of horseradish peroxidase (HRP) protein and their digested glycopeptides. PMID:28337401

  9. Electrical detection of spin coherence in silicon.

    PubMed

    Boehme, Christoph; Lips, Klaus

    2003-12-12

    Experimental evidence is presented showing that photocurrents in silicon can be used as highly sensitive readout probes for coherent spin states of localized electrons, the prime candidates for quantum bits in various semiconductor based quantum computer concepts. Conduction electrons are subjected to fast Rabi oscillation induced by means of pulsed electron spin resonance. The collective spin motion of the charge carrier ensemble is reflected by a spin-dependent recombination rate and therefore by the sample conductivity. Because of inhomogeneities, the Rabi oscillation dephases rapidly. However, a microwave induced rephasing is possible causing an echo effect whose intensity contains information about the charge carrier spin state and the coherence decay.

  10. A sensitive gel-based method combining distinct cyclophellitol-based probes for the identification of acid/base residues in human retaining β-glucosidases.

    PubMed

    Kallemeijn, Wouter W; Witte, Martin D; Voorn-Brouwer, Tineke M; Walvoort, Marthe T C; Li, Kah-Yee; Codée, Jeroen D C; van der Marel, Gijsbert A; Boot, Rolf G; Overkleeft, Herman S; Aerts, Johannes M F G

    2014-12-19

    Retaining β-exoglucosidases operate by a mechanism in which the key amino acids driving the glycosidic bond hydrolysis act as catalytic acid/base and nucleophile. Recently we designed two distinct classes of fluorescent cyclophellitol-type activity-based probes (ABPs) that exploit this mechanism to covalently modify the nucleophile of retaining β-glucosidases. Whereas β-epoxide ABPs require a protonated acid/base for irreversible inhibition of retaining β-glucosidases, β-aziridine ABPs do not. Here we describe a novel sensitive method to identify both catalytic residues of retaining β-glucosidases by the combined use of cyclophellitol β-epoxide- and β-aziridine ABPs. In this approach putative catalytic residues are first substituted to noncarboxylic amino acids such as glycine or glutamine through site-directed mutagenesis. Next, the acid/base and nucleophile can be identified via classical sodium azide-mediated rescue of mutants thereof. Selective labeling with fluorescent β-aziridine but not β-epoxide ABPs identifies the acid/base residue in mutagenized enzyme, as only the β-aziridine ABP can bind in its absence. The Absence of the nucleophile abolishes any ABP labeling. We validated the method by using the retaining β-glucosidase GBA (CAZy glycosylhydrolase family GH30) and then applied it to non-homologous (putative) retaining β-glucosidases categorized in GH1 and GH116: GBA2, GBA3, and LPH. The described method is highly sensitive, requiring only femtomoles (nanograms) of ABP-labeled enzymes.

  11. Quantum limited heterodyne detection of spin noise

    NASA Astrophysics Data System (ADS)

    Cronenberger, S.; Scalbert, D.

    2016-09-01

    Spin noise spectroscopy is a powerful technique for studying spin relaxation in semiconductors. In this article, we propose an extension of this technique based on optical heterodyne detection of spin noise, which provides several key advantages compared to conventional spin noise spectroscopy: detection of high frequency spin noise not limited by detector bandwidth or sampling rates of digitizers, quantum limited sensitivity even in case of very weak probe power, and possible amplification of the spin noise signal. Heterodyne detection of spin noise is demonstrated on insulating n-doped GaAs. From measurements of spin noise spectra up to 0.4 Tesla, we determined the distribution of g-factors, Δg/g = 0.49%.

  12. Probing Metal Carbonation Reactions of CO2 in a Model System Containing Forsterite and H2O Using Si-29, C-13 Magic Angle Sample Spinning NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hu, J.; Kwak, J.; Hoyt, D. W.; Sears, J. A.; Rosso, K. M.; Felmy, A. R.

    2009-12-01

    Ex situ solid state NMR have been used for the first time to study fundamental mineral carbonation processes and reaction extent relevant to geologic carbon sequestration using a model silicate mineral forsterite (Mg2SiO4)+scCO2 with and without H2O. Run conditions were 80C and 96 bar. Si-29 NMR clearly shows that in the absence of CO2, the role of H2O is to hydrolyze surface Mg-O-Si bonds to produce Mg2+, and mono- and oligomeric hydroxylated silica species. The surface hydrolysis products contain only Q0 (Si(OH)4) and Q1 (Si(OH)3OSi) species. An equilibrium between Q0, Q1 and Mg2+ with a saturated concentration equivalent to less than 3.2% of the Mg2SiO4 conversion is obtained at a reaction time of up to 7 days. Using scCO2 without H2O, no reaction is observed within 7 days. Using both scCO2 and H2O, the surface reaction products for silica are mainly Q3 (SiOH(OSi)3) species accompanied by a lesser amount of Q2 (Si(OH)2(OSi)2) and Q4 (Si(OSi)4). However, no Q0 and Q1 were detected, indicating the carbonic acid formation/deprotonation and magnesite (MgCO3) precipitation reactions are faster than the forsterite hydrolysis process. Thus it can be concluded that the Mg2SiO4 hydrolysis process is the rate limiting step of the overall mineral carbonation process. Si-29 NMR combined with XRD, TEM, SAED and EDX further reveal that the reaction is a surface reaction with the Mg2SiO4 crystallite in the core and with condensed Q2-Q4 species forming amorphous surface layers. C-13 MAS NMR identified a possible reaction intermediates as (MgCO3)4*Mg(OH)2*5H2O. However, at long reaction times only crystallite magnesite MgCO3 products are observed. This research is part of a broader effort at PNNL to develop experimental tools and fundamental insights into chemical transformations affecting subsurface CO2 reactive transport. Si-29 (left) and C-13 (right) MAS NMR spectra of Mg2SiO4 under various reaction conditions. Si-29 NMR reveals that in scCO2 without H2O, no reaction is

  13. Nuclear spin noise in NMR revisited

    SciTech Connect

    Ferrand, Guillaume; Luong, Michel

    2015-09-07

    The theoretical shapes of nuclear spin-noise spectra in NMR are derived by considering a receiver circuit with finite preamplifier input impedance and a transmission line between the preamplifier and the probe. Using this model, it becomes possible to reproduce all observed experimental features: variation of the NMR resonance linewidth as a function of the transmission line phase, nuclear spin-noise signals appearing as a “bump” or as a “dip” superimposed on the average electronic noise level even for a spin system and probe at the same temperature, pure in-phase Lorentzian spin-noise signals exhibiting non-vanishing frequency shifts. Extensive comparisons to experimental measurements validate the model predictions, and define the conditions for obtaining pure in-phase Lorentzian-shape nuclear spin noise with a vanishing frequency shift, in other words, the conditions for simultaneously obtaining the spin-noise and frequency-shift tuning optima.

  14. Studying the Proton Spin Puzzle with PHENIX

    NASA Astrophysics Data System (ADS)

    Daugherity, Michael

    2012-03-01

    The proton spin puzzle remains one of the biggest mysteries in fundamental particle physics today. This talk will explore how the PHENIX Collaboration's forward W-boson program uses RHIC, the world's only polarized proton-proton collider, to probe the spin structure of the proton.

  15. A comparative IR characterization of acidic sites on HY zeolite by pyridine and CO probes with silica-alumina and γ-alumina references.

    PubMed

    Kondo, Junko N; Nishitani, Ryoko; Yoda, Eisuke; Yokoi, Toshiyuki; Tatsumi, Takashi; Domen, Kazunari

    2010-10-07

    Using IR spectroscopy, three different surface states of HY zeolite were probed by successive adsorption of CO at 143 K followed by evacuation and pyridine adsorption at 523 K: HY zeolite [1] without strong Lewis acid sites (LAS); [2] after high temperature (873 K) evacuation to convert Brønsted acid sites (BAS) to strong LAS; and [3] after water re-adsorption on HY zeolite [2] to recover BAS from LAS. The original surface of HY zeolite [1] seemed to be recovered on HY zeolite [3] after high temperature evacuation and water treatment by CO adsorption, while a part of generated LAS on HY zeolite [2] seemed irreversible on HY zeolite [3] to HY zeolite [1] by pyridine adsorption. To clarify this discrepancy, re-examination of the IR spectra of adsorbed CO and pyridine on γ-alumina and silica-alumina after similar treatments to those on HY zeolite was conducted. Based on the results of CO adsorption on γ-alumina and silica-alumina, the presence of extra-framework aluminium sites on HY zeolite [1] was confirmed. High temperature evacuation of HY zeolite [1] formed very strong LAS, a part of which was irreversible to BAS by water re-adsorption at room temperature. The irreversible sites on HY zeolite [3] were assigned to non-acidic OH groups attributed to silica-alumina. The non-acidic OH groups on HY zeolite [3], which were BAS on HY zeolite [1], hydrogen-bonded to pyridine to show IR spectra similar to those adsorbed on LAS. Thus, LAS on HY zeolite [3] seemed irreversible by pyridine adsorption after water re-adsorption. On the other hand, CO adsorbed on non-acidic OH groups showed a band at only slightly lower frequency (2160 cm(-1)) than that of BAS (2178 cm(-1)), resulting in overlapps and ignoring their presence. Thus, CO adsorption seemed to show that complete recovery of LAS to BAS occurred.

