Topics in Chemical Instrumentation. The Fourier Transform in Chemistry-NMR: Part 4. Two-Dimensional Methods.

ERIC Educational Resources Information Center

Williams, Kathryn R.; King, Roy W.

1990-01-01

Examined are some of the types of two-dimensional spectra. Their application to nuclear magnetic resonance for the elucidation of molecular structure is discussed. Included are J spectroscopy, H-H correlation spectroscopy, heteronuclear correlation spectroscopy, carbon-carbon correlation, nuclear Overhauser effect correlation, experimental…

Spectrum of the Nuclear Environment for GaAs Spin Qubits.

PubMed

Malinowski, Filip K; Martins, Frederico; Cywiński, Łukasz; Rudner, Mark S; Nissen, Peter D; Fallahi, Saeed; Gardner, Geoffrey C; Manfra, Michael J; Marcus, Charles M; Kuemmeth, Ferdinand

2017-04-28

Using a singlet-triplet spin qubit as a sensitive spectrometer of the GaAs nuclear spin bath, we demonstrate that the spectrum of Overhauser noise agrees with a classical spin diffusion model over 6 orders of magnitude in frequency, from 1 mHz to 1 kHz, is flat below 10 mHz, and falls as 1/f^{2} for frequency f≳1  Hz. Increasing the applied magnetic field from 0.1 to 0.75 T suppresses electron-mediated spin diffusion, which decreases the spectral content in the 1/f^{2} region and lowers the saturation frequency, each by an order of magnitude, consistent with a numerical model. Spectral content at megahertz frequencies is accessed using dynamical decoupling, which shows a crossover from the few-pulse regime (≲16π pulses), where transverse Overhauser fluctuations dominate dephasing, to the many-pulse regime (≳32 π pulses), where longitudinal Overhauser fluctuations with a 1/f spectrum dominate.

The low cost Proton Precession Magnetometer developed at the Indian Institute of Geomagnetism

NASA Astrophysics Data System (ADS)

Mahavarkar, P.; Singh, S.; Labde, S.; Dongre, V.; Patil, A.

2017-05-01

Proton magnetometers are the oldest scalar magnetometers. The first commercial units were produced in early 1960s as portable instruments. In continuation airborne instruments appeared with optimized speed of readings and sensitivity, large sensors etc. Later development of Overhauser and optically pumped magnetometers has eliminated Proton magnetometers from airborne surveys. However they remain very popular in various ground surveys and observatories. With this primary purpose of generating the ground based magnetic data, the Indian Institute of Geomagnetism (IIG) for the last 3 decades have been developing low cost Proton Precession Magnetometers (PPM). Beginning with the 1 nT PPM which has undergone several changes in design, the successor PM7 the advanced version has been successfully developed by the institute and is installed at various observatories of the institute. PM7 records the total field `F' with accuracy of 0.1 nT and a sampling rate of 10 seconds/sample. This article briefly discusses the design and development of this IIG make PM7 and compares the data recorded by this instrument with one of the commercially available Overhauser magnetometer in the world market. The quality of data recorded by PM7 is in excellent agreement with the Overhauser. With the available quality of data generated by this instrument, PM7 is an affordable PPM for scientific institutions, schools and colleges intending to carry out geomagnetic studies. The commercial cost of PM7 is ≈ 20% of the cost of Overhauser available in market.

Polarized electrons, trions, and nuclei in charged quantum dots

NASA Astrophysics Data System (ADS)

Bracker, A. S.; Tischler, J. G.; Korenev, V. L.; Gammon, D.

2003-07-01

We have investigated spin polarization in GaAs quantum dots. Excitons and trions are polarized directly by optical excitation and studied through polarization of photoluminescence. Electrons and nuclei are polarized indirectly through subsequent relaxation processes. Polarized electrons are identified by the Hanle effect for exciton and trion photoluminescence, while polarized nuclei are identified through the Overhauser effect in individual charged quantum dots.

Water accessibility in a membrane-inserting peptide comparing Overhauser DNP and pulse EPR methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Segawa, Takuya F., E-mail: takuya.segawa@alumni.ethz.ch; Doppelbauer, Maximilian; Garbuio, Luca

2016-05-21

Water accessibility is a key parameter for the understanding of the structure of biomolecules, especially membrane proteins. Several experimental techniques based on the combination of electron paramagnetic resonance (EPR) spectroscopy with site-directed spin labeling are currently available. Among those, we compare relaxation time measurements and electron spin echo envelope modulation (ESEEM) experiments using pulse EPR with Overhauser dynamic nuclear polarization (DNP) at X-band frequency and a magnetic field of 0.33 T. Overhauser DNP transfers the electron spin polarization to nuclear spins via cross-relaxation. The change in the intensity of the {sup 1}H NMR spectrum of H{sub 2}O at a Larmormore » frequency of 14 MHz under a continuous-wave microwave irradiation of the nitroxide spin label contains information on the water accessibility of the labeled site. As a model system for a membrane protein, we use the hydrophobic α-helical peptide WALP23 in unilamellar liposomes of DOPC. Water accessibility measurements with all techniques are conducted for eight peptides with different spin label positions and low radical concentrations (10–20 μM). Consistently in all experiments, the water accessibility appears to be very low, even for labels positioned near the end of the helix. The best profile is obtained by Overhauser DNP, which is the only technique that succeeds in discriminating neighboring positions in WALP23. Since the concentration of the spin-labeled peptides varied, we normalized the DNP parameter ϵ, being the relative change of the NMR intensity, by the electron spin concentration, which was determined from a continuous-wave EPR spectrum.« less

Water accessibility in a membrane-inserting peptide comparing Overhauser DNP and pulse EPR methods.

PubMed

Segawa, Takuya F; Doppelbauer, Maximilian; Garbuio, Luca; Doll, Andrin; Polyhach, Yevhen O; Jeschke, Gunnar

2016-05-21

Water accessibility is a key parameter for the understanding of the structure of biomolecules, especially membrane proteins. Several experimental techniques based on the combination of electron paramagnetic resonance (EPR) spectroscopy with site-directed spin labeling are currently available. Among those, we compare relaxation time measurements and electron spin echo envelope modulation (ESEEM) experiments using pulse EPR with Overhauser dynamic nuclear polarization (DNP) at X-band frequency and a magnetic field of 0.33 T. Overhauser DNP transfers the electron spin polarization to nuclear spins via cross-relaxation. The change in the intensity of the (1)H NMR spectrum of H2O at a Larmor frequency of 14 MHz under a continuous-wave microwave irradiation of the nitroxide spin label contains information on the water accessibility of the labeled site. As a model system for a membrane protein, we use the hydrophobic α-helical peptide WALP23 in unilamellar liposomes of DOPC. Water accessibility measurements with all techniques are conducted for eight peptides with different spin label positions and low radical concentrations (10-20 μM). Consistently in all experiments, the water accessibility appears to be very low, even for labels positioned near the end of the helix. The best profile is obtained by Overhauser DNP, which is the only technique that succeeds in discriminating neighboring positions in WALP23. Since the concentration of the spin-labeled peptides varied, we normalized the DNP parameter ϵ, being the relative change of the NMR intensity, by the electron spin concentration, which was determined from a continuous-wave EPR spectrum.

Proton-decoupled, Overhauser-enhanced, spatially localized carbon-13 spectroscopy in humans.

PubMed

Bottomley, P A; Hardy, C J; Roemer, P B; Mueller, O M

1989-12-01

Spatially localized, natural abundance, carbon (13C) NMR spectroscopy has been combined with proton (1H) decoupling and nuclear Overhauser enhancement to improve 13C sensitivity up to five-fold in the human leg, liver, and heart. Broadhand-decoupled 13C spectra were acquired in 1 s to 17 min with a conventional 1.5-T imaging/spectroscopy system, an auxiliary 1H decoupler, an air-cooled dual-coil coplanar surface probe, and both depth-resolved surface coil spectroscopy (DRESS) and one-dimensional phase-encoding gradient NMR pulse sequences. The surface coil probe comprised circular and figure-eight-shaped coils to eliminate problems with mutual coupling of coils at high decoupling power levels applied during 13C reception. Peak decoupler RF power deposition in tissue was computed numerically from electromagnetic theory assuming a semi-infinite plane of uniform biological conductor. Peak values at the surface were calculated at 4 to 6 W/kg in any gram of tissue for each watt of decoupler power input excluding all coil and cable losses, warning of potential local RF heating problems in these and related experiments. The average power deposition was about 9 mW/kg per watt input, which should present no systemic hazard. At 3 W input, human 13C spectra were decoupled to a depth of about 5 cm while some Overhauser enhancement was sustained up to about 3 cm depth, without ill effect. The observation of glycogen in localized natural abundance 13C spectra of heart and muscle suggests that metabolites in the citric acid cycle should be observable noninvasively using 13C-labeled substrates.

Determination of the chirality of the saturated pyrrole in sulfmyoglobin using the nuclear Overhauser effect.

PubMed

Parker, W O; Chatfield, M J; La Mar, G N

1989-02-21

The interproton nuclear Overhauser effect (NOE) and paramagnetic dipolar relaxation rates for hyperfine-shifted resonances in the proton NMR spectra of sperm whale met-cyano sulfmyoglobin have led to the location and assignment of the proton signals of the heme pocket residue isoleucine 99 (FG5) in two sulfmyoglobin isomers. Dipolar relaxation rates of these protein signals indicate a highly conserved geometry of the heme pocket upon sulfmyoglobin formation, while the similar upfield direction of dipolar shifts for this residue to that observed in native sperm whale myoglobin reflects largely retained magnetic properties. Dipolar connectivity of this protein residue to the substituents of the reacted heme pyrrole ring B defines the stereochemistry of the puckered thiolene ring found in one isomer, with the 3-CH3 tilted out of the heme plane proximally. The chirality of the saturated carbons of pyrrole ring B in both the initial sulfmyoglobin product and the terminal alkaline product is consistent with a mechanism of formation in which an atom of sulfur is incorporated distally to form an episulfide across ring B, followed by reaction of the vinyl group to yield the thiolene ring that retains the C3 chirality.

Spin-lattice relaxation of 13C in solid amino acids using the CP-MAS technique

NASA Astrophysics Data System (ADS)

Naito, A.; Ganapathy, S.; Akasaka, K.; McDowell, C. A.

It is shown by a simple application of relaxation theory that the 13C magnetization decays nonexponentially, in principle, in the CP-MAS experiment because of the distribution of the spin-lattice relaxation times; however, the deviation from the exponential decay is quite small. The transient Overhauser effect also contributes appreciably to the nonexponential decay of the 13C magnetization when the protons are not saturated during the 13C T1 measurements and the correlation time of the group rotational motion satisfies the condition, ω2τc2 ≦ 1. It is shown by both experiment and theory that the transient Overhauser effect in the solid state is much smaller than that expected for the liquid state. The 13C spin-lattice relaxation times of L-alanine, deutero- L-alanine, glycine, and L-serine were determined for the individual carbon atoms. The experimentally obtained 13C T1 values agree well with calculated ones, showing that the CH 3 group rotation provides the main source of the relaxation in alanine, while the NH 3+ group motion plays an important role for the relaxation in glycine and serene.

SHMUTZ & PROTON-DIAMANT H + Irradiated/Written-Hyper/Super-conductivity(HC/SC) Precognizance/Early Experiments Connections: Wet-Graphite Room-Tc & Actualized MgB2 High-Tc: Connection to Mechanical Bulk-Moduli/Hardness: Diamond Hydrocarbon-Filaments, Disorder, Nano-Powders:C,Bi,TiB2,TiC

NASA Astrophysics Data System (ADS)

Wunderman, Irwin; Siegel, Edward Carl-Ludwig; Lewis, Thomas; Young, Frederic; Smith, Adolph; Dresschhoff-Zeller, Gieselle

2013-03-01

SHMUTZ: ``wet-graphite''Scheike-....[Adv.Mtls.(7/16/12)]hyper/super-SCHMUTZ-conductor(S!!!) = ``wet''(?)-``graphite''(?) = ``graphene''(?) = water(?) = hydrogen(?) =ultra-heavy proton-bands(???) = ...(???) claimed room/high-Tc/high-Jc superconductOR ``p''-``wave''/ BAND(!!!) superconductIVITY and actualized/ instantiated MgB2 high-Tc superconductors and their BCS- superconductivity: Tc Siegel[ICMAO(77);JMMM 7,190(78)] connection to SiegelJ.Nonxline-Sol.40,453(80)] disorder/amorphous-superconductivity in nano-powders mechanical bulk/shear(?)-moduli/hardness: proton-irradiated diamond, powders TiB2, TiC,{Siegel[Semis. & Insuls.5:39,47, 62 (79)])-...``VS''/concommitance with Siegel[Phys.Stat.Sol.(a)11,45(72)]-Dempsey [Phil.Mag. 8,86,285(63)]-Overhauser-(Little!!!)-Seitz-Smith-Zeller-Dreschoff-Antonoff-Young-...proton-``irradiated''/ implanted/ thermalized-in-(optimal: BOTH heat-capacity/heat-sink & insulator/maximal dielectric-constant) diamond: ``VS'' ``hambergite-borate-mineral transformable to Overhauser optimal-high-Tc-LiBD2 in Overhauser-(NW-periodic-table)-Land: CO2/CH4-ETERNAL-sequestration by-product: WATER!!!: physics lessons from

Microtesla MRI with dynamic nuclear polarization

NASA Astrophysics Data System (ADS)

Zotev, Vadim S.; Owens, Tuba; Matlashov, Andrei N.; Savukov, Igor M.; Gomez, John J.; Espy, Michelle A.

2010-11-01

Magnetic resonance imaging at microtesla fields is a promising imaging method that combines the pre-polarization technique and broadband signal reception by superconducting quantum interference device (SQUID) sensors to enable in vivo MRI at microtesla-range magnetic fields similar in strength to the Earth magnetic field. Despite significant advances in recent years, the potential of microtesla MRI for biomedical imaging is limited by its insufficient signal-to-noise ratio due to a relatively low sample polarization. Dynamic nuclear polarization (DNP) is a widely used approach that allows polarization enhancement by 2-4 orders of magnitude without an increase in the polarizing field strength. In this work, the first implementation of microtesla MRI with Overhauser DNP and SQUID signal detection is described. The first measurements of carbon-13 NMR spectra at microtesla fields are also reported. The experiments were performed at the measurement field of 96 μT, corresponding to Larmor frequency of 4 kHz for protons and 1 kHz for carbon-13. The Overhauser DNP was carried out at 3.5-5.7 mT fields using rf irradiation at 120 MHz. Objects for imaging included water phantoms and a cactus plant. Aqueous solutions of metabolically relevant sodium bicarbonate, pyruvate, alanine, and lactate, labeled with carbon-13, were used for NMR studies. All the samples were doped with TEMPO free radicals. The Overhauser DNP enabled nuclear polarization enhancement by factor as large as -95 for protons and as large as -200 for carbon-13, corresponding to thermal polarizations at 0.33 T and 1.1 T fields, respectively. These results demonstrate that SQUID-based microtesla MRI can be naturally combined with Overhauser DNP in one system, and that its signal-to-noise performance is greatly improved in this case. They also suggest that microtesla MRI can become an efficient tool for in vivo imaging of hyperpolarized carbon-13, produced by low-temperature dissolution DNP.

Nuclear Overhauser effect studies on the conformation of magnesium adenosine 5'-triphosphate bound to rabbit muscle creatine kinase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosevear, P.R.; Powers, V.M.; Dowhan, D.

1987-08-25

Nuclear Overhauser effects were used to determine interproton distances on MgATP bound to rabbit muscle creatine kinase. The internuclear distances were used in a distance geometry program that objectively determines both the conformation of the bound MgATP and its uniqueness. Two classes of structures were found that satisfied the measured interproton distances. Both classes had the same anti glycosidic torsional angle (X = 78 +/- 10/sup 0/) but differed in their ribose ring puckers (O1'-endo or C4'-exo). The uniqueness of the glycosidic torsional angle is consistent with the preference of creatine kinase for adenine nucleotides. One of these conformations ofmore » MgATP bound to creatine kinase is indistinguishable from the conformation found for Co(NH/sub 3/)/sub 4/ ATP bound to the catalytic subunit of protein kinase, which also has a high specificity for adenine nucleotides. Distance geometry calculations also suggest that upper limit distances, when low enough (less than or equal to 3.4 A), can be used instead of measured distances to define, within experimental error, the glycosidic torsional angle of bound nucleotides. However, this approach does not permit an evaluation of the ribose ring pucker.« less

Comparison of generation 3 polyamidoamine dendrimer and generation 4 polypropylenimine dendrimer on drug loading, complex structure, release behavior, and cytotoxicity

PubMed Central

Shao, Naimin; Su, Yunzhang; Hu, Jingjing; Zhang, Jiahai; Zhang, Hongfeng; Cheng, Yiyun

2011-01-01

Background Polyamidoamine (PAMAM) and polypropylenimine (PPI) dendrimers are the commercially available and most widely used dendrimers in pharmaceutical sciences and biomedical engineering. In the present study, the loading and release behaviors of generation 3 PAMAM and generation 4 PPI dendrimers with the same amount of surface amine groups (32 per dendrimer) were compared using phenylbutazone as a model drug. Methods The dendrimer-phenylbutazone complexes were characterized by 1H nuclear magnetic resonance and nuclear Overhauser effect techniques, and the cytotoxicity of each dendrimer was evaluated. Results Aqueous solubility results suggest that the generation 3 PAMAM dendrimer has a much higher loading ability towards phenylbutazone in comparison with the generation 4 PPI dendrimer at high phenylbutazone-dendrimer feeding ratios. Drug release was much slower from the generation 3 PAMAM matrix than from the generation 4 PPI dendrimer. In addition, the generation 3 PAMAM dendrimer is at least 50-fold less toxic than generation 4 PPI dendrimer on MCF-7 and A549 cell lines. Conclusion Although the nuclear Overhauser effect nuclear magnetic resonance results reveal that the generation 4 PPI dendrimer with a more hydrophobic interior encapsulates more phenylbutazone, the PPI dendrimer-phenylbutazone inclusion is not stable in aqueous solution, which poses a great challenge during drug development. PMID:22267921

Matrix decompositions of two-dimensional nuclear magnetic resonance spectra.

PubMed

Havel, T F; Najfeld, I; Yang, J X

1994-08-16

Two-dimensional NMR spectra are rectangular arrays of real numbers, which are commonly regarded as digitized images to be analyzed visually. If one treats them instead as mathematical matrices, linear algebra techniques can also be used to extract valuable information from them. This matrix approach is greatly facilitated by means of a physically significant decomposition of these spectra into a product of matrices--namely, S = PAPT. Here, P denotes a matrix whose columns contain the digitized contours of each individual peak or multiple in the one-dimensional spectrum, PT is its transpose, and A is an interaction matrix specific to the experiment in question. The practical applications of this decomposition are considered in detail for two important types of two-dimensional NMR spectra, double quantum-filtered correlated spectroscopy and nuclear Overhauser effect spectroscopy, both in the weak-coupling approximation. The elements of A are the signed intensities of the cross-peaks in a double quantum-filtered correlated spectrum, or the integrated cross-peak intensities in the case of a nuclear Overhauser effect spectrum. This decomposition not only permits these spectra to be efficiently simulated but also permits the corresponding inverse problems to be given an elegant mathematical formulation to which standard numerical methods are applicable. Finally, the extension of this decomposition to the case of strong coupling is given.

Matrix decompositions of two-dimensional nuclear magnetic resonance spectra.

PubMed Central

Havel, T F; Najfeld, I; Yang, J X

1994-01-01

Two-dimensional NMR spectra are rectangular arrays of real numbers, which are commonly regarded as digitized images to be analyzed visually. If one treats them instead as mathematical matrices, linear algebra techniques can also be used to extract valuable information from them. This matrix approach is greatly facilitated by means of a physically significant decomposition of these spectra into a product of matrices--namely, S = PAPT. Here, P denotes a matrix whose columns contain the digitized contours of each individual peak or multiple in the one-dimensional spectrum, PT is its transpose, and A is an interaction matrix specific to the experiment in question. The practical applications of this decomposition are considered in detail for two important types of two-dimensional NMR spectra, double quantum-filtered correlated spectroscopy and nuclear Overhauser effect spectroscopy, both in the weak-coupling approximation. The elements of A are the signed intensities of the cross-peaks in a double quantum-filtered correlated spectrum, or the integrated cross-peak intensities in the case of a nuclear Overhauser effect spectrum. This decomposition not only permits these spectra to be efficiently simulated but also permits the corresponding inverse problems to be given an elegant mathematical formulation to which standard numerical methods are applicable. Finally, the extension of this decomposition to the case of strong coupling is given. PMID:8058742

Transferred nuclear Overhauser enhancement experiments show that the monoclonal antibody strep 9 selects a local minimum conformation of a Streptococcus group A trisaccharide-hapten.

PubMed

Weimar, T; Harris, S L; Pitner, J B; Bock, K; Pinto, B M

1995-10-17

Transferred nuclear Overhauser enhancement (TRNOE) experiments have been performed to investigate the bound conformation of the trisaccharide repeating unit of the Streptococcus Group A cell-wall polysaccharide. Thus, the conformations of propyl 3-O-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-2-O-(alpha-L-rhamnopyran osyl)- alpha-L-rhamnopyranoside [C(A')B] (1) as a free ligand and when complexed to the monoclonal antibody Strep 9 were examined. Improved insights about the conformational preferences of the glycosidic linkages of the trisaccharide ligand showed that the free ligand populates various conformations in aqueous solution, thus displaying relatively flexible behavior. The NOE HNAc-H2A', which was not detected in previous work, accounts for a conformation at the beta-(1-->3) linkage with a phi angle of approximately 180 degrees. Observed TRNOEs for the complex are weak, and their analysis was further complicated by spin diffusion. With the use of transferred rotating-frame Overhauser enhancement (TRROE) experiments, the amount of spin diffusion was assessed experimentally, proving that all of the observed long-range TRNOEs arose through spin diffusion. Four interglycosidic distances, derived from the remaining TRNOEs and TRROEs, together with repulsive constraints, derived from the absence of TRROE effects, were used as input parameters in simulated annealing and molecular mechanics calculations to determine the bound conformation of the trisaccharide. Complexation by the antibody results in the selection of one defined conformation of the carbohydrate hapten. This bound conformation, which is a local energy minimum on the energy maps calculated for the trisaccharide ligand, shows only a change from a +gauche to a -gauche orientation at the psi angle of the alpha-(1-->2) linkage when compared to the global minimum conformation. The results infer that the bound conformation of the Streptococcus Group A cell-wall polysaccharide is different from its previously proposed solution structure (Kreis et al., 1995).

Template Based Design of Anti-Metastatic Drugs from the Active Conformation of Laminin Peptide 11

DTIC Science & Technology

2002-01-01

spectrometry, and the success of refolding column, lane D = molecular weight markers. the domain by circular dichroism (CD) spectroscopy . The recombinant...determine the active conformation of peptide 11 utilized Tr-NOESY (Transferred Nuclear Overhauser Effect Spectroscopy ) experiments where the peptide...activity. RNAase Nothing activity assayed for 20 hours of refolding using 2’:3’-cyclic cytidine monophosphate 0 01𔃺 1,5 2𔃺 Time, hrs A Final report

New Methods of Low-Field Magnetic Resonance Imaging for Application to Traumatic Brain Injury

DTIC Science & Technology

2013-02-01

magnet based ), the development of novel high-speed parallel imaging detection systems, and work on advanced adaptive reconstruction methods ...signal many times within the acquisition time . We present here a new method for 3D OMRI based on b-SSFP at a constant field of 6.5 mT that provides up...developing injury-sensitive MRI based on the detection of free radicals associat- ed with injury using the Overhauser effect and subsequently imaging that

Solution conformation of a peptide fragment representing a proposed RNA-binding site of a viral coat protein studied by two-dimensional NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

van der Graaf, M.; van Mierlo, C.P.M.; Hemminga, M.A.

1991-06-11

The first 25 amino acids of the coat protein of cowpea chlorotic mottle virus are essential for binding the encapsidated RNA. Although an {alpha}-helical conformation has been predicted for this highly positively charged N-terminal region. No experimental evidence for this conformation has been presented so far. In this study, two-dimensional proton NMR experiments were performed on a chemically synthesized pentacosapeptide containing the first 25 amino acids of this coat protein. All resonances could be assigned by a combined use of two-dimensional correlated spectroscopy and nuclear Overhauser enhancement spectroscopy carried out at four different temperatures. Various NMR parameters indicate the presencemore » of a conformational ensemble consisting of helical structures rapidly converting into more extended states. Differences in chemical shifts and nuclear Overhauser effects indicate that lowering the temperature induces a shift of the dynamic equilibrium toward more helical structures. At 10{degrees}C, a perceptible fraction of the conformational ensemble consists of structures with an {alpha}-helical conformation between residues 9 and 17, likely starting with a turnlike structure around Thr9 and Arg10. Both the conformation and the position of this helical region agree well with the secondary structure predictions mentioned above.« less

Optical pumping of electron and nuclear spin in a negatively-charged quantum dot

NASA Astrophysics Data System (ADS)

Bracker, Allan; Gershoni, David; Korenev, Vladimir

2005-03-01

We report optical pumping of electron and nuclear spins in an individual negatively-charged quantum dot. With a bias-controlled heterostructure, we inject one electron into the quantum dot. Intense laser excitation produces negative photoluminescence polarization, which is easily erased by the Hanle effect, demonstrating optical pumping of a long-lived resident electron. The electron spin lifetime is consistent with the influence of nuclear spin fluctuations. Measuring the Overhauser effect in high magnetic fields, we observe a high degree of nuclear spin polarization, which is closely correlated to electron spin pumping.

Nuclear Spin Nanomagnet in an Optically Excited Quantum Dot

NASA Astrophysics Data System (ADS)

Korenev, V. L.

2007-12-01

Linearly polarized light tuned slightly below the optical transition of the negatively charged exciton (trion) in a single quantum dot causes the spontaneous nuclear spin polarization (self-polarization) at a level close to 100%. The effective magnetic field of spin-polarized nuclei shifts the optical transition energy close to resonance with photon energy. The resonantly enhanced Overhauser effect sustains the stability of the nuclear self-polarization even in the absence of spin polarization of the quantum dot electron. As a result the optically selected single quantum dot represents a tiny magnet with the ferromagnetic ordering of nuclear spins—the nuclear spin nanomagnet.

Optical pumping of the electronic and nuclear spin of single charge-tunable quantum dots.

PubMed

Bracker, A S; Stinaff, E A; Gammon, D; Ware, M E; Tischler, J G; Shabaev, A; Efros, Al L; Park, D; Gershoni, D; Korenev, V L; Merkulov, I A

2005-02-04

We present a comprehensive examination of optical pumping of spins in individual GaAs quantum dots as we change the net charge from positive to neutral to negative with a charge-tunable heterostructure. Negative photoluminescence polarization memory is enhanced by optical pumping of ground state electron spins, which we prove with the first measurements of the Hanle effect on an individual quantum dot. We use the Overhauser effect in a high longitudinal magnetic field to demonstrate efficient optical pumping of nuclear spins for all three charge states of the quantum dot.

Optical Pumping of the Electronic and Nuclear Spin of Single Charge-Tunable Quantum Dots

NASA Astrophysics Data System (ADS)

Bracker, A. S.; Stinaff, E. A.; Gammon, D.; Ware, M. E.; Tischler, J. G.; Shabaev, A.; Efros, Al. L.; Park, D.; Gershoni, D.; Korenev, V. L.; Merkulov, I. A.

2005-02-01

We present a comprehensive examination of optical pumping of spins in individual GaAs quantum dots as we change the net charge from positive to neutral to negative with a charge-tunable heterostructure. Negative photoluminescence polarization memory is enhanced by optical pumping of ground state electron spins, which we prove with the first measurements of the Hanle effect on an individual quantum dot. We use the Overhauser effect in a high longitudinal magnetic field to demonstrate efficient optical pumping of nuclear spins for all three charge states of the quantum dot.

Nuclear spin nanomagnet in an optically excited quantum dot.

PubMed

Korenev, V L

2007-12-21

Linearly polarized light tuned slightly below the optical transition of the negatively charged exciton (trion) in a single quantum dot causes the spontaneous nuclear spin polarization (self-polarization) at a level close to 100%. The effective magnetic field of spin-polarized nuclei shifts the optical transition energy close to resonance with photon energy. The resonantly enhanced Overhauser effect sustains the stability of the nuclear self-polarization even in the absence of spin polarization of the quantum dot electron. As a result the optically selected single quantum dot represents a tiny magnet with the ferromagnetic ordering of nuclear spins-the nuclear spin nanomagnet.

Features of the reaction of heterocyclic analogs of chalcone with lanthanide shift reagents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turov, A.V.; Khilya, V.P.

1994-10-01

The PMR spectra of heterocyclic analogs of 2-hydroxychalcone containing thiazole, benzofuran, triazole, imidazole, benzodioxane, or pyridine rings in the presence of lanthanide shift reagents are studied. It is found that the most effective reagent for modifying the spectra of these compounds is Yb(fod)3. The broadening of the spectra of 2-hydroxy chalcones in the presence of lanthanide shift reagents is explained by the dynamic effects of complex formation. An example is given of the determination of the conformation of molecules of 2-hydroxychalcone by the simultaneous use of lanthanide shift reagents and the homonuclear Overhauser effect. 9 refs., 1 fig., 1 tab.

Identification of New Diterpenes as Putative Marker Compounds Distinguishing Agnus Castus Fruit (Chaste Tree) from Shrub Chaste Tree Fruit (Viticis Fructus).

PubMed

Oshima, Naohiro; Masada, Sayaka; Suzuki, Ryuta; Yagi, Kanae; Matsufuji, Hiroshi; Suenaga, Emi; Takahashi, Yutaka; Yahagi, Tadahiro; Watanabe, Masato; Yahara, Shoji; Iida, Osamu; Kawahara, Nobuo; Maruyama, Takuro; Goda, Yukihiro; Hakamatsuka, Takashi

2016-01-01

Agnus Castus Fruit is defined in the European Pharmacopoeia as the dried ripe fruit of Vitex agnus-castus. In Europe it is used as a medicine targeting premenstrual syndrome and climacteric disorder. In Japan, Agnus Castus Fruit is becoming popular as a raw material for over-the-counter drugs and health food products, though its congenic species, Vitex rotundifolia and Vitex trifolia, have been used as Shrub Chaste Tree Fruit in traditional medicines. Therefore, it is important to discriminate these Vitex plants from the viewpoint of regulatory science. Here we tried to identify putative marker compounds that distinguish between Agnus Castus Fruit and Shrub Chaste Tree Fruit. We analyzed extracts of each crude drug by liquid chromatography-mass spectrometry, and performed differential analysis by comparison of each chromatogram to find one or more peaks characteristic of Agnus Castus Fruit. A peak was isolated and identified as an equilibrium mixture of new compounds named chastol (1) and epichastol (1a). The planar structures of 1 and 1a were determined spectroscopically. Their relative configurations were revealed by nuclear Overhauser effect spectroscopy and differential nuclear Overhauser effect-NMR data. Since avoiding contamination from closely related species is needed for the quality control of natural pharmaceuticals, this information will be valuable to establish a method for the quality control of both, Agnus Castus Fruit and Shrub Chaste Tree Fruit products. Georg Thieme Verlag KG Stuttgart · New York.

NMR study of the transforming growth factor-alpha (TGF-alpha)-epidermal growth factor receptor complex. Visualization of human TGF-alpha binding determinants through nuclear Overhauser enhancement analysis.

PubMed

McInnes, C; Hoyt, D W; Harkins, R N; Pagila, R N; Debanne, M T; O'Connor-McCourt, M; Sykes, B D

1996-12-13

The study of human transforming growth factor-alpha (TGF-alpha) in complex with the epidermal growth factor (EGF) receptor extracellular domain has been undertaken in order to generate information on the interactions of these molecules. Analysis of 1H NMR transferred nuclear Overhauser enhancement data for titration of the ligand with the receptor has yielded specific data on the residues of the growth factor involved in contact with the larger protein. Significant increases and decreases in nuclear Overhauser enhancement cross-peak intensity occur upon complexation, and interpretation of these changes indicates that residues of the A- and C-loops of TGF-alpha form the major binding interface, while the B-loop provides a structural scaffold for this site. These results corroborate the conclusions from NMR relaxation studies (Hoyt, D. W., Harkins, R. N., Debanne, M. T., O'Connor-McCourt, M., and Sykes, B. D. (1994) Biochemistry 33, 15283-15292), which suggest that the C-terminal residues of the polypeptide are immobilized upon receptor binding, while the N terminus of the molecule retains considerable flexibility, and are consistent with structure-function studies of the TGF-alpha/EGF system indicating a multidomain binding model. These results give a visualization, for the first time, of native TGF-alpha in complex with the EGF receptor and generate a picture of the ligand-binding site based upon the intact molecule. This will undoubtedly be of utility in the structure-based design of TGF-alpha/EGF agonists and/or antagonists.

Suppression of Overhauser Effect in the Exciton-Nuclear Spin System of GaAs Quantum Dot

DTIC Science & Technology

2001-06-01

the exciton-nuclear spin system of GaAs quantum dot V L. Korenevt, I. A. Merkulovt, D. Gammonj, Al. L. Efrosj, T. A. Kennedyl, M. Rosenj, D. S ...Katzerj and S . W. Brown§ t loffe Physico-Technical Institute, St Petersburg, Russia I Naval Research Laboratory, Washington DC 20375, USA § NIST...2.5 s -1 for N - 105 nuclei in the quantum dot [51 and rb - 0.1 ns [9]. The estimation is in agreement with experiment (Texp ; 3 s ). Coupling of

Separation of enilconazole enantiomers in capillary electrophoresis with cyclodextrin-type chiral selectors and investigation of structure of selector-selectand complexes by using nuclear magnetic resonance spectroscopy.

PubMed

Gogolashvili, Ann; Tatunashvili, Elene; Chankvetadze, Lali; Sohajda, Tamas; Szeman, Julianna; Salgado, Antonio; Chankvetadze, Bezhan

2017-08-01

In the present study, the enantiomer migration order (EMO) of enilconazole in the presence of various cyclodextrins (CDs) was investigated by capillary electrophoresis (CE). Opposite EMO of enilconazole were observed when β-CD or the sulfated heptakis(2-O-methyl-3,6-di-O-sulfo)-β-CD (HMDS-β-CD) was used as the chiral selectors. Nuclear magnetic resonance (NMR) spectroscopy was used to study the mechanism of chiral recognition between enilconazole enantiomers and those two cyclodextrins. On the basis of rotating frame nuclear Overhauser (ROESY) experiments, the structure of an inclusion complex between enilconazole and β-CD was derived, in which (+)-enilconazole seemed to form a tighter complex than the (-)-enantiomer. This correlates well with the migration order of enilconazole enantiomers observed in CE. No evidence of complexation between enilconazole and HMDS-β-CD could be gathered due to lack of intermolecular nuclear Overhauser effect (NOE). Most likely the interaction between enilconazole and HMDS-β-CD leads to formation of a shallow external complex that is sufficient for separation of enantiomers in CE but cannot be evidenced based on ROESY experiment. Thus, in this particular case CE documents the presence of intermolecular interactions which are at least very difficult to be evidenced by other instrumental techniques. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

FRAMING Linguistics: ``SEANCES"(!!!) Martin-Bradshaw-Siegel ``Buzzwordism, Bandwagonism, Sloganeering For:Fun, Profit, Survival, Ego": Rampant UNethics Sociological-DYSfunctionality!!!