  16. Single glass nanopore-based regenerable sensing platforms with a non-immobilized polyglutamic acid probe for selective detection of cupric ions.

    PubMed

    Chen, Lizhen; He, Haili; Xu, Xiaolong; Jin, Yongdong

    2015-08-19

    A single glass capillary nanopore-based sensing platform for rapid and selective detection of cupric ions is demonstrated by utilizing polyglutamic acid (PGA) as a non-immobilized probe. The detection is based on the significant decrease of ionic current through nanopore and the reversal of ion current rectification responses induced by the chelated cupric ions on the probes when in the presence of cupric ions. PGA shows high selectivity for detecting cupric ions rather than other metal ions. The sensitivity of the sensing platform can be improved about 1-2 orders of magnitude by employing asymmetric salt gradients during the measurements. And the PGA-based nanopore sensing platform shows excellent regenerability for Cu(2+) sensing applications. In addition, the method is found effective and reliable for the detection of cupric ions in real samples with small volume down to 20 μL. This nanopore-based sensing platform will find promising practical applications for the detection of cupric ions.

  17. Probing metal ion complexation with salicylic acid and its derivatives with excited state proton transfer and luminescence anisotropy

    SciTech Connect

    Wang, Z.; Friedrich, D.M.; Ainsworth, C.C.

    1996-10-01

    Salicylic acid and its derivatives in which the phenolic proton is preserved show a characteristic dual fluorescence: one band in the UV, due to a {open_quotes}normal{close_quotes} excited state emission, and the other in the visible range, is assigned to excited state intramolecular proton transfer (ESIPT). The transition energy, quantum yield and fluorescence lifetime as well as fluorescence anisotropy are sensitive to the solvent environment, temperature and properties of the substituents (complexation) at the phenolic and carboxylic oxygens. The ESIPT band disappears in molecules in which the intramolecular hydrogen bond between phenolic hydrogen and the carbonyl oxygen is prohibited. In this work, the complexation of Na(I), Ca(II), Al(III) and La(III) with salicylic acid, 3-hydroxybenzoic acid, methylsalicylate and anisic acid in both aqueous and non-aqueous solvents has been studied by absorption and steady state luminescence spectroscopy, picosecond to nanosecond luminescence lifetimes and luminescence anisotropy measurements in a range of solvent and in ethanol at 77 K. Speciation in these complex systems, binding characteristics between the metal ion and the ligand, and ligand-centered energetics are discussed in terms of the spectroscopic properties, luminescence and anisotropy decay kinetics.

  18. Probing thermal stability of the β-lactoglobulin-oleic acid complex by fluorescence spectroscopy and molecular modeling

    NASA Astrophysics Data System (ADS)

    Simion (Ciuciu), Ana-Maria; Aprodu, Iuliana; Dumitrașcu, Loredana; Bahrim, Gabriela Elena; Alexe, Petru; Stănciuc, Nicoleta

    2015-09-01

    Bovine β-lactoglobulin is able to interact with different bioactive compounds, thus being an important candidate in the development of delivery systems with improved functionality. The heat induced changes in the β-lactoglobulin-oleic acid complex were examined by means of fluorescence spectroscopy and molecular modeling techniques. Fluorescence spectroscopy results indicated a rigid protein structure in the temperature range 25-70 °C, whereas at temperatures over 75 °C, the rearrangements of the polypeptide chains led to higher exposure of hydrophobic residues. The most significant increase of the accessible surface area with temperature increase was identified in case of Tyr99 and Tyr102. The phase diagram method indicated an all or none transition between two conformations. Due to conformational changes, no contact between Ile56 or Lys60 and the fatty acid could be identified at 85 °C, but new non-bonding interaction were established with Ile12 and Val15. The results obtained in this study provide important details about thermal induced changes in the conformation of β-lactoglobulin-oleic acid complex. Significant conformational changes were registered above 75 °C, suggesting the possibility of obtaining highly functional complexes between whey proteins and natural unsaturated fatty acids.

  19. Probing High School Students' Cognitive Structures and Key Areas of Learning Difficulties on Ethanoic Acid Using the Flow Map Method

    ERIC Educational Resources Information Center

    Zhou, Qing; Wang, Tingting; Zheng, Qi

    2015-01-01

    The purpose of this study was primarily to explore high school students' cognitive structures and to identify their learning difficulties on ethanoic acid through the flow map method. The subjects of this study were 30 grade 1 students from Dong Yuan Road Senior High School in Xi'an, China. The interviews were conducted a week after the students…

  20. Spectrophotometric probe

    DOEpatents

    Prather, W.S.; O'Rourke, P.E.

    1994-08-02

    A support structure is described bearing at least one probe for making spectrophotometric measurements of a fluid using a source of light and a spectrophotometer. The probe includes a housing with two optical fibers and a planoconvex lens. A sleeve bearing a mirror surrounds the housing. The lens is separated from the mirror by a fixed distance, defining an interior space for receiving a volume of the fluid sample. A plurality of throughholes extending through the sleeve communicate between the sample volume and the exterior of the probe, all but one hole bearing a screen. A protective jacket surrounds the probe. A hollow conduit bearing a tube is formed in the wall of the probe for venting any air in the interior space when fluid enters. The probe is held at an acute angle so the optic fibers carrying the light to and from the probe are not bent severely on emergence from the probe. 3 figs.

  1. Spectrophotometric probe

    DOEpatents

    Prather, William S.; O'Rourke, Patrick E.

    1994-01-01

    A support structure bearing at least one probe for making spectrophotometric measurements of a fluid using a source of light and a spectrophotometer. The probe includes a housing with two optical fibers and a planoconvex lens. A sleeve bearing a mirror surrounds the housing. The lens is separated from the mirror by a fixed distance, defining an interior space for receiving a volume of the fluid sample. A plurality of throughholes extending through the sleeve communicate between the sample volume and the exterior of the probe, all but one hole bearing a screen. A protective jacket surrounds the probe. A hollow conduit bearing a tube is formed in the wall of the probe for venting any air in the interior space when fluid enters. The probe is held at an acute angle so the optic fibers carrying the light to and from the probe are not bent severely on emergence from the probe.

  2. Probing pH and pressure effects on the apomyoglobin heme pocket with the 2'-(N,N-dimethylamino)-6-naphthoyl-4-trans-cyclohexanoic acid fluorophore.

    PubMed Central

    Sire, O; Alpert, B; Royer, C A

    1996-01-01

    The environmentally sensitive fluorophore 2'-(N,N-dimethylamino)-6-naphthoyl-4-trans-cyclohexanoic acid (DANCA) has been used to probe the apomyoglobin heme pocket. The unexpected polarity of this domain is generally interpreted as arising from dynamic dipolar relaxation of the peptide dipoles surrounding the heme pocket. In the present work we reexamine the photophysical properties of DANCA in a variety of solvents and complexed with apomyoglobin (apoMb) to further probe the heme pocket environment as a function of external solvent conditions. Absorption and excitation spectra in a number of solvents are consistent with the well-known pi*<--pi (LE) and pi*<--n (CT) electronic absorption transitions observed for naphthylamine derivatives. Dual emission is also a well-documented property of such derivatives. Based on the time scale of the heterogeneity in the decay of the DANCA fluorophore observed in a series of solvents, we propose that the emission properties of DANCA in apoMb are not uniquely attributable to dynamic relaxation events, but also reflect dual emission from both a long-lived, red CT state and the shorter-lived, blue LE state. The pH studies in the range of pH 5-9 of the emission properties of DANCA in apoMb support this hypothesis. They also suggest a specific interaction of DANCA with one or both of the pocket histidyl residues, which leads to a drastic static quenching and red shift of the bound DANCA fluorescence upon protonation. Similar effects are observed with increasing pressure, indicating that these two perturbations alter the DANCA-apoMb complex in a similar fashion. The pressure-induced form of the protein is distinct both energetically and structurally from the previously characterized acid intermediate, in that it is populated above pH 5 and retains a significant degree of integrity of the heme pocket. PMID:8744328