NASA Astrophysics Data System (ADS)

Bradshaw, John; Siegel, E.

2010-03-01

``Sciences''/SEANCES(!!!) rampant UNethics!!! WITNESS: Yau v Perelman Poincare-conj.-pf. [Naser, NewYorker(8/06)]; digits log- law Siegel[AMS Nat.Mtg.(02)-Abs.973-60-124] inversion to ONLY BEQS: Newcomb(1881)<<

Magnetization transfer contrast-suppressed imaging of amide proton transfer and relayed nuclear overhauser enhancement chemical exchange saturation transfer effects in the human brain at 7T.

PubMed

Xu, Xiang; Yadav, Nirbhay N; Zeng, Haifeng; Jones, Craig K; Zhou, Jinyuan; van Zijl, Peter C M; Xu, Jiadi

2016-01-01

To use the variable delay multipulse (VDMP) chemical exchange saturation transfer (CEST) approach to obtain clean amide proton transfer (APT) and relayed Nuclear Overhauser enhancement (rNOE) CEST images in the human brain by suppressing the conventional magnetization transfer contrast (MTC) and reducing the direct water saturation contribution. The VDMP CEST scheme consists of a train of RF pulses with a specific mixing time. The CEST signal with respect to the mixing time shows distinguishable characteristics for protons with different exchange rates. Exchange rate filtered CEST images are generated by subtracting images acquired at two mixing times at which the MTC signals are equal, while the APT and rNOE-CEST signals differ. Because the subtraction is performed at the same frequency offset for each voxel and the CEST signals are broad, no B0 correction is needed. MTC-suppressed APT and rNOE-CEST images of human brain were obtained using the VDMP method. The APT-CEST data show hyperintensity in gray matter versus white matter, whereas the rNOE-CEST images show negligible contrast between gray and white matter. The VDMP approach provides a simple and rapid way of recording MTC-suppressed APT-CEST and rNOE-CEST images without the need for B0 field correction. © 2015 Wiley Periodicals, Inc.

Exploiting Electric and Magnetic Fields for Underwater Characterization

DTIC Science & Technology

2011-03-01

geophysical surveys are primarily limited to passive magnetic systems towed from a surface vessel. These systems utilize fluxgate , Overhauser, or atomic... magnetometer sensors, often deployed in arrays towed from the stern of small to moderate-size vessels. Active source electromagnetic methods have been

Dynamics of glass-forming di-n-butyl phthalate as studied by NMR.

PubMed

Szcześniak, E; Głowinkowski, S; Suchański, W; Jurga, S

1997-04-01

Spin-lattice relaxation times T1 and nuclear Overhauser effect (NOE) enhancement factors for the individual ring carbons in di-n-butyl phthalate (DBF) show that the reorientational correlation function corresponding to the global dynamics in supercooled liquid can be described by a Davidson-Cole distribution. Measurements of proton spin-lattice relaxation times T1 and T1p, as well as 1H NMR spectra at temperatures below the glass transition temperature, Tg, reveal that the same distribution holds also for description of local dynamics in glassy DBF. The activation parameters of the motions detected are derived.

Three new 7.3',8.5'-connected bicyclo[3.2.1]octanoids and other neolignans from leaves of Nectandra amazonum NEES. (Lauraceae).

PubMed

Coy Barrera, Ericsson David; Cuca Suárez, Luis Enrique

2009-06-01

Three new 7.3',8.5'-connected (macrophyllin-type) bicyclo[3.2.1]octanoid neolignans (nectamazins A-C, 1-3) were isolated from leaves of Nectandra amazonum NEES., along with seven known neolignans (4-10). The structures of 1-3 were characterized by spectroscopic methods (1D, 2D NMR) and the absolute configuration was assigned on the basis of circular dichroism (CD) spectra supported by nuclear Overhauser effect spectroscopy (NOESY) correlations. The new compounds showed inhibition activity against platelet activating factor (PAF)-induced aggregation of rabbit platelets.

INTRAMOLECULAR MOTION AND REORIENTATIONAL BARRIERS IN 9-FLUORENONE, 4-METHYL-9-FLUORENONE AND 4,5-DIMETHYL-9-FLUORENONE

EPA Science Inventory

Carbon-13 nuclear magnetic resonance spin-lattice relaxation times and nuclear Overhauser enhancements were measured as functions of temperature for the hydrogen-bearing carbons in 9-fluorenone, 4-methyl-9-fluorenone, and 4,5-dimethyl-9-fluorenone. Reorientational diffusion const...

What's in a Name?FRAMING:Martin-Bradshaw DYSfunctionality = Siegel ``Buzzwordism,Bandwagonism&Sloganeering For: Fun, Profit,Survival,Ego": From SOC to FLT Proof to High-Tc to Spintronics to Giant-Magnetoresistance: Ethics??? SHMETHICS!!! Rampant Sociolog

NASA Astrophysics Data System (ADS)

Siegel, Edward

2008-03-01

Buzzwordism,Bandwagonism,Sloganeering for:Fun,Profit,Survival, Ego=ethics DYSunctionality: Digits log-law: Siegel INVERSION: bosons=digits; Excluded d=0? P(0)=oo V P(1)

A quasi-optical and corrugated waveguide microwave transmission system for simultaneous dynamic nuclear polarization NMR on two separate 14.1 T spectrometers

PubMed Central

Dubroca, Thierry; Smith, Adam N.; Pike, Kevin J.; Froud, Stuart; Wylde, Richard; Trociewitz, Bianca; McKay, Johannes; Mentink-Vigier, Frederic; van Tol, Johan; Wi, Sungsool; Brey, William; Long, Joanna R.; Frydman, Lucio; Hill, Stephen

2018-01-01

Nuclear magnetic resonance (NMR) is an intrinsically insensitive technique, with Boltzmann distributions of nuclear spin states on the order of parts per million in conventional magnetic fields. To overcome this limitation, dynamic nuclear polarization (DNP) can be used to gain up to three orders of magnitude in signal enhancement, which can decrease experimental time by up to six orders of magnitude. In DNP experiments, nuclear spin polarization is enhanced by transferring the relatively larger electron polarization to NMR active nuclei via microwave irradiation. Here, we describe the design and performance of a quasi-optical system enabling the use of a single 395 GHz gyrotron microwave source to simultaneously perform DNP experiments on two different 14.1 T (1H 600 MHz) NMR spectrometers: one configured for magic angle spinning (MAS) solid state NMR; the other configured for solution state NMR experiments. In particular, we describe how the high power microwave beam is split, transmitted, and manipulated between the two spectrometers. A 13C enhancement of 128 is achieved via the cross effect for alanine, using the nitroxide biradical AMUPol, under MAS-DNP conditions at 110 K, while a 31P enhancement of 160 is achieved via the Overhauser effect for triphenylphosphine using the monoradical BDPA under solution NMR conditions at room temperature. The latter result is the first demonstration of Overhauser DNP in the solution state at a field of 14.1 T (1H 600 MHz). Moreover these results have been produced with large sample volumes (~100 μL, i.e. 3 mm diameter NMR tubes). PMID:29459343

A quasi-optical and corrugated waveguide microwave transmission system for simultaneous dynamic nuclear polarization NMR on two separate 14.1 T spectrometers

NASA Astrophysics Data System (ADS)

Dubroca, Thierry; Smith, Adam N.; Pike, Kevin J.; Froud, Stuart; Wylde, Richard; Trociewitz, Bianca; McKay, Johannes; Mentink-Vigier, Frederic; van Tol, Johan; Wi, Sungsool; Brey, William; Long, Joanna R.; Frydman, Lucio; Hill, Stephen

2018-04-01

Nuclear magnetic resonance (NMR) is an intrinsically insensitive technique, with Boltzmann distributions of nuclear spin states on the order of parts per million in conventional magnetic fields. To overcome this limitation, dynamic nuclear polarization (DNP) can be used to gain up to three orders of magnitude in signal enhancement, which can decrease experimental time by up to six orders of magnitude. In DNP experiments, nuclear spin polarization is enhanced by transferring the relatively larger electron polarization to NMR active nuclei via microwave irradiation. Here, we describe the design and performance of a quasi-optical system enabling the use of a single 395 GHz gyrotron microwave source to simultaneously perform DNP experiments on two different 14.1 T (1H 600 MHz) NMR spectrometers: one configured for magic angle spinning (MAS) solid state NMR; the other configured for solution state NMR experiments. In particular, we describe how the high power microwave beam is split, transmitted, and manipulated between the two spectrometers. A 13C enhancement of 128 is achieved via the cross effect for alanine, using the nitroxide biradical AMUPol, under MAS-DNP conditions at 110 K, while a 31P enhancement of 160 is achieved via the Overhauser effect for triphenylphosphine using the monoradical BDPA under solution NMR conditions at room temperature. The latter result is the first demonstration of Overhauser DNP in the solution state at a field of 14.1 T (1H 600 MHz). Moreover these results have been produced with large sample volumes (∼100 μL, i.e. 3 mm diameter NMR tubes).

Nuclear magnetic resonance studies on yeast tRNAPhe. II. Assignment of the iminoproton resonances of the anticodon and T stem by means of nuclear Overhauser effect experiments at 500 MHz.

PubMed Central

Heerschap, A; Haasnoot, C A; Hilbers, C W

1983-01-01

Resonances of the water exchangeable iminoprotons of the T and anticodon stem of yeast tRNAPhe were assigned by means of Nuclear Overhauser Effects (NOE's). Together with our previous assignments of iminoproton resonances from the acceptor and D stem (A. Heerschap, C.A.G. Haasnoot and C.W. Hilbers (1982) Nucleic Acids Res. 10, 6981-7000) the present results constitute a complete assignment of all resonances of iminoprotons involved in the secondary structure of yeast tRNAPhe with a reliability and spectral resolution not reached heretofore. Separate identification of the methylprotons in m5C40 and m5C49 was also possible due to specific NOE patterns in the lowfield part of the spectrum. Our experiments indicate that in solution the psi 39 residue in the anticodon stem is orientated in a syn conformation in contrast to the normally observed anti orientation of the uracil base in AU basepairs. Evidence is presented that in solution the acceptor stem is stacked upon the T stem. Furthermore, it turns out that in a similar way the anticodon stem forms a continuous stack with the D stem, but here the m2(2)G26 residue is located between the latter two stems (as is found in the X-ray crystal structure). The stacking of these stems is not strictly dependent on the presence of magnesium ions. NOE experiments show that these structural features are preserved when proceeding from a buffer with magnesium ions to a buffer without magnesium ions although differences in chemical shifts and NOE intensities indicate changes in the conformation of the tRNA. PMID:6346268

A quasi-optical and corrugated waveguide microwave transmission system for simultaneous dynamic nuclear polarization NMR on two separate 14.1 T spectrometers.

PubMed

Dubroca, Thierry; Smith, Adam N; Pike, Kevin J; Froud, Stuart; Wylde, Richard; Trociewitz, Bianca; McKay, Johannes; Mentink-Vigier, Frederic; van Tol, Johan; Wi, Sungsool; Brey, William; Long, Joanna R; Frydman, Lucio; Hill, Stephen

2018-04-01

Nuclear magnetic resonance (NMR) is an intrinsically insensitive technique, with Boltzmann distributions of nuclear spin states on the order of parts per million in conventional magnetic fields. To overcome this limitation, dynamic nuclear polarization (DNP) can be used to gain up to three orders of magnitude in signal enhancement, which can decrease experimental time by up to six orders of magnitude. In DNP experiments, nuclear spin polarization is enhanced by transferring the relatively larger electron polarization to NMR active nuclei via microwave irradiation. Here, we describe the design and performance of a quasi-optical system enabling the use of a single 395 GHz gyrotron microwave source to simultaneously perform DNP experiments on two different 14.1 T ( 1 H 600 MHz) NMR spectrometers: one configured for magic angle spinning (MAS) solid state NMR; the other configured for solution state NMR experiments. In particular, we describe how the high power microwave beam is split, transmitted, and manipulated between the two spectrometers. A 13 C enhancement of 128 is achieved via the cross effect for alanine, using the nitroxide biradical AMUPol, under MAS-DNP conditions at 110 K, while a 31 P enhancement of 160 is achieved via the Overhauser effect for triphenylphosphine using the monoradical BDPA under solution NMR conditions at room temperature. The latter result is the first demonstration of Overhauser DNP in the solution state at a field of 14.1 T ( 1 H 600 MHz). Moreover these results have been produced with large sample volumes (∼100 µL, i.e. 3 mm diameter NMR tubes). Copyright © 2018 Elsevier Inc. All rights reserved.

Design of an Active Ultrastable Single-chain Insulin Analog

PubMed Central

Hua, Qing-xin; Nakagawa, Satoe H.; Jia, Wenhua; Huang, Kun; Phillips, Nelson B.; Hu, Shi-quan; Weiss, Michael A.

2008-01-01

Single-chain insulin (SCI) analogs provide insight into the inter-relation of hormone structure, function, and dynamics. Although compatible with wild-type structure, short connecting segments (<3 residues) prevent induced fit upon receptor binding and so are essentially without biological activity. Substantial but incomplete activity can be regained with increasing linker length. Here, we describe the design, structure, and function of a single-chain insulin analog (SCI-57) containing a 6-residue linker (GGGPRR). Native receptor-binding affinity (130 ± 8% relative to the wild type) is achieved as hindrance by the linker is offset by favorable substitutions in the insulin moiety. The thermodynamic stability of SCI-57 is markedly increased (ΔΔGu = 0.7 ± 0.1 kcal/mol relative to the corresponding two-chain analog and 1.9 ± 0.1 kcal/mol relative to wild-type insulin). Analysis of inter-residue nuclear Overhauser effects demonstrates that a native-like fold is maintained in solution. Surprisingly, the glycine-rich connecting segment folds against the insulin moiety: its central Pro contacts ValA3 at the edge of the hydrophobic core, whereas the final Arg extends the A1-A8 α-helix. Comparison between SCI-57 and its parent two-chain analog reveals striking enhancement of multiple native-like nuclear Overhauser effects within the tethered protein. These contacts are consistent with wild-type crystal structures but are ordinarily attenuated in NMR spectra of two-chain analogs, presumably due to conformational fluctuations. Linker-specific damping of fluctuations provides evidence for the intrinsic flexibility of an insulin monomer. In addition to their biophysical interest, ultrastable SCIs may enhance the safety and efficacy of insulin replacement therapy in the developing world. PMID:18332129

France’s New NATO Policy: Leveraging a Realignment of the Alliance?

DTIC Science & Technology

2009-01-01

things that others only think. Former Socialist foreign minister, Hubert Védrine, put it in particularly stark terms: Were France to become a...see Ronja Kempin and Marco Overhaus, “Kein grosser Sprung in der Entwicklung der ESVP: Lehren aus der französischen Ratpräsidentschaft” [“No great

Reduction process of nitroxyl spin probes used in Overhauser-enhanced magnetic resonance imaging: An ESR study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meenakumari, V.; Premkumar, S.; Benial, A. Milton Franklin, E-mail: miltonfranklin@yahoo.com

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 line width, hyperfine coupling constant, g-factor, signal intensity ratio and rotational correlation time were estimated. The 3-carbamoyl-PROXYL radical has narrowest line width and fast tumbling motion compared with 3-carboxy-PROXYL, 4-methoxy-TEMPO, and 4-acetamido-TEMPO radicals. The half life time and decay rate were estimated for 1mM concentration of {sup 14}N- labeled nitroxyl radicals in 1 mM concentration ofmore » ascorbic acid. From the results, the 3-carbamoyl-PROXYL has long half life time and high stability compared with 3-carboxy-PROXYL, 4-methoxy-TEMPO and 4-acetamido-TEMPO radicals. Therefore, this study reveals that the 3-carbamoyl-PROXYL radical can act as a good redox sensitive spin probe for Overhauser-enhanced Magnetic Resonance Imaging.« less

Reduction process of nitroxyl spin probes used in Overhauser-enhanced magnetic resonance imaging: An ESR study

NASA Astrophysics Data System (ADS)

Meenakumari, V.; Jawahar, A.; Premkumar, S.; Benial, A. Milton Franklin

2016-05-01

The Electron spin resonance studies on the reduction process of nitroxyl spin probes were carried out for 1mM 14N- 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 line width, hyperfine coupling constant, g-factor, signal intensity ratio and rotational correlation time were estimated. The 3-carbamoyl-PROXYL radical has narrowest line width and fast tumbling motion compared with 3-carboxy-PROXYL, 4-methoxy-TEMPO, and 4-acetamido-TEMPO radicals. The half life time and decay rate were estimated for 1mM concentration of 14N- labeled nitroxyl radicals in 1 mM concentration of ascorbic acid. From the results, the 3-carbamoyl-PROXYL has long half life time and high stability compared with 3-carboxy-PROXYL, 4-methoxy-TEMPO and 4-acetamido-TEMPO radicals. Therefore, this study reveals that the 3-carbamoyl-PROXYL radical can act as a good redox sensitive spin probe for Overhauser-enhanced Magnetic Resonance Imaging.