  3. Reaction Fields in the Environment of Fluorescent Probes: Polarity Profiles in Membranes

    PubMed Central

    Marsh, Derek

    2009-01-01

    Fluorescent probes in biological systems are sensitive to environmental polarity by virtue of their response to the reaction field created by polarization of the dielectric medium. Classically, fluorophore solvatochromism is analyzed in terms of the Lippert equation and later variants, all of which rely upon the original reaction field of Onsager. A recent survey of the solvent dependence of EPR spin-label probes, which are responsive solely to the reaction field in the ground state without the complication of excited states, shows that the reaction field of Block and Walker performs best in describing the polarity dependence. In this model, the step-function transition to the bulk dielectric medium used by Onsager is replaced by a graded transition. Analysis of the Stokes shifts for representative fluorescent membrane probes, such as PRODAN, DANSYL, and anthroyl fatty acid, reveals that, of several different reaction fields (including that of Onsager), the Block-Walker model best describes the dependence on solvent dielectric constant and refractive index for the different probes simultaneously. This is after full allowance is made for all contributions involving polarizability of the fluorophore, a point that is frequently neglected or treated incorrectly in studies using biological fluorescent probes. By using the full range of polar and apolar solvents, it is then possible to establish a common reference for the polarity dependence of different fluorophores and to relate this also to the polarity dependence of biologically relevant spin-label EPR probes. An important application is calibration of the transmembrane polarity profile recorded by fluorescent probes in terms of the high-resolution profile obtained from site-specifically spin-labeled lipid chains. PMID:19348740

  4. Reaction fields in the environment of fluorescent probes: polarity profiles in membranes.

    PubMed

    Marsh, Derek

    2009-04-08

    Fluorescent probes in biological systems are sensitive to environmental polarity by virtue of their response to the reaction field created by polarization of the dielectric medium. Classically, fluorophore solvatochromism is analyzed in terms of the Lippert equation and later variants, all of which rely upon the original reaction field of Onsager. A recent survey of the solvent dependence of EPR spin-label probes, which are responsive solely to the reaction field in the ground state without the complication of excited states, shows that the reaction field of Block and Walker performs best in describing the polarity dependence. In this model, the step-function transition to the bulk dielectric medium used by Onsager is replaced by a graded transition. Analysis of the Stokes shifts for representative fluorescent membrane probes, such as PRODAN, DANSYL, and anthroyl fatty acid, reveals that, of several different reaction fields (including that of Onsager), the Block-Walker model best describes the dependence on solvent dielectric constant and refractive index for the different probes simultaneously. This is after full allowance is made for all contributions involving polarizability of the fluorophore, a point that is frequently neglected or treated incorrectly in studies using biological fluorescent probes. By using the full range of polar and apolar solvents, it is then possible to establish a common reference for the polarity dependence of different fluorophores and to relate this also to the polarity dependence of biologically relevant spin-label EPR probes. An important application is calibration of the transmembrane polarity profile recorded by fluorescent probes in terms of the high-resolution profile obtained from site-specifically spin-labeled lipid chains.

  5. Acid-base interactions and secondary structures of poly-L-lysine probed by 15N and 13C solid state NMR and Ab initio model calculations.

    PubMed

    Dos, Alexandra; Schimming, Volkmar; Tosoni, Sergio; Limbach, Hans-Heinrich

    2008-12-11

    The interactions of the 15N-labeled amino groups of dry solid poly-L-lysine (PLL) with various halogen and oxygen acids HX and the relation to the secondary structure have been studied using solid-state 15N and 13C CPMAS NMR spectroscopy (CP = cross polarization and MAS = magic angle spinning). For comparison, 15N NMR spectra of an aqueous solution of PLL were measured as a function of pH. In order to understand the effects of protonation and hydration on the 15N chemical shifts of the amino groups, DFT and chemical shielding calculations were performed on isolated methylamine-acid complexes and on periodic halide clusters of the type (CH3NH3(+)X(-))n. The combined experimental and computational results reveal low-field shifts of the amino nitrogens upon interaction with the oxygen acids HX = HF, H2SO4, CH3COOH, (CH3)2POOH, H3PO4, HNO3, and internal carbamic acid formed by reaction of the amino groups with gaseous CO2. Evidence is obtained that only hydrogen-bonded species of the type (Lys-NH2***H-X)n are formed in the absence of water. 15N chemical shifts are maximum when H is located in the hydrogen bond center and then decrease again upon full protonation, as found for aqueous solution at low pH. By contrast, halogen acids interact in a different way. They form internal salts of the type (Lys-NH3(+)X(-))n via the interaction of many acid-base pairs. This salt formation is possible only in the beta-sheet conformation. By contrast, the formation of hydrogen-bonded complexes can occur both in beta-sheet domains as well as in alpha-helical domains. The 15N chemical shifts of the protonated ammonium groups increase when the size of the interacting halogen anions is increased from chloride to iodide and when the number of the interacting anions is increased. Thus, the observed high-field 15N shift of ammonium groups upon hydration is the consequence of replacing interacting halogen atoms by oxygen atoms.

  6. Spin-SILC: CMB polarization component separation with spin wavelets

    NASA Astrophysics Data System (ADS)

    Rogers, Keir K.; Peiris, Hiranya V.; Leistedt, Boris; McEwen, Jason D.; Pontzen, Andrew

    2016-12-01

    We present Spin-SILC, a new foreground component separation method that accurately extracts the cosmic microwave background (CMB) polarization E and B modes from raw multifrequency Stokes Q and U measurements of the microwave sky. Spin-SILC is an internal linear combination method that uses spin wavelets to analyse the spin-2 polarization signal P = Q + iU. The wavelets are additionally directional (non-axisymmetric). This allows different morphologies of signals to be separated and therefore the cleaning algorithm is localized using an additional domain of information. The advantage of spin wavelets over standard scalar wavelets is to simultaneously and self-consistently probe scales and directions in the polarization signal P = Q + iU and in the underlying E and B modes, therefore providing the ability to perform component separation and E-B decomposition concurrently for the first time. We test Spin-SILC on full-mission Planck simulations and data and show the capacity to correctly recover the underlying cosmological E and B modes. We also demonstrate a strong consistency of our CMB maps with those derived from existing component separation methods. Spin-SILC can be combined with the pseudo- and pure E-B spin wavelet estimators presented in a companion paper to reliably extract the cosmological signal in the presence of complicated sky cuts and noise. Therefore, it will provide a computationally efficient method to accurately extract the CMB E and B modes for future polarization experiments.

  7. Long-lived spin-correlated pairs generated by photolysis of naphthalene occluded in non-Brønsted acidic ZSM-5 zeolites.

    PubMed

    Moissette, Alain; Marquis, Séverine; Cornu, David; Vezin, Hervé; Brémard, Claude

    2005-11-09

    Long-lived spin-correlated pairs were generated by laser irradiation of naphthalene (NAP) occluded as intact molecule within non-Brønsted acidic MnZSM-5 zeolites with MnSiO(2))(96-n)(AlO(2)n formula per unit cell. The laser UV photoionization generates primary NAP.+-electron pair as a fast phenomenon. These charge carriers exhibit lifetimes that extend over less than 1 h at room temperature and disappear according to two parallel competitive ways: direct charge recombination and electron transfer. This subsequent electron transfer takes place between the electron-deficient radical cation (NAP.+) and the electron-donor oxygen atom of zeolite framework. The aluminum rich MnZSM-5 zeolites (n = 3.4, 6.6) hinder efficiently the charge recombination and promote the electron transfer to generate a very long electron-hole pair which exceeds several weeks at room temperature in NAP@Li(6.6)ZSM-5. The electron-hole pair exhibits broad visible absorption bands at 482 and 525 nm. The electron-hole distance, 1.3 nm, was deduced from the dipolar interaction term (D) value. The spin density of trapped electron appears spread over (27)Al, (29)Si, (7)Li, and (1)H nuclei as deduced by two-dimensional approach of hyperfine sublevel correlation (HYSCORE). The very low recombination rate by tunneling effect was found to be in agreement with the very low value (J approximately 0) of the magnetic exchange. The combined effects of tight fit between NAP size and straight-channel dimension, the high aluminum content of the framework, and the highly polarizing cation Li(+) trapped efficiently the ejected electron in the conduction band and the hole in the valence band of the porous materials.

  8. A new dual-channel optical signal probe for Cu2+ detection based on morin and boric acid.

    PubMed

    Wang, Peng; Yuan, Bin Fang; Li, Nian Bing; Luo, Hong Qun

    2014-01-01

    In this work we utilized the common analytical reagent morin to develop a new a dual-channel, cost-effective, and sensitive method for determination of Cu(2+). It is found that morin is only weakly fluorescent by itself, but forms highly fluorescent complexes with boric acid. Moreover, the fluorescence of complexes of morin with boric acid is quenched linearly by Cu(2+) in a certain concentration range. Under optimum conditions, the fluorescence quenching efficiency was linearly proportional to the concentration of cupric ions in the range of 0.5-25 μM with high sensitivity, and the detection limit for Cu(2+) was 0.38 μM. The linear range was 1-25 μM determined by spectrophotometry, and the detection limit for cupric ions was 0.8 μM. Furthermore, the mechanism of sensitive fluorescence quenching response of morin to Cu(2+) is discussed.