Tigloylshikonin, a new minor Shikonin derivative, from the roots and the commercial root extract of lithospermum erythrorhizon.

PubMed

Ito, Yusai; Onobori, Kenichi; Yamazaki, Takeshi; Kawamura, Yoko

2011-01-01

Tigloylshikonin, a new shikonin derivative esterified with tiglic acid ((E)-2-methylbut-2-enoic acid), was isolated as a minor pigment from a food colorant "Shikon color," a commercial root extract from Lithospermum erythrorhizon SIEBOLD et ZUCCARINI. The structure of tigloylshikonin was elucidated using (1)H, (13)C, the difference nuclear Overhauser effect (NOE), and 2D NMR techniques. Its stereochemistry was determined by chiral-phase HPLC analysis. Tigloylshikonin was also found in the roots of L. erythrorhizon, which indicated that this new shikonin derivative is a typical component of naphthoquinone pigments in the roots of L. erythrorhizon.

The EU and U.S. Strategies against Terrorism and Proliferation of WMD: A Comparative Study

DTIC Science & Technology

2007-01-01

attitude, which they see as simplistic. As French Foreign Minister Hubert Vedrine said in 2002, “For George W. Bush all the world’s problems come...EU’s Emerging Role in Nuclear Non-proliferation. Ed. by Marco Overhaus, Hanns W. Maull and Sebastian Harnisch, Volume 6, Newsletter No. 17, October

Surface water retardation around single-chain polymeric nanoparticles: critical for catalytic function?

PubMed

Stals, Patrick J M; Cheng, Chi-Yuan; van Beek, Lotte; Wauters, Annelies C; Palmans, Anja R A; Han, Songi; Meijer, E W

2016-03-01

A library of water-soluble dynamic single-chain polymeric nanoparticles (SCPN) was prepared using a controlled radical polymerisation technique followed by the introduction of functional groups, including probes at targeted positions. The combined tools of electron paramagnetic resonance (EPR) and Overhauser dynamic nuclear polarization (ODNP) reveal that these SCPNs have structural and surface hydration properties resembling that of enzymes.

1H NMR study of inclusion compounds of phenylurea derivatives in β-cyclodextrin

NASA Astrophysics Data System (ADS)

Dupuy, N.; Barbry, D.; Bria, M.; Marquis, S.; Vrielynck, L.; Kister, J.

2005-04-01

Proton nuclear magnetic resonance spectroscopy ( 1H NMR), which has become an important tool for the study "in situ" of β-cyclodextrin (β-CD) complexes, was used to study and structurally characterize the inclusion complexes formed between β-CD and isoproturon, fenuron, monuron and diuron. The high variation of the chemical shifts from the proton located inside the cavity (H-3, H-5 and H-6) coupled with the non variation of the one located outer sphere of the β-CD (H-1, H-2 and H-4) provided clear evidence of the inclusion phenomena. Two-dimensional rotating frame Overhauser effect spectroscopy (ROESY) experiments were carried out to further support the proposed inclusion mode.

Monomeric Aβ1–40 and Aβ1–42 Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil

PubMed Central

2016-01-01

The pathogenesis of Alzheimer’s disease is characterized by the aggregation and fibrillation of amyloid peptides Aβ1–40 and Aβ1–42 into amyloid plaques. Despite strong potential therapeutic interest, the structural pathways associated with the conversion of monomeric Aβ peptides into oligomeric species remain largely unknown. In particular, the higher aggregation propensity and associated toxicity of Aβ1–42 compared to that of Aβ1–40 are poorly understood. To explore in detail the structural propensity of the monomeric Aβ1–40 and Aβ1–42 peptides in solution, we recorded a large set of nuclear magnetic resonance (NMR) parameters, including chemical shifts, nuclear Overhauser effects (NOEs), and J couplings. Systematic comparisons show that at neutral pH the Aβ1–40 and Aβ1–42 peptides populate almost indistinguishable coil-like conformations. Nuclear Overhauser effect spectra collected at very high resolution remove assignment ambiguities and show no long-range NOE contacts. Six sets of backbone J couplings (3JHNHα, 3JC′C′, 3JC′Hα, 1JHαCα, 2JNCα, and 1JNCα) recorded for Aβ1–40 were used as input for the recently developed MERA Ramachandran map analysis, yielding residue-specific backbone ϕ/ψ torsion angle distributions that closely resemble random coil distributions, the absence of a significantly elevated propensity for β-conformations in the C-terminal region of the peptide, and a small but distinct propensity for αL at K28. Our results suggest that the self-association of Aβ peptides into toxic oligomers is not driven by elevated propensities of the monomeric species to adopt β-strand-like conformations. Instead, the accelerated disappearance of Aβ NMR signals in D2O over H2O, particularly pronounced for Aβ1–42, suggests that intermolecular interactions between the hydrophobic regions of the peptide dominate the aggregation process. PMID:26780756

Monomeric Aβ(1-40) and Aβ(1-42) Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil.

PubMed

Roche, Julien; Shen, Yang; Lee, Jung Ho; Ying, Jinfa; Bax, Ad

2016-02-09

The pathogenesis of Alzheimer's disease is characterized by the aggregation and fibrillation of amyloid peptides Aβ(1-40) and Aβ(1-42) into amyloid plaques. Despite strong potential therapeutic interest, the structural pathways associated with the conversion of monomeric Aβ peptides into oligomeric species remain largely unknown. In particular, the higher aggregation propensity and associated toxicity of Aβ(1-42) compared to that of Aβ(1-40) are poorly understood. To explore in detail the structural propensity of the monomeric Aβ(1-40) and Aβ(1-42) peptides in solution, we recorded a large set of nuclear magnetic resonance (NMR) parameters, including chemical shifts, nuclear Overhauser effects (NOEs), and J couplings. Systematic comparisons show that at neutral pH the Aβ(1-40) and Aβ(1-42) peptides populate almost indistinguishable coil-like conformations. Nuclear Overhauser effect spectra collected at very high resolution remove assignment ambiguities and show no long-range NOE contacts. Six sets of backbone J couplings ((3)JHNHα, (3)JC'C', (3)JC'Hα, (1)JHαCα, (2)JNCα, and (1)JNCα) recorded for Aβ(1-40) were used as input for the recently developed MERA Ramachandran map analysis, yielding residue-specific backbone ϕ/ψ torsion angle distributions that closely resemble random coil distributions, the absence of a significantly elevated propensity for β-conformations in the C-terminal region of the peptide, and a small but distinct propensity for αL at K28. Our results suggest that the self-association of Aβ peptides into toxic oligomers is not driven by elevated propensities of the monomeric species to adopt β-strand-like conformations. Instead, the accelerated disappearance of Aβ NMR signals in D2O over H2O, particularly pronounced for Aβ(1-42), suggests that intermolecular interactions between the hydrophobic regions of the peptide dominate the aggregation process.

A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data

PubMed Central

Zeng, Jianyang; Roberts, Kyle E.; Zhou, Pei

2011-01-01

Abstract A major bottleneck in protein structure determination via nuclear magnetic resonance (NMR) is the lengthy and laborious process of assigning resonances and nuclear Overhauser effect (NOE) cross peaks. Recent studies have shown that accurate backbone folds can be determined using sparse NMR data, such as residual dipolar couplings (RDCs) or backbone chemical shifts. This opens a question of whether we can also determine the accurate protein side-chain conformations using sparse or unassigned NMR data. We attack this question by using unassigned nuclear Overhauser effect spectroscopy (NOESY) data, which records the through-space dipolar interactions between protons nearby in three-dimensional (3D) space. We propose a Bayesian approach with a Markov random field (MRF) model to integrate the likelihood function derived from observed experimental data, with prior information (i.e., empirical molecular mechanics energies) about the protein structures. We unify the side-chain structure prediction problem with the side-chain structure determination problem using unassigned NMR data, and apply the deterministic dead-end elimination (DEE) and A* search algorithms to provably find the global optimum solution that maximizes the posterior probability. We employ a Hausdorff-based measure to derive the likelihood of a rotamer or a pairwise rotamer interaction from unassigned NOESY data. In addition, we apply a systematic and rigorous approach to estimate the experimental noise in NMR data, which also determines the weighting factor of the data term in the scoring function derived from the Bayesian framework. We tested our approach on real NMR data of three proteins: the FF Domain 2 of human transcription elongation factor CA150 (FF2), the B1 domain of Protein G (GB1), and human ubiquitin. The promising results indicate that our algorithm can be applied in high-resolution protein structure determination. Since our approach does not require any NOE assignment, it can accelerate the NMR structure determination process. PMID:21970619

ESR Detection of optical dynamic nuclear polarization in GaAs/Al{sub x}Ga{sub 1-x}As quantum wells at unity filling factor in the quantum Hall effect

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vitkalov, Sergey A.; Bowers, C. Russell; Simmons, Jerry A.

2000-02-15

This paper presents a study of the enhancement of the Zeeman energy of two-dimensional (2D) conduction electrons near the {nu}=1 filling factor of the quantum Hall effect by optical dynamic nuclear polarization. The change in the Zeeman energy is determined from the Overhauser shift of the transport detected electron spin resonance in GaAs/Al{sub x}Ga{sub 1-x}As multiquantum wells. In a separate experiment the NMR signal enhancement factor is obtained by radio frequency detected nuclear magnetic resonance under similar conditions in the same sample. These measurements afford an estimation of the hyperfine coupling constant between the nuclei and 2D conduction electrons. (c)more » 2000 The American Physical Society.« less

Is there any difference in Amide and NOE CEST effects between white and gray matter at 7 T?

NASA Astrophysics Data System (ADS)

Khlebnikov, Vitaliy; Siero, Jeroen C. W.; Wijnen, Jannie; Visser, Fredy; Luijten, Peter R.; Klomp, Dennis W. J.; Hoogduin, Hans

2016-11-01

Measurement of Chemical Exchange Saturation Transfer (CEST) is providing tissue physiology dependent contrast, e.g. by looking at Amide and NOE (Nuclear Overhauser Enhancement) effects. CEST is unique in providing quantitative metabolite information at high imaging resolution. However, direct comparison of Amide and NOE effects between different tissues may result in wrong conclusions on the metabolite concentration due to the additional contributors to the observed CEST contrast, such as water content (WC) and water T1 relaxation (T1w). For instance, there are multiple contradictory reports in the literature on Amide and NOE effects in white matter (WM) and gray matter (GM) at 7 T. This study shows that at 7 T, tissue water T1 relaxation is a stronger contributor to CEST contrasts than WC. After water T1 correction, there was no difference in Amide effects between WM and GM, whereas WM/GM contrast was enhanced for NOE effects.

NMR and rotational angles in solution conformation of polypeptides

NASA Astrophysics Data System (ADS)

Bystrov, V. F.

1985-01-01

Professor San-Ichiro Mizushima and Professor Yonezo Morino's classical contributions provided unique means and firm basis for understanding of conformational states and internal rotation in polypeptide molecules. Now the NMR spectroscopy is the best choice to study molecular conformation, mechanism of action and structure-functional relationships of peptide and proteins in solution under conditions approaching those of their physiological environments. Crucial details of spatial structure and interactions of these molecules in solution are revealed by using proton-proton and carbon-proton vicinal coupling constants, proton nuclear Overhauser effect and spectral perturbation techniques. The results of NMR conformational analysis are presented for valinomycin "bracelet", gramicidin A double helices, honey-bee neurotoxin apamin, scorpion insectotoxins and snake neurotoxins of long and short types.

The structure of myristoylated Mason-Pfizer monkey virus matrix protein and the role of phosphatidylinositol-(4,5)-bisphosphate in its membrane binding.

PubMed

Prchal, Jan; Srb, Pavel; Hunter, Eric; Ruml, Tomáš; Hrabal, Richard

2012-10-26

We determined the solution structure of myristoylated Mason-Pfizer monkey virus matrix protein by NMR spectroscopy. The myristoyl group is buried inside the protein and causes a slight reorientation of the helices. This reorientation leads to the creation of a binding site for phosphatidylinositols. The interaction between the matrix protein and phosphatidylinositols carrying C(8) fatty acid chains was monitored by observation of concentration-dependent chemical shift changes of the affected amino acid residues, a saturation transfer difference experiment and changes in (31)P chemical shifts. No differences in the binding mode or affinity were observed with differently phosphorylated phosphatidylinositols. The structure of the matrix protein-phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P(2)] complex was then calculated with HADDOCK software based on the intermolecular nuclear Overhauser enhancement contacts between the ligand and the matrix protein obtained from a (13)C-filtered/(13)C-edited nuclear Overhauser enhancement spectroscopy experiment. PI(4,5)P(2) binding was not strong enough for triggering of the myristoyl-switch. The structural changes of the myristoylated matrix protein were also found to result in a drop in the oligomerization capacity of the protein. Copyright © 2012. Published by Elsevier Ltd.

A novel diarylheptanoid-bearing sesquiterpene moiety from the rhizomes of Alpinia officinarum.

PubMed

Wei, Na; Zhou, Zhonglin; Wei, Qing; Wang, Yong; Jiang, Jun; Zhang, Junqing; Wu, Lixiang; Dai, Shuiping; Li, Youbin

2016-10-01

A new diarylheptanoid analogue-bearing sesquiterpene moiety, named Alpinisin A, was isolated from the rhizomes of Alpinia officinarum Hance. The new structure was determined by various spectroscopic techniques (1)H-nuclear magnetic resonance ((1)H NMR), (13)C-attached proton test ((13)C-APT), heteronuclear single quantum coherence (HSQC), heteronuclear multiple bond correlation (HMBC), (1)H-(1)H correlation spectroscopy ((1)H-(1)HCOSY), nuclear overhauser effect spectroscopy (NOESY) and high resolution electrospray ionization mass spectrometry (HR-ESI-MS). The compound was tested for cytotoxic activity in vitro against human tumour cell lines (gastric carcinoma cell -7901 (SGC-7901), Michigan Cancer Foundation-7 (MCF-7) and Caski), which showed significant inhibitory effects with IC50 levels of 11.42, 15.14 and 14.78 μM, respectively. The novel chemical structure characterised with a diarylheptanoid linked to a chain-like sesquiterpenoid should be highlighted.

Mechanisms of Dynamic Nuclear Polarization in Insulating Solids

PubMed Central

Can, T.V.; Ni, Q.Z.; Griffin, R.G.

2015-01-01

Dynamic nuclear polarization (DNP) is a technique used to enhance signal intensities in NMR experiments by transferring the high polarization of electrons to their surrounding nuclei. The past decade has witnessed a renaissance in the development of DNP, especially at high magnetic fields, and its application in several areas including biophysics, chemistry, structural biology and materials science. Recent technical and theoretical advances have expanded our understanding of established experiments: for example, the cross effect DNP in samples spinning at the magic angle. Furthermore, new experiments suggest that our understanding of the Overhauser effect and its applicability to insulating solids needs to be re-examined. In this article, we summarize important results of the past few years and provide quantum mechanical explanations underlying these results. We also discuss future directions of DNP and current limitations, including the problem of resolution in protein spectra recorded at 80–100 K. PMID:25797002

Hepatoprotective activity of twelve novel 7'-hydroxy lignan glucosides from Arctii Fructus.

PubMed

Yang, Ya-Nan; Huang, Xiao-Ying; Feng, Zi-Ming; Jiang, Jian-Shuang; Zhang, Pei-Cheng

2014-09-17

Twelve novel 7'-hydroxy lignan glucosides (1-12), including two benzofuran-type neolignans, two 8-O-4' neolignans, two dibenzylbutyrolactone lignans, and six tetrahydrofuranoid lignans, together with six known lignan glucosides (13-18), were isolated from the fruit of Arctium lappa L. (Asteraceae), commonly known as Arctii Fructus. Their structures were elucidated using spectroscopy (1D and 2D NMR, MS, IR, ORD, and UV) and on the basis of chemical evidence. The absolute configurations of compounds 1-12 were confirmed using rotating frame nuclear overhauser effect spectroscopy (ROESY), the circular dichroic (CD) exciton chirality method, and Rh2(OCOCF3)4-induced CD spectrum analysis. All of the isolated compounds were tested for hepatoprotective effects against D-galactosamine-induced cytotoxicity in HL-7702 hepatic cells. Compounds 1, 2, 7-12, and 17 showed significantly stronger hepatoprotective activity than the positive control bicyclol at a concentration of 1 × 10(-5) M.

Direct NOE simulation from long MD trajectories.

PubMed

Chalmers, G; Glushka, J N; Foley, B L; Woods, R J; Prestegard, J H

2016-04-01

A software package, MD2NOE, is presented which calculates Nuclear Overhauser Effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected. Copyright © 2016 Elsevier Inc. All rights reserved.

Colloidal 3-Mercaptopropionic Acid Capped Lead Sulfide Quantum Dots in a Low Boiling Point Solvent.

PubMed

Reinhart, Chase C; Johansson, Erik

2017-04-26

Colloidal 3-mercaptopropionic acid (3-MPA) capped lead sulfide quantum dots were prepared in a variety of organic solvents stabilized with a quaternary ammonium halide salt. The stabilized colloids' optical properties were studied through optical absorption and emission spectroscopy and found to be dependent on both the concentration of a new ligand and stabilizer, and sample age. Nanocrystal ligand chemistry was studied through a combination of 1 H NMR and two-dimensional Nuclear Overhauser Effect Spectroscopy (NOESY) which revealed full displacement of the original oleate ligand to form a dynamically exchanging ligand shell. The colloids were studied optically and via NMR as they aged and revealed a quantitative conversion of monomeric 3-mercaptopropionic acid to its dimer, dithiodipropionic acid (dTdPA).

Theory and experimental results of transfer-NOE experiments. 1. The influence of the off rate versus cross-relaxation rates

NASA Astrophysics Data System (ADS)

Lippens, R. M.; Cerf, C.; Hallenga, K.

The theory of the transferred nuclear Overhauser effect is presented in the framework of an extended relaxation matrix representation. This matrix representation allows a coherent description of all one- and two-dimensional experiments. We present analytical solutions for the buildup of magnetization in the 2D transfer-NOE experiment, for all ratios of the off rate k to the cross-relaxation rates R involved. We show that systematic deviations in distance determination occur when the off rate becomes comparable to or smaller than the relaxation rates. Experimental results on the peptide/protein system oxytocin/neurophysin confirming this analysis are presented. The importance of residual mobility in the bound ligand, as demonstrated by the experimental data, is also discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Munro, S.L.; Andrews, P.R.; Craik, D.J.

The solution dynamics of a series of clinically potent antidepressants have been investigated by measuring /sup 13/C NMR relaxation parameters. Correlation times and internal motional rates were calculated from spin-lattice relaxation times and nuclear Overhauser effects for the protonated carbons in mianserin, imipramine-like antidepressants, and amitriptyline-like antidepressants. These data were interpreted in terms of overall molecular tumbling, internal rotations, and inherent flexibility of these structures. Of particular interest was the conformational variability of the tricyclic nucleus of the tricyclic antidepressants, where the data indicated a fivefold difference in mobility of the dimethylene bridge of imipramine-like antidepressants relative to amitriptyline-like compounds.more » The implications of such a difference in internal motions is discussed in relation to previous NMR studies and to the reported differences in pharmacological activity of these antidepressants.« less

New sesquiterpenes from Euonymus europaeus (Celastraceae).

PubMed

Descoins, Charles; Bazzocchi, Isabel López; Ravelo, Angel Gutiérrez

2002-02-01

A new sesquiterpene evoninate alkaloid (1), and two sesquiterpenes (2, 3) with a dihydro-beta-agarofuran skeleton, along with three known sesquiterpenes (4-6), were isolated from the seeds of Euonymus europaeus. Their structures were elucidated by high resolution mass analysis, and one- and two-dimensional (1D and 2D) NMR spectroscopy, including homonuclear and heteronuclear correlation [correlation spectroscopy (COSY), rotating frame Overhauser enhancement spectroscopy (ROESY), heteronuclear single quantum coherence (HSQC), and heteronuclear multiple bond correlation (HMBC)] experiments.

Characterization of an antibiotic produced by Bacillus subtilis JW-1 that suppresses Ralstonia solanacearum.

PubMed

Kwon, Jae Won; Kim, Shin Duk

2014-01-01

Bacillus subtilis JW-1 was isolated from rhizosphere soil as a potential biocontrol agent of bacterial wilt caused by Ralstonia solanacearum. Seed treatment followed by a soil drench application with this strain resulted in >80% reduction in bacterial wilt disease compared with that in the untreated control under greenhouse conditions. The antibacterial compound produced by strain JW-1 was purified by bioactivity-guided fractionation. Based on mass spectroscopy and nuclear magnetic resonance spectral data ((1)H, (13)C, (1)H-(1)H correlation spectroscopies, rotating frame nuclear Overhauser effect spectroscopy, and heteronuclear multiple-bond correlation spectroscopy), the structure of this compound was elucidated as a cyclic lipopeptide composed of a heptapeptide (Gln-Leu-Leu-Val-Asp-Leu-Leu) bonded to a β-hydroxy-iso-hexadecanoic acid arranged in a lactone ring system.

Overhauser enhanced magnetic resonance imaging for tumor oximetry: Coregistration of tumor anatomy and tissue oxygen concentration

NASA Astrophysics Data System (ADS)

Krishna, Murali C.; English, Sean; Yamada, Kenichi; Yoo, John; Murugesan, Ramachandran; Devasahayam, Nallathamby; Cook, John A.; Golman, Klaes; Ardenkjaer-Larsen, Jan Henrik; Subramanian, Sankaran; Mitchell, James B.

2002-02-01

An efficient noninvasive method for in vivo imaging of tumor oxygenation by using a low-field magnetic resonance scanner and a paramagnetic contrast agent is described. The methodology is based on Overhauser enhanced magnetic resonance imaging (OMRI), a functional imaging technique. OMRI experiments were performed on tumor-bearing mice (squamous cell carcinoma) by i.v. administration of the contrast agent Oxo63 (a highly derivatized triarylmethyl radical) at nontoxic doses in the range of 2-7 mmol/kg either as a bolus or as a continuous infusion. Spatially resolved pO2 (oxygen concentration) images from OMRI experiments of tumor-bearing mice exhibited heterogeneous oxygenation profiles and revealed regions of hypoxia in tumors (<10 mmHg; 1 mmHg = 133 Pa). Oxygenation of tumors was enhanced on carbogen (95% O2/5% CO2) inhalation. The pO2 measurements from OMRI were found to be in agreement with those obtained by independent polarographic measurements using a pO2 Eppendorf electrode. This work illustrates that anatomically coregistered pO2 maps of tumors can be readily obtained by combining the good anatomical resolution of water proton-based MRI, and the superior pO2 sensitivity of EPR. OMRI affords the opportunity to perform noninvasive and repeated pO2 measurements of the same animal with useful spatial (≈1 mm) and temporal (2 min) resolution, making this method a powerful imaging modality for small animal research to understand tumor physiology and potentially for human applications.

Influence of the nuclear Zeeman effect on mode locking in pulsed semiconductor quantum dots

NASA Astrophysics Data System (ADS)

Beugeling, Wouter; Uhrig, Götz S.; Anders, Frithjof B.

2017-09-01

The coherence of the electron spin in a semiconductor quantum dot is strongly enhanced by mode locking through nuclear focusing, where the synchronization of the electron spin to periodic pulsing is slowly transferred to the nuclear spins of the semiconductor material, mediated by the hyperfine interaction between these. The external magnetic field that drives the Larmor oscillations of the electron spin also subjects the nuclear spins to a Zeeman-like coupling, albeit a much weaker one. For typical magnetic fields used in experiments, the energy scale of the nuclear Zeeman effect is comparable to that of the hyperfine interaction, so that it is not negligible. In this work, we analyze the influence of the nuclear Zeeman effect on mode locking quantitatively. Within a perturbative framework, we calculate the Overhauser-field distribution after a prolonged period of pulsing. We find that the nuclear Zeeman effect can exchange resonant and nonresonant frequencies. We distinguish between models with a single type and with multiple types of nuclei. For the latter case, the positions of the resonances depend on the individual g factors, rather than on the average value.

Preventing Small Molecule Nucleation and Crystallization by Sequestering in a Micelle Corona

NASA Astrophysics Data System (ADS)

Li, Ziang; Johnson, Lindsay; Ricarte, Ralm; Yao, Letitia; Hillmyer, Marc; Bates, Frank; Lodge, Timothy

We exploited a blend of hydroxypropyl methylcellulose acetate succinate and poly(N-isopropylacrylamide) (PNIPAm) to improve the solubility and dissolution of a rapidly crystallizing model drug molecule phenytoin and observed synergistic effect in vitro at constant drug loading by varying the blending ratio. Dynamic and static light scattering experiments showed that PNIPAm self-assembled into micelles in aqueous solution. We believe that adding these PNIPAm micelles inhibited both nucleation and crystal growth of phenytoin based on the polarized light micrographs taken from the dissolution media. The drug-polymer intermolecular interaction was revealed by nuclear Overhauser effect spectroscopy and further quantified by diffusion ordered spectroscopy. We found that the phenytoin molecules were sequestered in aqueous solution by partitioning into the corona of the micelle. The blend strategy through the use of self-assembled micelles showcased in this study offers a new platform for designing advanced excipients for oral drug delivery. This study was funded by The Dow Chemical Company through Agreement 224249AT with the University of Minnesota.

New Butyrolactone Type Lignans from Arctii Fructus and Their Anti-inflammatory Activities.

PubMed

Yang, Ya-Nan; Huang, Xiao-Ying; Feng, Zi-Ming; Jiang, Jian-Shuang; Zhang, Pei-Cheng

2015-09-16

Arctiidilactone (1), a novel rare butyrolactone lignan with a 6-carboxyl-2-pyrone moiety, and 11 new butyrolactone lignans (2-12) were isolated from the fruits of Arctium lappa L., together with 5 known compounds (13-17). Their structures were elucidated by interpretation of their spectroscopic data (1D and 2D NMR, UV, IR, ORD, and HRESIMS) and comparison to literature data. The absolute configurations of compounds 1-12 were determined by a combination of rotating-frame nuclear Overhauser effect spectroscopy (ROESY), circular dichroism (CD) spectroscopy, and Rh2(OCOCF3)4-induced CD spectroscopy. All of the compounds were tested for their anti-inflammatory properties in terms of suppressing the production of NO in lipopolysaccharide-induced BV2 cells. Compounds 1, 6, 8, and 10 exhibited stronger anti-inflammatory effects than the positive control curcumin, particularly 1, which exhibited 75.51, 70.72, and 61.17% inhibition at 10, 1, and 0.1 μM, respectively.

Strategic Studies Quarterly. An Air Force-Sponsored Strategic Forum on National and International Security. Winter 2009. Volume 3, Number 4

DTIC Science & Technology

2009-01-01

leader of a party which has not been the dominant voice in shaping American foreign policy since Richard Nixon defeated Hubert Humphrey in the...others only think. Former Socialist foreign minister, Hubert Védrine, put it in particularly stark terms: Were France to become a “normal ally...Renate Grasse (Baden-Baden: Nomos Verlag, 2008), 233–60. 29. Le Monde, 4 October 2008. For a critical view, see Ronja Kempin and Marco Overhaus, “Kein

STD-NMR-Based Protein Engineering of the Unique Arylpropionate-Racemase AMDase G74C.

PubMed

Gaßmeyer, Sarah Katharina; Yoshikawa, Hiroyuki; Enoki, Junichi; Hülsemann, Nadine; Stoll, Raphael; Miyamoto, Kenji; Kourist, Robert

2015-06-23

Structure-guided protein engineering achieved a variant of the unique racemase AMDase G74C, with 40-fold increased activity in the racemisation of several arylaliphatic carboxylic acids. Substrate binding during catalysis was investigated by saturation-transfer-difference NMR (STD-NMR) spectroscopy. All atoms of the substrate showed interactions with the enzyme. STD-NMR measurements revealed distinct nuclear Overhauser effects in experiments with and without molecular conversion. The spectroscopic analysis led to the identification of several amino acid residues whose substitutions increased the activity of G74C. Single amino acid exchanges increased the activity moderately; structure-guided saturation mutagenesis yielded a quadruple mutant with a 40 times higher reaction rate. This study presents STD-NMR as versatile tool for the analysis of enzyme-substrate interactions in catalytically competent systems and for the guidance of protein engineering. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Using indirect covariance spectra to identify artifact responses in unsymmetrical indirect covariance calculated spectra.

PubMed

Martin, Gary E; Hilton, Bruce D; Blinov, Kirill A; Williams, Antony J

2008-02-01

Several groups of authors have reported studies in the areas of indirect and unsymmetrical indirect covariance NMR processing methods. Efforts have recently focused on the use of unsymmetrical indirect covariance processing methods to combine various discrete two-dimensional NMR spectra to afford the equivalent of the much less sensitive hyphenated 2D NMR experiments, for example indirect covariance (icv)-heteronuclear single quantum coherence (HSQC)-COSY and icv-HSQC-nuclear Overhauser effect spectroscopy (NOESY). Alternatively, unsymmetrical indirect covariance processing methods can be used to combine multiple heteronuclear 2D spectra to afford icv-13C-15N HSQC-HMBC correlation spectra. We now report the use of responses contained in indirect covariance processed HSQC spectra as a means for the identification of artifacts in both indirect covariance and unsymmetrical indirect covariance processed 2D NMR spectra. Copyright (c) 2007 John Wiley & Sons, Ltd.

Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field

PubMed Central

Eggimann, Becky L.; Vostrikov, Vitaly V.; Veglia, Gianluigi; Siepmann, J. Ilja

2013-01-01

We present a fast and simple protocol to obtain moderate-resolution backbone structures of helical proteins. This approach utilizes a combination of sparse backbone NMR data (residual dipolar couplings and paramagnetic relaxation enhancements) or EPR data with a residue-based force field and Monte Carlo/simulated annealing protocol to explore the folding energy landscape of helical proteins. By using only backbone NMR data, which are relatively easy to collect and analyze, and strategically placed spin relaxation probes, we show that it is possible to obtain protein structures with correct helical topology and backbone RMS deviations well below 4 Å. This approach offers promising alternatives for the structural determination of proteins in which nuclear Overha-user effect data are difficult or impossible to assign and produces initial models that will speed up the high-resolution structure determination by NMR spectroscopy. PMID:24639619

Multiple stable states of a periodically driven electron spin in a quantum dot using circularly polarized light

NASA Astrophysics Data System (ADS)

Korenev, V. L.

2011-06-01

The periodical modulation of circularly polarized light with a frequency close to the electron spin resonance frequency induces a sharp change of the single electron spin orientation. Hyperfine interaction provides a feedback, thus fixing the precession frequency of the electron spin in the external and the Overhauser field near the modulation frequency. The nuclear polarization is bidirectional and the electron-nuclear spin system (ENSS) possesses a few stable states. The same physics underlie the frequency-locking effect for two-color and mode-locked excitations. However, the pulsed excitation with mode-locked laser brings about the multitudes of stable states in ENSS in a quantum dot. The resulting precession frequencies of the electron spin differ in these states by the multiple of the modulation frequency. Under such conditions ENSS represents a digital frequency converter with more than 100 stable channels.

Large spin accumulation and crystallographic dependence of spin transport in single crystal gallium nitride nanowires

PubMed Central

Park, Tae-Eon; Park, Youn Ho; Lee, Jong-Min; Kim, Sung Wook; Park, Hee Gyum; Min, Byoung-Chul; Kim, Hyung-jun; Koo, Hyun Cheol; Choi, Heon-Jin; Han, Suk Hee; Johnson, Mark; Chang, Joonyeon

2017-01-01

Semiconductor spintronics is an alternative to conventional electronics that offers devices with high performance, low power and multiple functionality. Although a large number of devices with mesoscopic dimensions have been successfully demonstrated at low temperatures for decades, room-temperature operation still needs to go further. Here we study spin injection in single-crystal gallium nitride nanowires and report robust spin accumulation at room temperature with enhanced spin injection polarization of 9%. A large Overhauser coupling between the electron spin accumulation and the lattice nuclei is observed. Finally, our single-crystal gallium nitride samples have a trigonal cross-section defined by the (001), () and () planes. Using the Hanle effect, we show that the spin accumulation is significantly different for injection across the (001) and () (or ()) planes. This provides a technique for increasing room temperature spin injection in mesoscopic systems. PMID:28569767

Two-dimensional sup 1 H NMR studies on HPr protein from Staphylococcus aureus: Complete sequential assignments and secondary structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalbitzer, H.R.; Neidig, K.P.; Hengstenberg, W.

1991-11-19

Complete sequence-specific assignments of the {sup 1}H NMR spectrum of HPr protein from Staphylococcus aureus were obtained by two-dimensional NMR methods. Important secondary structure elements that can be derived from the observed nuclear Overhauser effects are a large antiparallel {beta}-pleated sheet consisting of four strands, A, B, C, D, a segment S{sub AB} consisting of an extended region around the active-center histidine (His-15) and an {alpha}-helix, a half-turn between strands B and C, a segment S{sub CD} which shows no typical secondary structure, and the {alpha}-helical, C-terminal segment S{sub term}. These general structural features are similar to those found earliermore » in HPr proteins from different microorganisms such as Escherichia coli, Bacillus subtilis, and Streptococcus faecalis.« less

Optically transmitted and inductively coupled electric reference to access in vivo concentrations for quantitative proton-decoupled ¹³C magnetic resonance spectroscopy.

PubMed

Chen, Xing; Pavan, Matteo; Heinzer-Schweizer, Susanne; Boesiger, Peter; Henning, Anke

2012-01-01

This report describes our efforts on quantification of tissue metabolite concentrations in mM by nuclear Overhauser enhanced and proton decoupled (13) C magnetic resonance spectroscopy and the Electric Reference To access In vivo Concentrations (ERETIC) method. Previous work showed that a calibrated synthetic magnetic resonance spectroscopy-like signal transmitted through an optical fiber and inductively coupled into a transmit/receive coil represents a reliable reference standard for in vivo (1) H magnetic resonance spectroscopy quantification on a clinical platform. In this work, we introduce a related implementation that enables simultaneous proton decoupling and ERETIC-based metabolite quantification and hence extends the applicability of the ERETIC method to nuclear Overhauser enhanced and proton decoupled in vivo (13) C magnetic resonance spectroscopy. In addition, ERETIC signal stability under the influence of simultaneous proton decoupling is investigated. The proposed quantification method was cross-validated against internal and external reference standards on human skeletal muscle. The ERETIC signal intensity stability was 100.65 ± 4.18% over 3 months including measurements with and without proton decoupling. Glycogen and unsaturated fatty acid concentrations measured with the ERETIC method were in excellent agreement with internal creatine and external phantom reference methods, showing a difference of 1.85 ± 1.21% for glycogen and 1.84 ± 1.00% for unsaturated fatty acid between ERETIC and creatine-based quantification, whereas the deviations between external reference and creatine-based quantification are 6.95 ± 9.52% and 3.19 ± 2.60%, respectively. Copyright © 2011 Wiley Periodicals, Inc.