  9. Probing the "additive effect" in the proline and proline hydroxamic acid catalyzed asymmetric addition of nitroalkanes to cyclic enones.

    PubMed

    Hanessian, Stephen; Govindan, Subramaniyan; Warrier, Jayakumar S

    2005-11-01

    The effect of chirality and steric bulk of 2,5-disubstituted piperazines as additives in the conjugate addition of 2-nitropropane to cyclohexenone, catalyzed by l-proline, was investigated. Neither chirality nor steric bulk affects the enantioselectivity of addition, which gives 86-93% ee in the presence of achiral and chiral nonracemic 2,5-disubstituted piperazines. Proline hydroxamic acid is shown for the first time to be an effective organocatalyst in the same Michael reaction.

  10. Charge-to-Spin Conversion and Spin Diffusion in Bi/Ag Bilayers Observed by Spin-Polarized Positron Beam

    NASA Astrophysics Data System (ADS)

    Zhang, H. J.; Yamamoto, S.; Gu, B.; Li, H.; Maekawa, M.; Fukaya, Y.; Kawasuso, A.

    2015-04-01

    Charge-to-spin conversion induced by the Rashba-Edelstein effect was directly observed for the first time in samples with no magnetic layer. A spin-polarized positron beam was used to probe the spin polarization of the outermost surface electrons of Bi /Ag /Al2O3 and Ag /Bi /Al2O3 when charge currents were only associated with the Ag layers. An opposite surface spin polarization was found between Bi /Ag /Al2O3 and Ag /Bi /Al2O3 samples with the application of a charge current in the same direction. The surface spin polarizations of both systems decreased exponentially with the outermost layer thickness, suggesting the occurrence of spin diffusion from the Bi/Ag interface to the outermost surfaces. This work provides a new technique to measure spin diffusion length.

  11. Probing the chemical mechanism and critical regulatory amino acid residues of Drosophila melanogaster arylalkylamine N-acyltransferase like 2.

    PubMed

    Dempsey, Daniel R; Carpenter, Anne-Marie; Ospina, Santiago Rodriguez; Merkler, David J

    2015-11-01

    Arylalkylamine N-acyltransferase like 2 (AANATL2) catalyzes the formation of N-acylarylalkylamides from the corresponding acyl-CoA and arylalkylamine. The N-acylation of biogenic amines in Drosophila melanogaster is a critical step for the inactivation of neurotransmitters, cuticle sclerotization, and melatonin biosynthesis. In addition, D. melanogaster has been used as a model system to evaluate the biosynthesis of fatty acid amides: a family of potent cell signaling lipids. We have previously showed that AANATL2 catalyzes the formation of N-acylarylakylamides, including long-chain N-acylserotonins and N-acyldopamines. Herein, we define the kinetic mechanism for AANATL2 as an ordered sequential mechanism with acetyl-CoA binding first followed by tyramine to generate the ternary complex prior to catalysis. Bell shaped kcat,app - acetyl-CoA and (kcat/Km)app - acetyl-CoA pH-rate profiles identified two apparent pKa,app values of ∼7.4 and ∼8.9 that are critical to catalysis, suggesting the AANATL2-catalyzed formation of N-acetyltyramine occurs through an acid/base chemical mechanism. Site-directed mutagenesis of a conserved glutamate that corresponds to the catalytic base for other D. melanogaster AANATL enzymes did not produce a substantial depression in the kcat,app value nor did it abolish the pKa,app value attributed to the general base in catalysis (pKa ∼7.4). These data suggest that AANATL2 catalyzes the formation of N-acylarylalkylamides using either different catalytic residues or a different chemical mechanism relative to other D. melanogaster AANATL enzymes. In addition, we constructed other site-directed mutants of AANATL2 to help define the role of targeted amino acids in substrate binding and/or enzyme catalysis.

  12. Folic acid-targeted magnetic Tb-doped CeF3 fluorescent nanoparticles as bimodal probes for cellular fluorescence and magnetic resonance imaging.

    PubMed

    Ma, Zhi-Ya; Liu, Yu-Ping; Bai, Ling-Yu; An, Jie; Zhang, Lin; Xuan, Yang; Zhang, Xiao-Shuai; Zhao, Yuan-Di

    2015-10-07

    Magnetic fluorescent nanoparticles (NPs) have great potential applications for diagnostics, imaging and therapy. We developed a facile polyol method to synthesize multifunctional Fe3O4@CeF3:Tb@CeF3 NPs with small size (<20 nm), high water solubility and good biocompatibility. The NPs were modified by ligand exchange reactions with citric acid (CA) to obtain carboxyl-functionalized NPs (Fe3O4@CeF3:Tb@CeF3-COOH). Folic acid (FA) as an affinity ligand was then covalently conjugated onto NPs to yield Fe3O4@CeF3:Tb@CeF3-FA NPs. They were then applied as multimodal imaging agents for simultaneous in vitro targeted fluorescence imaging and magnetic resonance imaging (MRI) of HeLa cells with overexpressed folate receptors (FR). The results indicated that these NPs had strong luminescence and enhanced T2-weighted MR contrast and would be promising candidates as multimodal probes for both fluorescence and MRI imaging.

  13. Probing of the combined effect of bisquaternary ammonium antimicrobial agents and acetylsalicylic acid on model phospholipid membranes: differential scanning calorimetry and mass spectrometry studies.

    PubMed

    Kasian, N A; Pashynska, V A; Vashchenko, O V; Krasnikova, A O; Gömöry, A; Kosevich, M V; Lisetski, L N

    2014-12-01

    A model molecular biosystem of hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers that mimics cell biomembranes is used to probe combined membranotropic effects of drugs by instrumental techniques of molecular biophysics. Differential scanning calorimetry reveals that doping of the DPPC model membrane with individual bisquaternary ammonium compounds (BQAC) decamethoxinum, ethonium, thionium and acetylsalicylic acid (ASA) leads to lowering of the membrane melting temperature (Tm) pointing to membrane fluidization. Combined application of the basic BQAC and acidic ASA causes an opposite effect on Tm (increase), corresponding to the membrane densification. Thus, modulation of the membranotropic effects upon combined use of the drugs studied can be revealed at the level of model membranes. Formation of noncovalent supramolecular complexes of the individual BQACs and ASA with DPPC molecules, which may be involved in the mechanism of the drug-membrane interaction at the molecular level, is demonstrated by electrospray ionization (ESI) mass spectrometry. In the ternary (DPPC + ASA + BQAC) model systems, the stable complexes of the BQAC dication with the ASA anion, which may be responsible for modulation of the membranotropic effects of the drugs, were recorded by ESI mass spectrometry. The proposed approach can be further developed for preliminary evaluation of the combined effects of the drugs at the level of model lipid membranes prior to tests on living organisms.

  14. Probing the Active Site of MIO-dependent Aminomutases, Key Catalysts in the Biosynthesis of amino Acids Incorporated in Secondary Metabolites

    SciTech Connect

    Cooke, H.; Bruner, S

    2010-01-01

    The tyrosine aminomutase SgTAM produces (S)-{beta}-tyrosine from L-tyrosine in the biosynthesis of the enediyne antitumor antibiotic C-1027. This conversion is promoted by the methylideneimidazole-5-one (MIO) prosthetic group. MIO was first identified in the homologous family of ammonia lyases, which deaminate aromatic amino acids to form {alpha},{beta}-unsaturated carboxylates. Studies of substrate specificity have been described for lyases but there have been limited reports in altering the substrate specificity of aminomutases. Furthermore, it remains unclear as to what structural properties are responsible for catalyzing the presumed readdition of the amino group into the {alpha},{beta}-unsaturated intermediates to form {beta}-amino acids. Attempts to elucidate specificity and mechanistic determinants of SgTAM have also proved to be difficult as it is recalcitrant to perturbations to the active site via mutagenesis. An X-ray cocrystal structure of the SgTAM mutant of the catalytic base with L-tyrosine verified important substrate binding residues as well as the enzymatic base. Further mutagenesis revealed that removal of these crucial interactions renders the enzyme inactive. Proposed structural determinants for mutase activity probed via mutagenesis, time-point assays and X-ray crystallography revealed a complicated role for these residues in maintaining key quaternary structure properties that aid in catalysis.

  15. Investigation of Humidity Dependent Surface Morphology and Proton Conduction in Multi-Acid Side Chain Membranes by Conductive Probe Atomic Force Microscopy.