Construction of 0.15 Tesla Overhauser Enhanced MRI.

PubMed

Tokunaga, Yuumi; Nakao, Motonao; Naganuma, Tatsuya; Ichikawa, Kazuhiro

2017-01-01

Overhauser enhanced MRI (OMRI) is one of the free radical imaging technologies and has been used in biomedical research such as for partial oxygen measurements in tumor, and redox status in acute oxidative diseases. The external magnetic field of OMRI is frequently in the range of 5-10 mTesla to ensure microwave penetration into small animals, and the S/N ratio is limited. In this study, a 0.15 Tesla OMRI was constructed and tested to improve the S/N ratio for a small sample, or skin measurement. Specification of the main magnet was as follows: 0.15 Tesla permanent magnet; gap size 160 mm; homogenous spherical volume of 80 mm in diameter. The OMRI resonator was designed based on TE 101 cavity mode and machined from a phosphorus deoxidized copper block for electron spin resonance (ESR) excitation and a solenoid transmission/receive resonator for NMR detection. The resonant frequencies and Q values were 6.38 MHz/150 and 4.31-4.41 GHz/120 for NMR and ESR, respectively. The Q values were comparable to those of conventional low field OMRI resonators at 15 mTesla. As expected, the MRI S/N ratio was improved by a factor of 30. Triplet dynamic nuclear polarization spectra were observed for 14 N carboxy-PROXYL, along the excitation microwave sweep. In the current setup, the enhancement factor was ca. 0.5. In conclusion, the results of this preliminary evaluation indicate that the 0.15 Tesla OMRI could be useful for free radical measurement for small samples.

Development of a PET/OMRI combined system for simultaneous imaging of positron and free radical probes for small animals.

PubMed

Yamamoto, Seiichi; Watabe, Tadashi; Ikeda, Hayato; Kanai, Yasukazu; Ichikawa, Kazuhiro; Nakao, Motonao; Kato, Katsuhiko; Hatazawa, Jun

2016-10-01

Positron emission tomography (PET) has high sensitivity for imaging radioactive tracer distributions in subjects. However, it is not possible to image free radical distribution in a subject by PET. Since free radicals are quite reactive, they are related to many diseases, including but not limited to cancer, inflammation, strokes, and heart disease. The Overhauser enhanced magnetic resonance imaging (OMRI) is so far the only method that images free radical distribution in vivo. By combining PET and OMRI, a new hybrid imaging modality might be developed that can simultaneously image the radioactive tracer and free radical distributions. For this purpose, the authors developed a PET/OMRI combined system for small animals. The developed PET/OMRI system used an optical fiber-based PET system combined with a permanent magnet-based OMRI system. The optical fiber-based PET system uses flexible optical fiber bundles. Eight optical fiber-based block detectors were arranged in a 56 mm diameter ring to form a PET system. The LGSO blocks were located inside the field-of-view (FOV) of the OMRI, and the position sensitive photomultiplier tubes were positioned behind the OMRI to minimize the interference between the PET and the OMRI. The OMRI system used a 0.0165 T permanent magnet. The system has an electron spin resonance coil to enhance the MRI signal using the Overhauser effect to image the free radical in the FOV of the PET/OMRI system. The spatial resolution and sensitivity of the optical fiber-based PET system were 1.2 mm FWHM and 1.2% at the central FOV, respectively. The OMRI system imaged the distribution of a nitroxyl radical (NXR) solution. The interference between PET and OMRI was small. Simultaneous imaging of the positron radiotracer and the NXR solution was successfully conducted with the developed PET/OMRI system for phantom and small animal studies. The authors developed a PET/OMRI combined system with the potential to provide interesting new results in molecular imaging research, such as in vivo molecular and free radical distributions.

Identification of Hepatoprotective Constituents in Limonium tetragonum and Development of Simultaneous Analysis Method using High-performance Liquid Chromatography

PubMed Central

Lee, Jae Sun; Kim, Yun Na; Kim, Na-Hyun; Heo, Jeong-Doo; Yang, Min Hye; Rho, Jung-Rae; Jeong, Eun Ju

2017-01-01

Background: Limonium tetragonum, a naturally salt-tolerant halophyte, has been studied recently and is of much interest to researchers due to its potent antioxidant and hepatoprotective activities. Objective: In the present study, we attempted to elucidate bioactive compounds from ethyl acetate (EtOAc) soluble fraction of L. tetragonum extract. Furthermore, the simultaneous analysis method of bioactive EtOAc fraction of L. tetragonum has been developed using high-performance liquid chromatography (HPLC). Materials and Methods: Thirteen compounds have been successfully isolated from EtOAc fraction of L. tetragonum, and the structures of 1–13 were elucidated by extensive one-dimensional and two-dimensional spectroscopic methods including 1H-NMR, 13C-NMR, 1H-1H COSY, heteronuclear single quantum coherence, heteronuclear multiple bond correlation, and nuclear Overhauser effect spectroscopy. Hepatoprotection of the isolated compounds against liver fibrosis was evaluated by measuring inhibition on hepatic stellate cells (HSCs) undergoing proliferation. Results: Compounds 1–13 were identified as gallincin (1), apigenin-3-O-β-D-galactopyranoside (2), quercetin (3), quercetin-3-O-β-D-galactopyranoside (4), (−)-epigallocatechin (5), (−)-epigallocatechin-3-gallate (6), (−)-epigallocatechin-3-(3″-O-methyl) gallate (7), myricetin-3-O-β-D-galactopyranoside (8), myricetin-3-O-(6″-O-galloyl)-β-D-galactopyranoside (9), myricetin-3-O-α-L-rhamnopyranoside (10), myricetin-3-O-(2″-O-galloyl)-α-L-rhamnopyranoside (11), myricetin-3-O-(3″-O-galloyl)-α-L-rhamnopyranoside (12), and myricetin-3-O-α-L-arabinopyranoside (13), respectively. All compounds except for 4, 8, and 10 are reported for the first time from this plant. Conclusion: Myricetin glycosides which possess galloyl substituent (9, 11, and 12) showed most potent inhibitory effects on the proliferation of HSCs. SUMMARY In the present study, we have successfully isolated 13 compounds from bioactive fraction of Limonium tetragonum. The structures of compounds isolated have been fully elucidated, and hepatoprotective activities of compounds against liver fibrosis were evaluated by measuring inhibition on hepatic stellate cells undergoing proliferation. Furthermore, the simultaneous analysis method of bioactive ethyl acetate fraction of L. tetragonum has been developed using HPLC. Ten compounds identified herein are reported for the first time from this plant. Abbreviations used: HSQC: Heteronuclear single quantum coherence; HMBC: Heteronuclear multiple bond correlation; NOESY: Nuclear Overhauser effect spectroscopy; EGCG: Epigallocatechin-3-gallate; EGC: Epigallocatechin; HSC: Hepatic stellate cell; MTT: 3-(4,5-dimethylthiazol-2-yl)-2.5-diphenyltetrazolium bromide. PMID:29200710

Nonlocal Nuclear Spin Quieting in Quantum Dot Molecules: Optically Induced Extended Two-Electron Spin Coherence Time.

PubMed

Chow, Colin M; Ross, Aaron M; Kim, Danny; Gammon, Daniel; Bracker, Allan S; Sham, L J; Steel, Duncan G

2016-08-12

We demonstrate the extension of coherence between all four two-electron spin ground states of an InAs quantum dot molecule (QDM) via nonlocal suppression of nuclear spin fluctuations in two vertically stacked quantum dots (QDs), while optically addressing only the top QD transitions. Long coherence times are revealed through dark-state spectroscopy as resulting from nuclear spin locking mediated by the exchange interaction between the QDs. Line shape analysis provides the first measurement of the quieting of the Overhauser field distribution correlating with reduced nuclear spin fluctuations.

Nonlocal Nuclear Spin Quieting in Quantum Dot Molecules: Optically Induced Extended Two-Electron Spin Coherence Time

NASA Astrophysics Data System (ADS)

Chow, Colin M.; Ross, Aaron M.; Kim, Danny; Gammon, Daniel; Bracker, Allan S.; Sham, L. J.; Steel, Duncan G.

2016-08-01

We demonstrate the extension of coherence between all four two-electron spin ground states of an InAs quantum dot molecule (QDM) via nonlocal suppression of nuclear spin fluctuations in two vertically stacked quantum dots (QDs), while optically addressing only the top QD transitions. Long coherence times are revealed through dark-state spectroscopy as resulting from nuclear spin locking mediated by the exchange interaction between the QDs. Line shape analysis provides the first measurement of the quieting of the Overhauser field distribution correlating with reduced nuclear spin fluctuations.

How hot? Systematic convergence of the replica exchange method using multiple reservoirs.

PubMed

Ruscio, Jory Z; Fawzi, Nicolas L; Head-Gordon, Teresa

2010-02-01

We have devised a systematic approach to converge a replica exchange molecular dynamics simulation by dividing the full temperature range into a series of higher temperature reservoirs and a finite number of lower temperature subreplicas. A defined highest temperature reservoir of equilibrium conformations is used to help converge a lower but still hot temperature subreplica, which in turn serves as the high-temperature reservoir for the next set of lower temperature subreplicas. The process is continued until an optimal temperature reservoir is reached to converge the simulation at the target temperature. This gradual convergence of subreplicas allows for better and faster convergence at the temperature of interest and all intermediate temperatures for thermodynamic analysis, as well as optimizing the use of multiple processors. We illustrate the overall effectiveness of our multiple reservoir replica exchange strategy by comparing sampling and computational efficiency with respect to replica exchange, as well as comparing methods when converging the structural ensemble of the disordered Abeta(21-30) peptide simulated with explicit water by comparing calculated Rotating Overhauser Effect Spectroscopy intensities to experimentally measured values. Copyright 2009 Wiley Periodicals, Inc.

Sesquiterpenes from the Saudi Red Sea: Litophyton arboreum with their cytotoxic and antimicrobial activities.

PubMed

Abou El-Kassem, Lamia T; Hawas, Usama W; El-Desouky, Samy K; Al-Farawati, Radwan

2018-01-26

A new pseudoguaiane-type sesquiterpene named litopharbol (1) was isolated from the methanolic extract of the Red Sea soft coral Litophyton arboreum, along with known sesquiterpenoids alismol (2), alismorientol B (3), teuhetenone A (4), and calamusin I (5); steroid, 24-methyl-cholesta-5,24(28)-diene-3β-ol (6), alkyl glyceryl ether, chimyl alcohol (7); sphingolipid, erythro-N-dodecanoyl-docosasphinga-(4E,8E)-dienine (8); and nitrogenous bases, thymine (9) and thymidine (10). The structures were determined on the basis of nuclear magnetic resonance (NMR) spectroscopic (1D and 2D NMR data including heteronuclear single quantum coherence spectroscopy, heteronuclear multiple-bond correlation spectroscopy, and nuclear Overhauser effect spectroscopy) and mass spectrometric analyses. Compounds 1-5 were explored for antimicrobial activity and cancer cell line sensitivity tests. Compound 1 exhibited antibacterial activity against Bacillus cereus with a minimum inhibition concentration of 1.8 μg/mL, whereas compound 3 showed significant potent cytotoxic effect against MCF-7 (breast cancer cells) with IC50 4.32 μM.

RDC-enhanced structure calculation of a β-heptapeptide in methanol.

PubMed

Rigling, Carla; Ebert, Marc-Olivier

2017-07-01

Residual dipolar couplings (RDCs) are a rich source of structural information that goes beyond the range covered by the nuclear Overhauser effect or scalar coupling constants. They can only be measured in partially oriented samples. RDC studies of peptides in organic solvents have so far been focused on samples in chloroform or DMSO. Here, we show that stretched poly(vinyl acetate) can be used for the partial alignment of a linear β-peptide with proteinogenic side chains in methanol. 1 D CH , 1 D NH , and 2 D HH RDCs were collected with this sample and included as restraints in a simulated annealing calculation. Incorporation of RDCs in the structure calculation process improves the long-range definition in the backbone of the resulting 3 14 -helix and uncovers side-chain mobility. Experimental side-chain RDCs of the central leucine and valine residues are in good agreement with predicted values from a local three-state model. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Individual Basepair Stability of DNA and RNA Studied by NMR-Detected Solvent Exchange

PubMed Central

Steinert, Hannah S.; Rinnenthal, Jörg; Schwalbe, Harald

2012-01-01

In this study, we have optimized NMR methodology to determine the thermodynamic parameters of basepair opening in DNA and RNA duplexes by characterizing the temperature dependence of imino proton exchange rates of individual basepairs. Contributions of the nuclear Overhauser effect to exchange rates measured with inversion recovery experiments are quantified, and the influence of intrinsic and external catalysis exchange mechanisms on the imino proton exchange rates is analyzed. Basepairs in DNA and RNA have an approximately equal stability, and the enthalpy and entropy values of their basepair dissociation are correlated linearly. Furthermore, the compensation temperature, Tc, which is derived from the slope of the correlation, coincides with the melting temperature, and duplex unfolding occurs at that temperature where all basepairs are equally thermodynamically stable. The impact of protium-deuterium exchange of the imino hydrogen on the free energy of RNA basepair opening is investigated, and it is found that two A·U basepairs show distinct fractionation factors. PMID:22713572

Solution Structure of Enterocin HF, an Antilisterial Bacteriocin Produced by Enterococcus faecium M3K31.

PubMed

Arbulu, Sara; Lohans, Christopher T; van Belkum, Marco J; Cintas, Luis M; Herranz, Carmen; Vederas, John C; Hernández, Pablo E

2015-12-16

The solution structure of enterocin HF (EntHF), a class IIa bacteriocin of 43 amino acids produced by Enterococcus faecium M3K31, was evaluated by CD and NMR spectroscopy. Purified EntHF was unstructured in water, but CD analysis supports that EntHF adopts an α-helical conformation when exposed to increasing concentrations of trifluoroethanol. Furthermore, NMR spectroscopy indicates that this bacteriocin adopts an antiparallel β-sheet structure in the N-terminal region (residues 1-17), followed by a well-defined central α-helix (residues 19-30) and a more disordered C-terminal end (residues 31-43). EntHF could be structurally organized into three flexible regions that might act in a coordinated manner. This is in agreement with the absence of long-range nuclear Overhauser effect signals between the β-sheet domain and the C-terminal end of the bacteriocin. The 3D structure recorded for EntHF fits emerging facts regarding target recognition and mode of action of class IIa bacteriocins.

A Novel Diterpene Glycoside with Nine Glucose Units from Stevia rebaudiana Bertoni

PubMed Central

Prakash, Indra; Ma, Gil; Bunders, Cynthia; Charan, Romila D.; Ramirez, Catherine; Devkota, Krishna P.; Snyder, Tara M.

2017-01-01

Following our interest in new diterpene glycosides with better taste profiles than that of Rebaudioside M, we have recently isolated and characterized Rebaudioside IX—a novel steviol glycoside—from a commercially-supplied extract of Stevia rebaudiana Bertoni. This molecule contains a hexasaccharide group attached at C-13 of the central diterpene core, and contains three additional glucose units when compared with Rebaudioside M. Here we report the complete structure elucidation—based on extensive Nuclear Magnetic Resonance (NMR) analysis (1H, 13C, Correlation Spectroscopy (COSY), Heteronuclear Single Quantum Coherence-Distortionless Enhancement Polarization Transfer (HSQC-DEPT), Heteronuclear Multiple Bond Correlation (HMBC), 1D Total Correlation Spectroscopy (TOCSY), Nuclear Overhauser Effect Spectroscopy (NOESY)) and mass spectral data—of this novel diterpene glycoside with nine sugar moieties and containing a relatively rare 1→6 α-linked glycoside. A steviol glycoside bearing nine glucose units is unprecedented in the literature, and could have an impact on the natural sweetener catalog. PMID:28146121

A Novel Diterpene Glycoside with Nine Glucose Units from Stevia rebaudiana Bertoni.

PubMed

Prakash, Indra; Ma, Gil; Bunders, Cynthia; Charan, Romila D; Ramirez, Catherine; Devkota, Krishna P; Snyder, Tara M

2017-01-31

Following our interest in new diterpene glycosides with better taste profiles than that of Rebaudioside M, we have recently isolated and characterized Rebaudioside IX-a novel steviol glycoside-from a commercially-supplied extract of Stevia rebaudiana Bertoni. This molecule contains a hexasaccharide group attached at C-13 of the central diterpene core, and contains three additional glucose units when compared with Rebaudioside M. Here we report the complete structure elucidation-based on extensive Nuclear Magnetic Resonance (NMR) analysis (1H, 13C, Correlation Spectroscopy (COSY), Heteronuclear Single Quantum Coherence-Distortionless Enhancement Polarization Transfer (HSQC-DEPT), Heteronuclear Multiple Bond Correlation (HMBC), 1D Total Correlation Spectroscopy (TOCSY), Nuclear Overhauser Effect Spectroscopy (NOESY)) and mass spectral data-of this novel diterpene glycoside with nine sugar moieties and containing a relatively rare 16 α-linked glycoside. A steviol glycoside bearing nine glucose units is unprecedented in the literature, and could have an impact on the natural sweetener catalog.