    PubMed

    Economou, Nicholas J; Barnes, Austin M; Wheat, Andrew J; Schaberg, Mark S; Hamrock, Steven J; Buratto, Steven K

    2015-11-05

    In this report, we employ phase-contrast tapping mode and conductive probe atomic force microscopy (cp-AFM) as tools to investigate the nanoscale morphology and proton conductance of a 3M perfluoro-imide acid (PFIA) membrane (625 EW) over a large range of relative humidity (3-95% RH). As a point of comparison, we also investigate 3M perfluorosulfonic acid (PFSA) (825 EW) and Nafion 212. With AFM, we assess the membrane's water retention and mechanical stability at low RH and high RH, respectively. Cp-AFM allows us to spatially resolve the hydrophilic and electrochemically active domains under a similar set of conditions and observe directly the ties between membrane morphology and proton conductance. From our data, we are able to correlate the improved water retention indicated by the size of the hydrophilic domains with the proton conductance in the PFIA membrane at elevated temperature and compare the result with that observed for the PFSA and Nafion. At high RH conditions, we see evidence of a nearly continuous hydrophilic phase, which indicates a high degree of swelling.

  16. Probing Nucleic Acid Interactions and Pre-mRNA Splicing by Förster Resonance Energy Transfer (FRET) Microscopy

    PubMed Central

    Šimková, Eva; Staněk, David

    2012-01-01

    Förster resonance energy transfer (FRET) microscopy is a powerful technique routinely used to monitor interactions between biomolecules. Here, we focus on the techniques that are used for investigating the structure and interactions of nucleic acids (NAs). We present a brief overview of the most commonly used FRET microscopy techniques, their advantages and drawbacks. We list experimental approaches recently used for either in vitro or in vivo studies. Next, we summarize how FRET contributed to the understanding of pre-mRNA splicing and spliceosome assembly. PMID:23203103

  17. Amorphous/nanocrystalline silicon biosensor for the specific identification of unamplified nucleic acid sequences using gold nanoparticle probes

    NASA Astrophysics Data System (ADS)

    Martins, Rodrigo; Baptista, Pedro; Raniero, Leandro; Doria, Gonçalo; Silva, Leonardo; Franco, Ricardo; Fortunato, Elvira

    2007-01-01

    Amorphous/nanocrystalline silicon pi 'ii'n devices fabricated on micromachined glass substrates are integrated with oligonucleotide-derivatized gold nanoparticles for a colorimetric detection method. The method enables the specific detection and quantification of unamplified nucleic acid sequences (DNA and RNA) without the need to functionalize the glass surface, allowing for resolution of single nucleotide differences between DNA and RNA sequences—single nucleotide polymorphism and mutation detection. The detector's substrate is glass and the sample is directly applied on the back side of the biosensor, ensuring a direct optical coupling of the assays with a concomitant maximum photon capture and the possibility to reuse the sensor.

  18. Characterisation of embroidered 3D electrodes by use of anthraquinone-1,5-disulfonic acid as probe system

    NASA Astrophysics Data System (ADS)

    Aguiló-Aguayo, Noemí; Bechtold, Thomas

    2014-05-01

    New electrode designs are required for electrochemical applications such as batteries or fuel cells. Embroidered 3D Cu porous electrodes with a geometric surface of 100 cm2 are presented and characterised by means of the anthraquinone-1,5-disfulfonic acid (AQDS2-) redox system in alkaline solution. The electrochemical behaviour of the 3D electrode is established by the comparison of cyclic voltammetry responses using a micro cell and a 100 cm2 plane Cu-plate electrode. Dependencies of the peak currents and peak-to-peak potential separation on scan rate and AQDS2- concentration are studied. The AQDS2- characterisation is also performed by means of spectroelectrochemical experiments.

  19. Spin transport and dynamics in all-oxide perovskite La2 /3Sr1 /3MnO3 /SrRuO3 bilayers probed by ferromagnetic resonance

    NASA Astrophysics Data System (ADS)

    Emori, Satoru; Alaan, Urusa S.; Gray, Matthew T.; Sluka, Volker; Chen, Yizhang; Kent, Andrew D.; Suzuki, Y.

    2016-12-01

    Thin films of perovskite oxides offer the possibility of combining emerging concepts of strongly correlated electron phenomena and spin current in magnetic devices. However, spin transport and magnetization dynamics in these complex oxide materials are not well understood. Here, we experimentally quantify spin transport parameters and magnetization damping in epitaxial perovskite ferromagnet/paramagnet bilayers of La2 /3Sr1 /3MnO3 /SrRuO3 (LSMO/SRO) by broadband ferromagnetic resonance spectroscopy. From the SRO thickness dependence of the Gilbert damping, we estimate a short spin diffusion length of ≲1 nm in SRO and an interfacial spin-mixing conductance comparable to other ferromagnet/paramagnetic-metal bilayers. Moreover, we find that anisotropic non-Gilbert damping due to two-magnon scattering also increases with the addition of SRO. Our results demonstrate LSMO/SRO as a spin-source/spin-sink system that may be a foundation for examining spin-current transport in various perovskite heterostructures.

  20. Strong spin-orbit fields and Dyakonov-Perel spin dephasing in supported metallic films

    NASA Astrophysics Data System (ADS)

    Long, Nguyen H.; Mavropoulos, Phivos; Bauer, David S. G.; Zimmermann, Bernd; Mokrousov, Yuriy; Blügel, Stefan

    2016-11-01

    Spin dephasing by the Dyakonov-Perel mechanism in metallic films deposited on insulating substrates is revealed, and quantitatively examined by means of density functional calculations combined with a kinetic equation. The surface-to-substrate asymmetry, probed by the metal wave functions in thin films, is found to produce strong spin-orbit fields and a fast Larmor precession, giving a dominant contribution to spin decay over the Elliott-Yafet spin relaxation up to a thickness of 70 nm. The spin dephasing is oscillatory in time with a rapid (subpicosecond) initial decay. However, parts of the Fermi surface act as spin traps, causing a persistent tail signal lasting 1000 times longer than the initial decay time. It is also found that the decay depends on the direction of the initial spin polarization, resulting in a spin-dephasing anisotropy of 200% in the examined cases.

  1. A novel magnetic field probing technique for determining state of health of sealed lead-acid batteries

    NASA Astrophysics Data System (ADS)

    Khare, Neeta; Singh, Pritpal; Vassiliou, John K.

    2012-11-01

    State of Health (SOH) is a critical index for a Sealed Lead-Acid (SLA) battery diagnostic which provides the information about battery replacement and aging effects. SOH is a complex function of chemical parameters of a battery such as stratification in electrolyte, electrode structure (sulfation and hard sulfation) in addition to electrical parameters of a battery. This paper describes a method of online determination of stratification, electrode structure, electrode polarization and current profile within the battery under the influence of a magnetic field. An AC magnetic field is used as a noninvasive tool during battery cycles. An induced emf in a secondary coil (SCV) is used as a measure of change in the magnetic field. The H+ proton density varies with change in sulfuric acid (electrolyte) concentration during battery cycles. The magnetic flux lines are affected by the density of H+ protons whose magnetic dipole moments try to align along the magnetic flux lines. The stratification is seen by a 12% decrease in magnetic flux linking from the top to the bottom of the electrolyte in a battery. Additional experimental results demonstrate the variation in magnetic flux linking which correlates with current profile across the electrode and electrode structure.

  2. Molecular dynamics approach to probe the allosteric inhibition of PTP1B by chlorogenic and cichoric acid.

    PubMed

    Baskaran, Sarath Kumar; Goswami, Nabajyoti; Selvaraj, Sudhagar; Muthusamy, Velusamy Shanmuganathan; Lakshmi, Baddireddi Subhadra

    2012-08-27

    Protein tyrosine phosphatase 1B (PTP1B), a major negative regulator of the insulin and leptin signaling pathway, is a potential target for therapeutic intervention against diabetes and obesity. The recent discovery of an allosteric site in PTP1B has created an alternate strategy in the development of PTP1B targeted therapy. The current study investigates the molecular interactions between the allosteric site of PTP1B with two caffeoyl derivatives, chlorogenic acid (CGA) and cichoric acid (CHA), using computational strategies. Molecular docking analysis with CGA and CHA at the allosteric site of PTP1B were performed and the resulting protein-ligand complexes used for molecular dynamics simulation studies for a time scale of 10 ns. Results show stable binding of CGA and CHA at the allosteric site of PTP1B. The flexibility of the WPD loop was observed to be constrained by CGA and CHA in the open (inactive), providing molecular mechanism of allosteric inhibition. The allosteric inhibition of CGA and CHA of PTP1B was shown to be favorable due to no restriction by the α-7 helix in the binding of CGA and CHA at the allosteric binding site. In conclusion, our results exhibit an inhibitory pattern of CGA and CHA against PTP1B through potent binding at the allosteric site.

  3. Proton spin: A topological invariant

    NASA Astrophysics Data System (ADS)

    Tiwari, S. C.

    2016-11-01

    Proton spin problem is given a new perspective with the proposition that spin is a topological invariant represented by a de Rham 3-period. The idea is developed generalizing Finkelstein-Rubinstein theory for Skyrmions/kinks to topological defects, and using non-Abelian de Rham theorems. Two kinds of de Rham theorems are discussed applicable to matrix-valued differential forms, and traces. Physical and mathematical interpretations of de Rham periods are presented. It is suggested that Wilson lines and loop operators probe the local properties of the topology, and spin as a topological invariant in pDIS measurements could appear with any value from 0 to ℏ 2, i.e. proton spin decomposition has no meaning in this approach.

  4. Using rumen probes to examine effects of conjugated linoleic acids and dietary concentrate proportion on rumen pH and rumen temperature of periparturient dairy cows.

    PubMed

    Petzold, M; Meyer, U; Spilke, J; Dänicke, S

    2014-08-01

    The study aimed to examine the influence of supplemented conjugated linoleic acids (CLA) to periparturient cows receiving different concentrate proportions antepartum on rumen pH (RpH) and rumen temperature (RT). Twenty pregnant German Holstein cows were equipped with rumen probes for continuous RpH and RT measurement in a frequency of 15 min to investigate effects of dietary concentrate and CLA around parturition and the impact of parturition itself on RpH and RT. Cows had ad libitum access to partial mixed rations, 3 weeks prior to calving until day 7 post-partum. Antepartum, cows received 100 g/day control fat (CON) or CLA supplement, either in low (20%; CON-20, CLA-20) or high concentrate diet (60%; CON-60, CLA-60). Post-partum, concentrate proportion was adjusted to 50% while fat supplementation continued. Compared with adapted feeding, high concentrate proportions antepartum tended to increase DMI and reduced RpH. Groups CON-60 and CLA-60 spent more than 4 h per day below RpH 5.6 during late pregnancy, indicating the presence of subacute rumen acidosis (SARA). The RT remained unaffected antepartum. Before calving, cows spent less time below RpH 5.6 and SARA could be detected in each group post-partum. Mean RpH increased slightly antepartum, whereas few hours before parturition a sharp decrease in RpH could be observed, accompanied with increased RT. Overall, it seems that CLA supplementation influences RpH and RT. Bearing in mind that rumen parameters fluctuate during day and herd level must be known, rumen probes for continuous RpH and RT measurement could be a useful management tool for animal health surveillance and may also help to predict parturition.

  5. Mn-doped ZnS quantum dot imbedded two-fragment imprinting silica for enhanced room temperature phosphorescence probing of domoic acid.

    PubMed

    Dan, Li; Wang, He-Fang

    2013-05-21

    A novel strategy was presented to construct the enhanced molecularly imprinted polymer (MIP)-based room temperature phosphorescence (RTP) probe by combining the RTP of Mn-doped ZnS quantum dots (Mn-ZnS QDs) and two-fragment imprinting. Two fragments or structurally similar parts of the target analytes were used as the dummy templates. Polyethyleneimine capped Mn-ZnS (PEI-Mn-ZnS) QDs, offering the binding sites to interact with the carboxyl groups of templates, were imbedded into MIPs by the hydrolysis of tetraethoxysilane. The rebinding of the target analytes to their fragments' cavities (recognition sites) modulated the selective aggregation of Mn-ZnS QDs in QDs-MIPs and resulted in the RTP enhancement. This new method was suitable for the selective enhanced RTP detection of nonphosphorescent analytes without any derivatization and inducers. The proposed methodology was applied to construct the high selective enhanced MIP-based RTP probe for domoic acid (DA) detection. The RTP enhancement of two-fragment imprinting silica was about 2 times of one-fragment imprinting silica and 4 times of the nonimprinting silica. The two-fragment imprinting silica exhibited the linear RTP enhancement to DA in the range of 0.25-3.5 μM in buffer and 0.25-1.5 μM in shellfish sample. The precision for 11 replicate detections of 1.25 μM DA was 0.65% (RSD), and the limit of detection was 67 nM in buffer and 2.0 μg g(-1) wet weight (w/w) in shellfish sample.

  6. Tensor spin observables and spin stucture at low Q{sup 2}

    SciTech Connect

    Slifer, K.

    2015-04-10

    We discuss recent spin structure results from Jefferson Lab, and outline an emerging program to study tensor spin observables using solid deuteron targets. These new experiments open the potential to study hidden color, the tensor nature of short range correlations, and to probe for exotic gluonic states.

  7. Germinal Center Marker GL7 Probes Activation-Dependent Repression of N-Glycolylneuraminic Acid, a Sialic Acid Species Involved in the Negative Modulation of B-Cell Activation▿ †

    PubMed Central

    Naito, Yuko; Takematsu, Hiromu; Koyama, Susumu; Miyake, Shizu; Yamamoto, Harumi; Fujinawa, Reiko; Sugai, Manabu; Okuno, Yasushi; Tsujimoto, Gozoh; Yamaji, Toshiyuki; Hashimoto, Yasuhiro; Itohara, Shigeyoshi; Kawasaki, Toshisuke; Suzuki, Akemi; Kozutsumi, Yasunori

    2007-01-01

    Sialic acid (Sia) is a family of acidic nine-carbon sugars that occupies the nonreducing terminus of glycan chains. Diversity of Sia is achieved by variation in the linkage to the underlying sugar and modification of the Sia molecule. Here we identified Sia-dependent epitope specificity for GL7, a rat monoclonal antibody, to probe germinal centers upon T cell-dependent immunity. GL7 recognizes sialylated glycan(s), the α2,6-linked N-acetylneuraminic acid (Neu5Ac) on a lactosamine glycan chain(s), in both Sia modification- and Sia linkage-dependent manners. In mouse germinal center B cells, the expression of the GL7 epitope was upregulated due to the in situ repression of CMP-Neu5Ac hydroxylase (Cmah), the enzyme responsible for Sia modification of Neu5Ac to Neu5Gc. Such Cmah repression caused activation-dependent dynamic reduction of CD22 ligand expression without losing α2,6-linked sialylation in germinal centers. The in vivo function of Cmah was analyzed using gene-disrupted mice. Phenotypic analyses showed that Neu5Gc glycan functions as a negative regulator for B-cell activation in assays of T-cell-independent immunization response and splenic B-cell proliferation. Thus, Neu5Gc is required for optimal negative regulation, and the reaction is specifically suppressed in activated B cells, i.e., germinal center B cells. PMID:17296732

  8. A Comprehensive Spectroscopic and Computational Investigation to Probe the Interaction of Antineoplastic Drug Nordihydroguaiaretic Acid with Serum Albumins.

    PubMed

    Nusrat, Saima; Siddiqi, Mohammad Khursheed; Zaman, Masihuz; Zaidi, Nida; Ajmal, Mohammad Rehan; Alam, Parvez; Qadeer, Atiyatul; Abdelhameed, Ali Saber; Khan, Rizwan Hasan

    2016-01-01

    Exogenous drugs that are used as antidote against chemotheray, inflammation or viral infection, gets absorbed and interacts reversibly to the major serum transport protein i.e. albumins, upon entering the circulatory system. To have a structural guideline in the rational drug designing and in the synthesis of drugs with greater efficacy, the binding mechanism of an antineoplastic and anti-inflammatory drug Nordihydroguaiaretic acid (NDGA) with human and bovine serum albumins (HSA & BSA) were examined by spectroscopic and computational methods. NDGA binds to site II of HSA with binding constant (Kb) ~105 M-1 and free energy (ΔG) ~ -7.5 kcal.mol-1. It also binds at site II of BSA but with lesser binding affinity (Kb) ~105 M-1 and ΔG ~ -6.5 kcal.mol-1. The negative value of ΔG, ΔH and ΔS for both the albumins at three different temperatures confirmed that the complex formation process between albumins and NDGA is spontaneous and exothermic. Furthermore, hydrogen bonds and hydrophobic interactions are the main forces involved in complex formation of NDGA with both the albumins as evaluated from fluorescence and molecular docking results. Binding of NDGA to both the albumins alter the conformation and causes minor change in the secondary structure of proteins as indicated by the CD spectra.

  9. Preparation of Au Nanoclusters-Modified Polylactic Acid Fiber with Bright Red Fluorescence and its Use as Sensing Probe.