Lichenysin, a cyclooctapeptide occurring in Chinese liquor jiannanchun reduced the headspace concentration of phenolic off-flavors via hydrogen-bond interactions.

PubMed

Zhang, Rong; Wu, Qun; Xu, Yan

2014-08-20

Nonvolatile compounds play important roles in the quality of alcoholic beverages. In our previous work, a type of cyclooctapeptide lichenysin was newly identified in Chinese strong-aroma type liquor. In this work, it was found that lichenysin could selectively affect aroma volatility in strong-aroma type (Jiannanchun) liquor. Interaction of lichenysin and volatile phenolic compounds (off-odors in strong-aroma type liquor) was characterized using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS). HS-SPME results indicated that lichenysin very efficiently suppressed the volatility of phenolic compounds by 36-48% (P < 0.05). Thermodynamic analysis showed that the binding process was mainly mediated by hydrogen bonding. Furthermore, the mixture of lichenysin and 4-ethylguaiacol revealed intermolecular cross peaks between the aH (Val) of lichenysin and the 1H of 4-ethylguaiacol, by using nuclear Overhauser effect spectroscopy. This study will help to further understand the interaction mechanisms between flavor and nonvolatile matrix components in Chinese liquors.

Interactions of a designed peptide with lipopolysaccharide: Bound conformation and anti-endotoxic activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhunia, Anirban; Chua, Geok Lin; Domadia, Prerna N.

Designed peptides that would selectively interact with lipopolysaccharide (LPS) or endotoxin and fold into specific conformations could serve as important scaffolds toward the development of antisepsis compounds. Here, we describe solution structure of a designed amphipathic peptide, H{sub 2}N-YVKLWRMIKFIR-CONH{sub 2} (YW12D) in complex with endotoxin as determined by transferred nuclear Overhauser effect spectroscopy. The conformation of the isolated peptide is highly flexible, but undergoes a dramatic structural stabilization in the presence of LPS. Structure calculations reveal that the peptide presents two amphipathic surfaces in its bound state to LPS whereby each surface is characterized by two positive charges and amore » number of aromatic and/or aliphatic residues. ITC data suggests that peptide interacts with two molecules of lipid A. In activity assays, YW12D exhibits neutralization of LPS toxicity with very little hemolysis of red blood cells. Structural and functional properties of YW12D would be applicable in designing low molecular weight non-toxic antisepsis molecules.« less

Nuclear magnetic resonance spectroscopy in the structure elucidation and biosynthesis of natural products

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meksuriyen, D.

1988-01-01

Examination of a chloroform extract of Dracaena loureiri Gagnep (Agavaceae), a Thia medicinal plant possessing antibacterial activity, has led to the isolation of fifteen flavenoids. The biogenic relationships among these flavenoids isolated were briefly discussed. Definition of the skeleton and the unambiguous assignment of all of the protons of the isolates was achieved through extensive 2D-homonuclear chemical shift correlation, nuclear Overhauser effect (NOE) difference spectroscopy and 2D-NOE experiments. The {sup 1}H and {sup 13}C NMR spectra of staurosporine, a potent biologically active agent from Streptomyces staurosporeus, were unambiguously assigned by using 2D homonuclear chemical shift correlation, NOE, {sup 1}H-detected heteronuclearmore » multiple-quantum coherence via direct coupling and via multiple-bond coupling for resonance assignments of protonated and nonprotonated carbons, respectively. S. Staurosporeus was found to utilize endogenous and exogenous D- and L-isomers of trytophan in the production of staurosporine. The biosynthesis of staurosporine was examined by employing carbon-14, tritium, and carbon-13 labeled precursors.« less

Nanometer-scale water- and proton-diffusion heterogeneities across water channels in polymer electrolyte membranes.

PubMed

Song, Jinsuk; Han, Oc Hee; Han, Songi

2015-03-16

Nafion, the most widely used polymer for electrolyte membranes (PEMs) in fuel cells, consists of a fluorocarbon backbone and acidic groups that, upon hydration, swell to form percolated channels through which water and ions diffuse. Although the effects of the channel structures and the acidic groups on water/ion transport have been studied before, the surface chemistry or the spatially heterogeneous diffusivity across water channels has never been shown to directly influence water/ion transport. By the use of molecular spin probes that are selectively partitioned into heterogeneous regions of the PEM and Overhauser dynamic nuclear polarization relaxometry, this study reveals that both water and proton diffusivity are significantly faster near the fluorocarbon and the acidic groups lining the water channels than within the water channels. The concept that surface chemistry at the (sub)nanometer scale dictates water and proton diffusivity invokes a new design principle for PEMs. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Compact oleic acid in HAMLET.

PubMed

Fast, Jonas; Mossberg, Ann-Kristin; Nilsson, Hanna; Svanborg, Catharina; Akke, Mikael; Linse, Sara

2005-11-07

HAMLET (human alpha-lactalbumin made lethal to tumor cells) is a complex between alpha-lactalbumin and oleic acid that induces apoptosis in tumor cells, but not in healthy cells. Heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine the structure of 13C-oleic acid in HAMLET, and to study the 15N-labeled protein. Nuclear Overhauser enhancement spectroscopy shows that the two ends of the fatty acid are in close proximity and close to the double bond, indicating that the oleic acid is bound to HAMLET in a compact conformation. The data further show that HAMLET is a partly unfolded/molten globule-like complex under physiological conditions.

Evaluation of the photoprotective effect of β-cyclodextrin on the emission of volatile degradation products of ranitidine.

PubMed

Jamrógiewicz, Marzena; Wielgomas, Bartosz; Strankowski, Michał

2014-09-01

The process of the photo-excitation of ranitidine hydrochloride (RAN) in a solid state makes visible changes to its colour and generates an unpleasant odour. The purpose of the present study was to observe the protective effects of β-cyclodextrin (CD) complexation as well as the effect of the mixture of two stoichiometries 1:1 and 1:2 (RAN:CD, IC) on the photostability of samples in a solid state. Samples of inclusion complexes (IC) and physical mixtures (PM) were prepared and irradiated for 48h in a Suntest CPS+ chamber. Irradiated samples were analyzed using nuclear magnetic resonance ((1)H NMR), infrared spectroscopy (FT-IR), the differential scanning calorimetry method (DSC) and thermogravimetry analysis (TGA). Volatiles were monitored with the use of headspace-solid phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). The protective effect of CD was noticed with respect to IC, and also PM. Achieved photostabilization of complexed RAN against photodegradation could be explained due to either the inclusion of the furan part of RAN into the CD cavity as shown by the (1)H NMR ROESY (rotation frame nuclear Overhauser effect spectroscopy) spectrum or the screening effect of CD. FT-IR spectra, DSC curves and microscope images of irradiated samples of protected RAN did not indicate any physical changes, such as phase transfer. Copyright © 2014 Elsevier B.V. All rights reserved.

Smart, Sustainable, and Ecofriendly Chemical Design of Fully Bio-Based Thermally Stable Thermosets Based on Benzoxazine Chemistry.

PubMed

Froimowicz, Pablo; R Arza, Carlos; Han, Lu; Ishida, Hatsuo

2016-08-09

A smart synthetic chemical design incorporating furfurylamine, a natural renewable amine, into a partially bio-based coumarin-containing benzoxazine is presented. The versatility of the synthetic approach is shown to be flexible and robust enough to be successful under more ecofriendly reaction conditions by replacing toluene with ethanol as the reaction solvent and even under solventless conditions. The chemical structure of this coumarin-furfurylamine-containing benzoxazine is characterized by FTIR, (1) H NMR spectroscopy and two-dimensional (1) H-(1) H nuclear Overhauser effect spectroscopy (2D (1) H-(1) H NOESY). The thermal properties of the resin toward polymerization are characterized by differential scanning calorimetry (DSC) and the thermal stability of the resulting polymers by thermogravimetric analysis (TGA). The results reveal that the furanic moiety induces a co-operative activating effect, thus lowering the polymerization temperature and also contributes to a better thermal stability of the resulting polymers. These results, in addition to those of natural renewable benzoxazine resins reviewed herein, highlight the positive and beneficial implication of designing novel bio-based polybenzoxazine and possibly other thermosets with desirable and competitive properties. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Double resonance calibration of g factor standards: Carbon fibers as a high precision standard

NASA Astrophysics Data System (ADS)

Herb, Konstantin; Tschaggelar, Rene; Denninger, Gert; Jeschke, Gunnar

2018-04-01

The g factor of paramagnetic defects in commercial high performance carbon fibers was determined by a double resonance experiment based on the Overhauser shift due to hyperfine coupled protons. Our carbon fibers exhibit a single, narrow and perfectly Lorentzian shaped ESR line and a g factor slightly higher than gfree with g = 2.002644 =gfree · (1 + 162ppm) with a relative uncertainty of 15ppm . This precisely known g factor and their inertness qualify them as a high precision g factor standard for general purposes. The double resonance experiment for calibration is applicable to other potential standards with a hyperfine interaction averaged by a process with very short correlation time.

A ocean bottom vector magnetometer

NASA Astrophysics Data System (ADS)

Wang, Xiaomei; Teng, Yuntian; Wang, Chen; Ma, Jiemei

2017-04-01

The new development instrument with a compact spherical coil system and Overhauser magnetometer for measuring the total strength of the magnetic field and the vectors of strength, Delta inclination - Delta declination, meanwhile we also use a triaxial fluxgate instrument of the traditional instrument for geomagnetic vector filed measurement. The advantages of this method are be calibrated by each other and get good performances with automatic operation, good stability and high resolution. Firstly, a brief description of the instrument measurement principles and the key technologies are given. The instrument used a spherical coil system with 34 coils to product the homogeneous volume inside the coils which is large enough to accommodate the sensor of Overhauser total field sensor; the rest of the footlocker-sized ocean-bottom vector magnetometer consists of equipment to run the sensors and records its data (batteries and a data logger), weight to sink it to the sea floor, a remote-controlled acoustic release and flotation to bring the instrument back to the surface. Finally, the accuracy of the instrument was tested in the Geomagnetic station, and the measurement accuracies of total strength and components were better than 0.2nT and 1nT respectively. The figure 1 shows the development instrument structure. it includes six thick glass spheres which protect the sensor, data logger and batteries from the pressures of the deep sea, meanwhile they also provide recycling positive buoyancy; To cushion the glass, the spheres then go inside yellow plastic "hardhats". The triaxial fluxgate is inside No.1 glass spheres, data logger and batteries are inside No.2 glass spheres, the new vector sensor is inside No.3 glass spheres, acoustic communication unit is inside No.4 glass spheres, No.5 and No.6 glass spheres are empty which only provide recycling positive buoyancy. The figure 2 shows the development instrument Physical photo.

Comparative NMR analysis of the decadeoxynucleotide d-(GCATTAATGC)2 and an analogue containing 2-aminoadenine.

PubMed Central

Chazin, W J; Rance, M; Chollet, A; Leupin, W

1991-01-01

The dodecadeoxynucleotide duplex d-(GCATTAATGC)2 has been prepared with all adenine bases replaced by 2-NH2-adenine. This modified duplex has been characterized by nuclear magnetic resonance (NMR) spectroscopy. Complete sequence-specific 1H resonance assignments have been obtained by using a variety of 2D NMR methods. Multiple quantum-filtered and multiple quantum experiments have been used to completely assign all sugar ring protons, including 5'H and 5'H resonances. The assignments form the basis for a detailed comparative analysis of the 1H NMR parameters of the modified and parent duplex. The structural features of both decamer duplexes in solution are characteristic of the B-DNA family. The spin-spin coupling constants in the sugar rings and the relative spatial proximities of protons in the bases and sugars (as determined from the comparison of corresponding nuclear Overhauser effects) are virtually identical in the parent and modified duplexes. Thus, substitution by this adenine analogue in oligonucleotides appears not to disturb the global or local conformation of the DNA duplex. PMID:1945828

Wightianines A-E, dihydro-β-agarofuran sesquiterpenes from Parnassia wightiana, and their antifungal and insecticidal activities.

PubMed

Wang, Dong-Mei; Zhang, Cheng-Chen; Zhang, Qiang; Shafiq, Nusrat; Pescitelli, Gennaro; Li, Deng-Wu; Gao, Jin-Ming

2014-07-16

Five new sesquiterpene polyol esters with a dihydro-β-agarofuran skeleton, designated as wightianines A-E (1-5), besides two known compounds, were isolated from the methanolic extract of the whole plant of the traditional herbal medicine Parnassia wightiana Wall. The structures of the isolated compounds were elucidated on the basis of spectroscopic analyses, including two-dimensional nuclear magnetic resonance techniques (correlation spectroscopy, heteronuclear multiple-quantum coherence, nuclear Overhauser effect spectrometry, and heteronuclear multiple-bond correlation) and electronic circular dichroism studies. The antifungal and insecticidal activities of five compounds were evaluated against several plant pathogenic fungi and armyworm larvae (Mythimna separata Walker). Among the test metabolites, compounds 2 and 7 both exhibited potent antifungal activity against the phytopathogenic fungus Cytospora sp. with minimum inhibitory concentration values of 0.78 μg/mL, which are equal to the two positive controls, hymexazol and carbendazim. However, no insecticidal activity of the test compounds was observed in the present study. Compounds 2 and 7 could be promising leads for developing new fungicides against agriculturally important fungus Cytospora sp.

A definitive analytical spectroscopic study of Indian yellow, an ancient pigment used for dating purposes.

PubMed

de Faria, Dalva L A; Edwards, Howell G M; Careaga, Valeria; Walt, Nicholas; Maier, Marta S

2017-02-01

The Raman spectrum of tartrazine has been mistakenly reported as being that of Indian yellow in the literature, which has serious consequences for the identification of this pigment in art works regarding their authentication. Unlike tartrazine, Indian yellow (a natural mixture of the magnesium and calcium salts of euxanthic acid) exhibits in its Raman spectrum a strong fluorescent background when visible excitation is used, however, excitation in the near infrared (1064nm) permitted the observation of the Raman bands from the raw pigment with the main features placed at 1346, 1368, 1425, 1441 and 1626cm -1 . Indian yellow identification was assured by 1 H and 13 C Nuclear Magnetic Resonance characterization and the complete assignment of the proton and carbon resonances was accomplished using heteronuclear single quantum correlation (HSQC), heteronuclear multiple bond correlation (HMBC), nuclear overhauser effect spectroscopy (NOESY) and 1 H- 1 H correlation spectroscopy (COSY). Scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) and X-ray fluorescence (XRF) analyzes were also conducted on a genuine sample of this historical pigment. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Structures and functions of proteins and nucleic acids in protein biosynthesis

NASA Astrophysics Data System (ADS)

Miyazawa, Tatsuo; Yokoyama, Shigeyuki

Infrared and Raman spectroscopy is useful for studying helical conformations of polypeptides, which are determined by molecular structure parameters. Nuclear magnetic resonance spectroscopy, as well as X-ray analysis, is now established to be important for conformation studies of proteins and nucleic acids in solution. This article is mainly concerned with the conformational aspect and function regulation in protein biosynthesis. The strict recognition of transfer ribonucleic acid (tRNA) by aminoacyl-tRNA synthetase (ARS) is achieved by multi-step mutual adaptation. The conformations of ARS-bound amino acids have been elucidated by transferred nuclear Overhauser effect analysis. Aminoacyl-tRNA takes the 3‧-isomeric form in the polypeptide chain elongation cycle. The regulation of codon recognition by post-transcriptional modification is achieved by conversion of the conformational characteristic of the anticodon of tRNA. The cytidine → lysidine modification of the anticodon of minor isoleucine tRNA concurrently converts the amino acid specificity and the codon specificity. As novel protein engineering, a basic strategy has been established for in vivo biosynthesis of proteins that are substituted with unnatural amino acids (alloproteins).

DNP enhanced NMR with flip-back recovery

NASA Astrophysics Data System (ADS)

Björgvinsdóttir, Snædís; Walder, Brennan J.; Pinon, Arthur C.; Yarava, Jayasubba Reddy; Emsley, Lyndon

2018-03-01

DNP methods can provide significant sensitivity enhancements in magic angle spinning solid-state NMR, but in systems with long polarization build up times long recycling periods are required to optimize sensitivity. We show how the sensitivity of such experiments can be improved by the classic flip-back method to recover bulk proton magnetization following continuous wave proton heteronuclear decoupling. Experiments were performed on formulations with characteristic build-up times spanning two orders of magnitude: a bulk BDPA radical doped o-terphenyl glass and microcrystalline samples of theophylline, L-histidine monohydrochloride monohydrate, and salicylic acid impregnated by incipient wetness. For these systems, addition of flip-back is simple, improves the sensitivity beyond that provided by modern heteronuclear decoupling methods such as SPINAL-64, and provides optimal sensitivity at shorter recycle delays. We show how to acquire DNP enhanced 2D refocused CP-INADEQUATE spectra with flip-back recovery, and demonstrate that the flip-back recovery method is particularly useful in rapid recycling regimes. We also report Overhauser effect DNP enhancements of over 70 at 592.6 GHz/900 MHz.