    PubMed

    Zhu, Wenli; Li, Huili; Wan, Ajun; Liu, Lanbo

    2017-01-01

    In present work, the Au nanoclusters-modified polylactic acid fiber (PLA-Au NCs) with bright red fluorescence were fabricated by the encapsulation of Au nanoclusters (Au NCs) in the PLA fiber treated with H2O2. The Au25 nanoclusters stabilized by bovine serum albumin (BSA-Au NCs) were prepared via an improved "green" synthetic routine. With pretreatment of the PLA fiber in H2O2 concentration of 12 and 18 %, the as-prepared PLA-Au NCs exhibited brighter red emission with a strong peak centered at ~640 nm than BSA-Au NCs. The fluorescence can be quenched by nitric oxide (NO). A good linear relationship between the relative fluorescence quenching intensity of the as-prepared PLA-Au NCs and the concentration of NO can be obtained in the range of 0.0732 to 0.7320 mM, and the detection limit was 0.0070 mM.

  10. A Comprehensive Spectroscopic and Computational Investigation to Probe the Interaction of Antineoplastic Drug Nordihydroguaiaretic Acid with Serum Albumins

    PubMed Central

    Nusrat, Saima; Siddiqi, Mohammad Khursheed; Zaman, Masihuz; Zaidi, Nida; Ajmal, Mohammad Rehan; Alam, Parvez; Qadeer, Atiyatul; Abdelhameed, Ali Saber

    2016-01-01

    Exogenous drugs that are used as antidote against chemotheray, inflammation or viral infection, gets absorbed and interacts reversibly to the major serum transport protein i.e. albumins, upon entering the circulatory system. To have a structural guideline in the rational drug designing and in the synthesis of drugs with greater efficacy, the binding mechanism of an antineoplastic and anti-inflammatory drug Nordihydroguaiaretic acid (NDGA) with human and bovine serum albumins (HSA & BSA) were examined by spectroscopic and computational methods. NDGA binds to site II of HSA with binding constant (Kb) ~105 M-1 and free energy (ΔG) ~ -7.5 kcal.mol-1. It also binds at site II of BSA but with lesser binding affinity (Kb) ~105 M-1 and ΔG ~ -6.5 kcal.mol-1. The negative value of ΔG, ΔH and ΔS for both the albumins at three different temperatures confirmed that the complex formation process between albumins and NDGA is spontaneous and exothermic. Furthermore, hydrogen bonds and hydrophobic interactions are the main forces involved in complex formation of NDGA with both the albumins as evaluated from fluorescence and molecular docking results. Binding of NDGA to both the albumins alter the conformation and causes minor change in the secondary structure of proteins as indicated by the CD spectra. PMID:27391941

  11. A novel turn-on fluorescent strategy for sensing ascorbic acid using graphene quantum dots as fluorescent probe.

    PubMed

    Liu, Hua; Na, Weidan; Liu, Ziping; Chen, Xueqian; Su, Xingguang

    2017-06-15

    In this paper, a facile and rapid fluorescence turn-on assay for fluorescent detection of ascorbic acid (AA) was developed by using the orange emission graphene quantum dots (GQDs). In the presence of horse radish peroxidase (HRP) and hydrogen peroxide (H2O2), catechol can be oxidized by hydroxyl radicals and converted to o-benzoquinone, which can significantly quench the fluorescence of GQDs. However, when AA present in the system, it can consume part of H2O2 and hydroxyl radicals to inhibit the generation of o-benzoquinone, resulting in fluorescence recovery. Under the optimized experimental conditions, the fluorescence intensity was linearly correlated with the concentration of H2O2 in the range of 3.33-500µM with a detection limit of 1.2µM. The linear detection for AA was in the range from 1.11 to 300µM with a detection limit of 0.32µM. The proposed method was applied to the determination of AA in human serum samples with satisfactory results.

  12. Sulphonic acid derivatives as probes of pore properties of volume-regulated anion channels in endothelial cells.

    PubMed

    Droogmans, G; Maertens, C; Prenen, J; Nilius, B

    1999-09-01

    1. We have used the whole-cell patch-clamp technique to study the effects of 4-sulphonic-calixarenes and some other poly-sulphonic acid agents, such as suramin and basilen blue, on volume-regulated anion channel (VRAC) currents in cultured endothelial cells (CPAE cells). 2. The 4-sulphonic-calixarenes induced a fast inhibition at positive potentials but were ineffective at negative potentials. At small positive potentials, 4-sulphonic-calix[4]arene was a more effective inhibitor than 4-sulphonic-calix[6]arene and -calix[8]arene, which became more effective at more positive potentials. 3. Also suramin and basilen blue induced a voltage dependent current inhibition, reaching a maximum around +40 mV and declining at more positive potentials. 4. The voltage dependence of inhibition was modelled by assuming that these negatively charged molecules bind to a site inside VRAC that senses a fraction delta of the applied electrical field, ranging beween 0.16 to 0.32. 4-Sulphonic-calix[4]arene, suramin and basilen blue bind and occlude VRAC at moderate potentials, but permeate the channel at more positive potentials. 4-Sulphonic-calix[6]arene and -calix[8]arene however do not permeate the channel. From the structural information of the calixarenes, we estimate a lower and upper limit of 11*12 and 17*12 A2 respectively for the cross-sectional area of the pore.

  13. Quantum spin liquids: a review

    NASA Astrophysics Data System (ADS)

    Savary, Lucile; Balents, Leon

    2017-01-01

    Quantum spin liquids may be considered ‘quantum disordered’ ground states of spin systems, in which zero-point fluctuations are so strong that they prevent conventional magnetic long-range order. More interestingly, quantum spin liquids are prototypical examples of ground states with massive many-body entanglement, which is of a degree sufficient to render these states distinct phases of matter. Their highly entangled nature imbues quantum spin liquids with unique physical aspects, such as non-local excitations, topological properties, and more. In this review, we discuss the nature of such phases and their properties based on paradigmatic models and general arguments, and introduce theoretical technology such as gauge theory and partons, which are conveniently used in the study of quantum spin liquids. An overview is given of the different types of quantum spin liquids and the models and theories used to describe them. We also provide a guide to the current status of experiments in relation to study quantum spin liquids, and to the diverse probes used therein.

  14. Molecularly imprinted ultrathin graphitic carbon nitride nanosheets-Based electrochemiluminescence sensing probe for sensitive detection of perfluorooctanoic acid.

    PubMed

    Chen, Sihua; Li, Aimin; Zhang, Lizhi; Gong, Jingming

    2015-10-08

    Driven by the urgent demand for the determination of low level perfluorooctanoic acid (PFOA) present in environment, a novel electrochemiluminescence (ECL) sensor has been first developed for the detection of PFOA using the molecularly imprinted polypyrrole modified two-dimensional ultrathin g-C3N4 (utg-C3N4) nanosheets as a cathodic ECL emitter with S2O8(2-) as coreactant. The prepared molecularly imprinted polymer (MIP) functionalized utg-C3N4 nanosheets (MIP@utg-C3N4) exhibit a stable and significantly amplified ECL signal. It is found that the targets of PFOA could be efficiently oxidized by the electro-generated strong oxidants of SO4(-) (from the reduction of coreactant S2O8(2-)), thus leading to a low yield of the excited utg-C3N4 (g-C3N4*) and finally a decrease in ECL signal. Based on this, a highly sensitive and selective MIP@utg-C3N4-based signal-off ECL sensor is developed for sensing PFOA. Such a newly designed ECL sensor exhibits highly linear over the PFOA concentration in two ranges, from 0.02 to 40.0 ng mL(-1) and 50.0-400.0 ng mL(-1). The detection limit (S/N = 3) is estimated to be 0.01 ng mL(-1) (i.e. 0.01 ppb), comparable to the results obtained by using well-established liquid chromatography-tandem mass spectrometry (LC-MS/MS). Toward practical applications, this low-cost and sensitive assay was successfully applied to measure PFOA in real water samples, showing fine applicability for the detection of PFOA in real samples.

  15. Probing the role of lysine 16 in ras p[sup 21] protein with unnatural amino acids

    SciTech Connect

    Chung, H.H.; Benson, D.R.; Schultz, P.G. )

    1993-07-14

    Mamalian proteins encoded by the ras gene are thought to function as regulators of various signal transduction processes involved in cell growth and differentiation. The chemical basis for the regulation is cycling of the protein between the inactive guanosine diphosphate (GDP)-bound state and the active guanosine triphophate (GTP)-bound state. Loop 1 of ras contains the GXXXXGK(S/T) motif (residues 10-17), which is found in all ras-related proteins, G proteins, and other nucleotide-binding proteins. Structural and biochemical studies have suggested that Lys 16 of loop 1 is critical for substrate binding and catalysis. The [epsilon]-amino group is involved in ion pair interactions with the [Beta]-and [gamma]-phosphates of GTP and forms hydrogen bonds with the main-chain oxygens of Gly 10 and Ala 11. In order to better understand the role of the key residue in ras function, we have replaced Lys 16 with a number of unnatural amino acid analogues, including (aminoethyl)cysteine, (hydroxyethyl)cysteine, (aminoethyl)homocysteine, and ornithine. We were surprised to find that the [open quotes]unnatural[close quotes] mutant ras proteins retained high levels of GAP-stimulated GTPase activity and GTP dissociation rates comparable to that of wild-type ras. These results may indicate that, in the GAP-activated form, Lys 16 is not involved in transition-state stabilization or GTP binding. However, replacement of Lys 16 with the isosteric uncharged Lys analogue, (hydroxyethyl)cysteine, led to a complete loss of GAP-stimulated GTPase activity, demonstrating the importance of the charged ammonium side chain. 22 refs., 1 fig., 1 tab.

  16. Using Unnatural Amino Acids to Probe the Energetics of Oxyanion Hole Hydrogen Bonds in the Ketosteroid Isomerase Active Site

    PubMed Central

    2015-01-01

    Hydrogen bonds are ubiquitous in enzyme active sites, providing binding interactions and stabilizing charge rearrangements on substrate groups over the course of a reaction. But understanding the origin and magnitude of their catalytic contributions relative to hydrogen bonds made in aqueous solution remains difficult, in part because of complexities encountered in energetic interpretation of traditional site-directed mutagenesis experiments. It has been proposed for ketosteroid isomerase and other enzymes that active site hydrogen bonding groups provide energetic stabilization via “short, strong” or “low-barrier” hydrogen bonds that are formed due to matching of their pKa or proton affinity to that of the transition state. It has also been proposed that the ketosteroid isomerase and other enzyme active sites provide electrostatic environments that result in larger energetic responses (i.e., greater “sensitivity”) to ground-state to transition-state charge rearrangement, relative to aqueous solution, thereby providing catalysis relative to the corresponding reaction in water. To test these models, we substituted tyrosine with fluorotyrosines (F-Tyr’s) in the ketosteroid isomerase (KSI) oxyanion hole to systematically vary the proton affinity of an active site hydrogen bond donor while minimizing steric or structural effects. We found that a 40-fold increase in intrinsic F-Tyr acidity caused no significant change in activity for reactions with three different substrates. F-Tyr substitution did not change the solvent or primary kinetic isotope effect for proton abstraction, consistent with no change in mechanism arising from these substitutions. The observed shallow dependence of activity on the pKa of the substituted Tyr residues suggests that the KSI oxyanion hole does not provide catalysis by forming an energetically exceptional pKa-matched hydrogen bond. In addition, the shallow dependence provides no indication of an active site electrostatic

  17. ANTS-anchored Zn-Al-CO3-LDH particles as fluorescent probe for sensing of folic acid

    NASA Astrophysics Data System (ADS)

    Liu, Pengfei; Liu, Dan; Liu, Yanhuan; Li, Lei

    2016-09-01

    A novel fluorescent nanosensor for detecting folic acid (FA) in aqueous media has been developed based on 8-aminonaphthalene-1,3,6-trisulfonate (ANTS) anchored to the surface of Zn-Al-CO3-layered double hydroxides (LDH) particles. The nanosensor showed high fluorescence intensity and good photostability due to a strong coordination interaction between surface Zn2+ ions of Zn-Al-CO3-LDH and N atoms of ANTS, which were verified by result of X-ray photoelectron spectroscopy (XPS). ANTS-anchored on the surface of Zn-Al-CO3-LDH restricted the intra-molecular rotation leading to ANTS-anchored J-type aggregation emission enhancement. ANTS-anchored Zn-Al-CO3-LDH particles exhibited highly sensitive and selective response to FA over other common metal ions and saccharides present in biological fluids. The proposed mechanism was that oxygen atoms of -SO3 groups in ANTS-anchored on the surface of Zn-Al-CO3-LDH were easily collided by FA molecules to form potential hydrogen bonds between ANTS-anchored and FA molecules, which could effectively quench the ANTS-anchored fluorescence. Under the simulated physiological conditions (pH of 7.4), the fluorescence quenching was fitted to Stern-Volmer equation with a linear response in the concentration range of 1 μM to 200 μM with a limit of detection of 0.1 μM. The results indicate that ANTS-anchored Zn-Al-CO3-LDH particles can afford a very sensitive system for the sensing FA in aqueous solution.

  18. Probing the conformation of a conserved glutamic acid within the Cl(-) pathway of a CLC H(+)/Cl(-) exchanger.

    PubMed

    Vien, Malvin; Basilio, Daniel; Leisle, Lilia; Accardi, Alessio

    2017-04-03

    The CLC proteins form a broad family of anion-selective transport proteins that includes both channels and exchangers. Despite extensive structural, functional, and computational studies, the transport mechanism of the CLC exchangers remains poorly understood. Several transport models have been proposed but have failed to capture all the key features of these transporters. Multiple CLC crystal structures have suggested that a conserved glutamic acid, Gluex, can adopt three conformations and that the interconversion of its side chain between these states underlies H(+)/Cl(-) exchange. One of these states, in which Gluex occupies the central binding site (Scen) while Cl(-) ions fill the internal and external sites (Sint and Sext), has only been observed in one homologue, the eukaryotic cmCLC. The existence of such a state in other CLCs has not been demonstrated. In this study, we find that during transport, the prototypical prokaryotic CLC exchanger, CLC-ec1, adopts a conformation with functional characteristics that match those predicted for a cmCLC-like state, with Gluex trapped in Scen between two Cl(-) ions. Transport by CLC-ec1 is reduced when [Cl(-)] is symmetrically increased on both sides of the membrane and mutations that disrupt the hydrogen bonds stabilizing Gluex in Scen destabilize this trapped state. Furthermore, inhibition of transport by high [Cl(-)] is abolished in the E148A mutant, in which the Gluex side chain is removed. Collectively, our results suggest that, during the CLC transport cycle, Gluex can occupy Scen as well as the Sext position in which it has been captured crystallographically and that hydrogen bonds with the side chains of residues that coordinate ion binding to Scen play a role in determining the equilibrium between these two conformations.

  19. Use of the beta-phase of poly(9,9-dioctylfluorene) as a probe into the interfacial interplay for the mixed bilayer films formed by sequential spin-coating.

    PubMed

    Zhu, Rui; Lin, Jian-Ming; Wang, Wei-Zhi; Zheng, Chao; Wei, Wei; Huang, Wei; Xu, Yun-Hua; Peng, Jun-Biao; Cao, Yong

    2008-02-14

    Spin-coating one polymer solution on another spin-cast polymer film is believed to result in unfavorable interfacial mixing. Here, we show some results to demonstrate that some interesting properties will be obtained in such mixed bilayer films formed by sequential spin-coating. Poly(9-vinylcarbazole) and poly(9,9-dioctylfluorene-2,7-diyl) were chosen as the first and second polymer layers, respectively. By varying the initial thickness of the first layer, some interesting variations were observed. The spectroscopic features of beta-phase polyfluorene were utilized to reflect the variations at the complicated interface. Morphologies were also presented to illustrate that the variations of spectroscopic features were accompanied with some interesting morphological changes. On the basis of these results, a schematic model was proposed to gain insight into the mixed interface formed by sequential spin-coating. Polymer light-emitting devices based on such films were also investigated.

  20. Detecting asymptomatic Trichomonas vaginalis in females using the BD ProbeTec™ Trichomonas vaginalis Q(x) nucleic acid amplification test.

    PubMed

    Lord, Emily; Newnham, Tana; Dorrell, Lucy; Jesuthasan, Gerald; Clarke, Lorraine; Jeffery, Katie; Sherrard, Jackie

    2017-03-01

    Trichomonas vaginalis (TV) rates in women are increasing and many are asymptomatic. Nucleic acid amplification tests (NAATs) are becoming the 'gold standard' for diagnosis. We aimed to establish our asymptomatic TV rates by testing all women attending Oxfordshire's Sexual Health service, regardless of symptoms, using the BD ProbeTec™ TV Q(x) NAATs (BDQ(x)). During BDQ(x)'s verification process, the sensitivity and specificity were calculated using results of 220 endocervical samples from symptomatic women, compared with culture. BDQ(x) was subsequently implemented and prospectively evaluated over 6 months in female attendees. Wet mount microscopy was also performed in symptomatics. Demographic and clinical characteristics of those diagnosed were analysed. From 220 samples tested by BDQ(x) and culture: 5 were positive on both and one solely using BDQ(x), giving a sensitivity and specificity of 100% and 99.53%, respectively. In the prospective cohort, of 5775 BDQ(x) tests, 33 (0.57%) were positive. 11/33 (33%) patients were asymptomatic. All patients diagnosed had risk factors: age >25 years (85%), residence in a deprived area (79%) and black ethnicity (21%). Despite BDQ(x) being highly sensitive and specific, with our low TV prevalence universal screening may not be justified. Targeted screening using local demographic data merits further investigation.