Blowpipe Mineralogy for Physics/Environment: Highest-Possible-Tc SuperConductor (Beyond: (but via!!!) MgB2, Cuprates, Pnictides) Quest; BOTH PERMANENT FOREVER Carb-IDES SOLID-State Sequestration AND Drought(s)-Elimination

NASA Astrophysics Data System (ADS)

Segler, Kurt; Williams, Wendell; Siegel, Edward

2011-03-01

Detailed are old blowpipe new applications: charcoal-block reduction of borates to yield ("N-NW" of MgB2) Overhauser-[PR 35,1,411(1987); Intl.J.Mod.Phys.1, 2 & 4, 927(1987)]-"land" predicted high-EST-POSSIBLE Tc SC "LiD2"; very-early: Siegel[Phys.Stat.Sol.(a)11,45(1972);Semiconductors.and Insulators 5: 39,47,62(1979)] carb-IDES SOLID-state phase-TRANSITIONED CHEMICALLY-REDOX"-REACTED STABLE PERMANENT LONG-term NOT "CO2" BUT C-sequestration: PROFITABLE "Grab and Sell" TRUMPS "cap and trade"!!!; Mott alloying/vertical metal-insulator transitions in "borax-(GLASS)-beads"; and very-earlySiegel [{3rd Intl.Conf.Alt.Energy }(1980)-vol.5/p.459!!!] "FLYING-WATER" Hindenberg-effect (H2-UP;H2O-DOWN) via Hydrogen-maximal-Archimedes-buoyancy "chemical-rain-in-pipelines", only via Siegel proprietary "magnetic-hydrogen-valve"(MHV): Renewables-Hydrogen-Water flexible versatile agile scaleable retrofitable integrated operating-system for PERMANENT drought(s)-elimination FOREVER!!!

Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding.

PubMed

Adrian, Michael; Winnerdy, Fernaldo Richtia; Heddi, Brahim; Phan, Anh Tuân

2017-08-22

Nucleic acids are dynamic molecules whose functions may depend on their conformational fluctuations and local motions. In particular, amino groups are dynamic components of nucleic acids that participate in the formation of various secondary structures such as G-quadruplexes. Here, we present a cost-efficient NMR method to quantify the rotational dynamics of guanine amino groups in G-quadruplex nucleic acids. An isolated spectrum of amino protons from a specific tetrad-bound guanine can be extracted from the nuclear Overhauser effect spectroscopy spectrum based on the close proximity between the intra-residue imino and amino protons. We apply the method in different structural contexts of G-quadruplexes and their complexes. Our results highlight the role of stacking and hydrogen-bond interactions in restraining amino-group rotation. The measurement of the rotation rate of individual amino groups could give insight into the dynamic processes occurring at specific locations within G-quadruplex nucleic acids, providing valuable probes for local structure, dynamics, and ligand binding. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Automation of NMR structure determination of proteins.

PubMed

Altieri, Amanda S; Byrd, R Andrew

2004-10-01

The automation of protein structure determination using NMR is coming of age. The tedious processes of resonance assignment, followed by assignment of NOE (nuclear Overhauser enhancement) interactions (now intertwined with structure calculation), assembly of input files for structure calculation, intermediate analyses of incorrect assignments and bad input data, and finally structure validation are all being automated with sophisticated software tools. The robustness of the different approaches continues to deal with problems of completeness and uniqueness; nevertheless, the future is very bright for automation of NMR structure generation to approach the levels found in X-ray crystallography. Currently, near completely automated structure determination is possible for small proteins, and the prospect for medium-sized and large proteins is good. Copyright 2004 Elsevier Ltd.

The first observation of Carbon-13 spin noise spectra

PubMed Central

Schlagnitweit, Judith; Müller, Norbert

2012-01-01

We demonstrate the first 13C NMR spin noise spectra obtained without any pulse excitation by direct detection of the randomly fluctuating noise from samples in a cryogenically cooled probe. Noise power spectra were obtained from 13C enriched methanol and glycerol samples at 176 MHz without and with 1H decoupling, which increases the sensitivity without introducing radio frequency interference with the weak spin noise. The multiplet amplitude ratios in 1H coupled spectra indicate that, although pure spin noise prevails in these spectra, the influence of absorbed circuit noise is still significant at the high concentrations used. In accordance with the theory heteronuclear Overhauser enhancements are absent from the 1H-decoupled 13C spin noise spectra. PMID:23041799

The binding domain of the HMGB1 inhibitor carbenoxolone: Theory and experiment

NASA Astrophysics Data System (ADS)

Mollica, Luca; Curioni, Alessandro; Andreoni, Wanda; Bianchi, Marco E.; Musco, Giovanna

2008-05-01

We present a combined computational and experimental study of the interaction of the Box A of the HMGB1 protein and carbenoxolone, an inhibitor of its pro-inflammatory activity. The computational approach consists of classical molecular dynamics (MD) simulations based on the GROMOS force field with quantum-refined (QRFF) atomic charges for the ligand. Experimental data consist of fluorescence intensities, chemical shift displacements, saturation transfer differences and intermolecular Nuclear Overhauser Enhancement signals. Good agreement is found between observations and the conformation of the ligand-protein complex resulting from QRFF-MD. In contrast, simple docking procedures and MD based on the unrefined force field provide models inconsistent with experiment. The ligand-protein binding is dominated by non-directional interactions.

Application of ex situ dynamic nuclear polarization in studying small molecules.

PubMed

Ludwig, Christian; Marin-Montesinos, Ildefonso; Saunders, Martin G; Emwas, Abdul-Hamid; Pikramenou, Zoe; Hammond, Stephen P; Günther, Ulrich L

2010-06-14

Dynamic nuclear polarization (DNP) has become an attractive technique to boost the sensitivity of NMR experiments. In the case of ex situ polarizations two-dimensional (2D) spectra are limited by the short lifetime of the polarization after dissolution and sample transfer to a high field NMR magnet. This limitation can be overcome by various approaches. Here we show how the use of (13)C-labelled acetyl tags can help to obtain 2D-HMQC spectra for many small molecules, owing to a nuclear Overhauser enhancement between (13)C spins originating from the long-lived carbonyl carbon, which extends the lifetimes of other (13)C spins with shorter longitudinal relaxation times. We also show an alternative approach of using an optimized polarization matrix.

Trifasciatosides A-J, Steroidal Saponins from Sansevieria trifasciata.

PubMed

Teponno, Rémy Bertrand; Tanaka, Chiaki; Jie, Bai; Tapondjou, Léon Azefack; Miyamoto, Tomofumi

2016-01-01

Four previously unreported steroidal saponins, trifasciatosides A-D (1-4), three pairs of previously undescribed steroidal saponins, trifasciatosides E-J (5a, b-7a, b) including acetylated ones, together with twelve known compounds were isolated from the n-butanol soluble fraction of the methanol extract of Sansevieria trifasciata. Their structures were elucidated on the basis of detailed spectroscopic analysis, including (1)H-NMR, (13)C-NMR, (1)H-(1)H correlated spectroscopy (COSY), heteronuclear single quantum coherence (HSQC), heteronuclear multiple bond connectivity (HMBC), total correlated spectroscopy (TOCSY), nuclear Overhauser enhancement and exchange spectroscopy (NOESY), electrospray ionization-time of flight (ESI-TOF)-MS and chemical methods. Compounds 2, 4, and 7a, b exhibited moderate antiproliferative activity against HeLa cells.

Self-sustaining dynamical nuclear polarization oscillations in quantum dots.

PubMed

Rudner, M S; Levitov, L S

2013-02-22

Early experiments on spin-blockaded double quantum dots revealed robust, large-amplitude current oscillations in the presence of a static (dc) source-drain bias. Despite experimental evidence implicating dynamical nuclear polarization, the mechanism has remained a mystery. Here we introduce a minimal albeit realistic model of coupled electron and nuclear spin dynamics which supports self-sustained oscillations. Our mechanism relies on a nuclear spin analog of the tunneling magnetoresistance phenomenon (spin-dependent tunneling rates in the presence of an inhomogeneous Overhauser field) and nuclear spin diffusion, which governs dynamics of the spatial profile of nuclear polarization. The proposed framework naturally explains the differences in phenomenology between vertical and lateral quantum dot structures as well as the extremely long oscillation periods.

MR imaging of a novel NOE-mediated magnetization transfer with water in rat brain at 9.4 T.

PubMed

Zhang, Xiao-Yong; Wang, Feng; Jin, Tao; Xu, Junzhong; Xie, Jingping; Gochberg, Daniel F; Gore, John C; Zu, Zhongliang

2017-08-01

To detect, map, and quantify a novel nuclear Overhauser enhancement (NOE)-mediated magnetization transfer (MT) with water at approximately -1.6 ppm [NOE(-1.6)] in rat brain using MRI. Continuous wave MT sequences with a variety of radiofrequency irradiation powers were optimized to achieve the maximum contrast of this NOE(-1.6) effect at 9.4 T. The distribution of effect magnitudes, resonance frequency offsets, and line widths in healthy rat brains and the differences of the effect between tumors and contralateral normal brains were imaged and quantified using a multi-Lorentzian fitting method. MR measurements on reconstituted model phospholipids as well as two cell lines (HEK293 and 9L) were also performed to investigate the possible molecular origin of this NOE. Our results suggest that the NOE(-1.6) effect can be detected reliably in rat brain. Pixel-wise fittings demonstrated the regional variations of the effect. Measurements in a rodent tumor model showed that the amplitude of NOE(-1.6) in brain tumor was significantly diminished compared with that in normal brain tissue. Measurements of reconstituted phospholipids suggest that this effect may originate from choline phospholipids. NOE(-1.6) could be used as a new biomarker for the detection of brain tumor. Magn Reson Med 78:588-597, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

(13)C MRS of human brain at 7 Tesla using [2-(13)C]glucose infusion and low power broadband stochastic proton decoupling.

PubMed

Li, Shizhe; An, Li; Yu, Shao; Ferraris Araneta, Maria; Johnson, Christopher S; Wang, Shumin; Shen, Jun

2016-03-01

Carbon-13 ((13)C) MR spectroscopy (MRS) of the human brain at 7 Tesla (T) may pose patient safety issues due to high radiofrequency (RF) power deposition for proton decoupling. The purpose of present work is to study the feasibility of in vivo (13)C MRS of human brain at 7 T using broadband low RF power proton decoupling. Carboxylic/amide (13)C MRS of human brain by broadband stochastic proton decoupling was demonstrated on a 7 T scanner. RF safety was evaluated using the finite-difference time-domain method. (13)C signal enhancement by nuclear Overhauser effect (NOE) and proton decoupling was evaluated in both phantoms and in vivo. At 7 T, the peak amplitude of carboxylic/amide (13)C signals was increased by a factor of greater than 4 due to the combined effects of NOE and proton decoupling. The 7 T (13)C MRS technique used decoupling power and average transmit power of less than 35 watts (W) and 3.6 W, respectively. In vivo (13)C MRS studies of human brain can be performed at 7 T, well below the RF safety threshold, by detecting carboxylic/amide carbons with broadband stochastic proton decoupling. © 2015 Wiley Periodicals, Inc.

Spin Choreography: Basic Steps in High Resolution NMR (by Ray Freeman)

NASA Astrophysics Data System (ADS)

Minch, Michael J.

1998-02-01

There are three orientations that NMR courses may take. The traditional molecular structure course focuses on the interpretation of spectra and the use of chemical shifts, coupling constants, and nuclear Overhauser effects (NOE) to sort out subtle details of structure and stereochemistry. Courses can also focus on the fundamental quantum mechanics of observable NMR parameters and processes such a spin-spin splitting and relaxation. More recently there are courses devoted to the manipulation of nuclear spins and the basic steps of one- and two-dimensional NMR experiments. Freeman's book is directed towards the latter audience. Modern NMR methods offer a myriad ways to extract information about molecular structure and motion by observing the behavior of nuclear spins under a variety of conditions. In Freeman's words: "We can lead the spins through an intricate dance, carefully programmed in advance, to enhance, simplify, correlate, decouple, edit or assign NMR spectra." This is a carefully written, well-illustrated account of how this dance is choreographed by pulse programming, double resonance, and gradient effects. Although well written, this book is not an easy read; every word counts. It is recommended for graduate courses that emphasize the fundamentals of magnetic resonance. It is not a text on interpretation of spectra.

Effect of bisecting GlcNAc and core fucosylation on conformational properties of biantennary complex-type N-glycans in solution.

PubMed

Nishima, Wataru; Miyashita, Naoyuki; Yamaguchi, Yoshiki; Sugita, Yuji; Re, Suyong

2012-07-26

The introduction of bisecting GlcNAc and core fucosylation in N-glycans is essential for fine functional regulation of glycoproteins. In this paper, the effect of these modifications on the conformational properties of N-glycans is examined at the atomic level by performing replica-exchange molecular dynamics (REMD) simulations. We simulate four biantennary complex-type N-glycans, namely, unmodified, two single-substituted with either bisecting GlcNAc or core fucose, and disubstituted forms. By using REMD as an enhanced sampling technique, five distinct conformers in solution, each of which is characterized by its local orientation of the Manα1-6Man glycosidic linkage, are observed for all four N-glycans. The chemical modifications significantly change their conformational equilibria. The number of major conformers is reduced from five to two and from five to four upon the introduction of bisecting GlcNAc and core fucosylation, respectively. The population change is attributed to specific inter-residue hydrogen bonds, including water-mediated ones. The experimental NMR data, including nuclear Overhauser enhancement and scalar J-coupling constants, are well reproduced taking the multiple conformers into account. Our structural model supports the concept of "conformer selection", which emphasizes the conformational flexibility of N-glycans in protein-glycan interactions.

13C MRS of Human Brain at 7 Tesla Using [2-13C]Glucose Infusion and Low Power Broadband Stochastic Proton Decoupling

PubMed Central

Li, Shizhe; An, Li; Yu, Shao; Araneta, Maria Ferraris; Johnson, Christopher S.; Wang, Shumin; Shen, Jun

2015-01-01

Purpose 13C magnetic resonance spectroscopy (MRS) of human brain at 7 Tesla (T) may pose patient safety issues due to high RF power deposition for proton decoupling. The purpose of present work is to study the feasibility of in vivo 13C MRS of human brain at 7 T using broadband low RF power proton decoupling. Methods Carboxylic/amide 13C MRS of human brain by broadband stochastic proton decoupling was demonstrated on a 7 T scanner. RF safety was evaluated using the finite-difference time-domain method. 13C signal enhancement by nuclear Overhauser effect (NOE) and proton decoupling was evaluated in both phantoms and in vivo. Results At 7 T, the peak amplitude of carboxylic/amide 13C signals was increased by a factor of greater than 4 due to the combined effects of NOE and proton decoupling. The 7 T 13C MRS technique used decoupling power and average transmit power of less than 35 W and 3.6 W, respectively. Conclusion In vivo 13C MRS studies of human brain can be performed at 7 T well below the RF safety threshold by detecting carboxylic/amide carbons with broadband stochastic proton decoupling. PMID:25917936

Measurement of a heavy-hole hyperfine interaction in InGaAs quantum dots using resonance fluorescence.

PubMed

Fallahi, P; Yilmaz, S T; Imamoğlu, A

2010-12-17

We measure the strength and the sign of hyperfine interaction of a heavy hole with nuclear spins in single self-assembled quantum dots. Our experiments utilize the locking of a quantum dot resonance to an incident laser frequency to generate nuclear spin polarization. By monitoring the resulting Overhauser shift of optical transitions that are split either by electron or exciton Zeeman energy with respect to the locked transition using resonance fluorescence, we find that the ratio of the heavy-hole and electron hyperfine interactions is -0.09 ± 0.02 in three quantum dots. Since hyperfine interactions constitute the principal decoherence source for spin qubits, we expect our results to be important for efforts aimed at using heavy-hole spins in quantum information processing.

Double resonance calibration of g factor standards: Carbon fibers as a high precision standard.

PubMed

Herb, Konstantin; Tschaggelar, Rene; Denninger, Gert; Jeschke, Gunnar

2018-04-01

The g factor of paramagnetic defects in commercial high performance carbon fibers was determined by a double resonance experiment based on the Overhauser shift due to hyperfine coupled protons. Our carbon fibers exhibit a single, narrow and perfectly Lorentzian shaped ESR line and a g factor slightly higher than g free with g=2.002644=g free ·(1+162ppm) with a relative uncertainty of 15ppm. This precisely known g factor and their inertness qualify them as a high precision g factor standard for general purposes. The double resonance experiment for calibration is applicable to other potential standards with a hyperfine interaction averaged by a process with very short correlation time. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Isolation and identification of flavonoids, including flavone rotamers, from the herbal drug 'Crataegi folium cum flore' (hawthorn).

PubMed

Rayyan, S; Fossen, T; Solheim Nateland, H; Andersen, O M

2005-01-01

Twelve flavonoids, including seven flavones, four flavonols and one flavanone, were isolated from methanolic extract of the herbal drug 'Crataegi folium cum flore' (hawthorn leaves and flowers) by a combination of CC (over Amberlite XAD-7 and Sephadex LH-20) and preparative HPLC. Their structures, including that of the novel flavonol 8-methoxykaempferol 3-O-(6"-malonyl-beta-glucopyranoside), were elucidated by homo- and heteronuclear NMR and electrospray/MS. The 1H- and 13C-NMR of all compounds, including rotameric pairs of five flavone C-glycosides, were assigned. The presence and relative proportion of each rotamer was shown by various NMR experiments, including two-dimensional nuclear Overhauser and exchange spectroscopy, to depend on solvent, linkage position and structure of the C-glycosyl substituent.

Neutron interferometry: The pioneering contributions of Samuel A. Werner

NASA Astrophysics Data System (ADS)

Klein, A. G.

2006-11-01

In 1975, Sam Werner, while on the staff of the Scientific Laboratory of the Ford Motor Company, and his collaborators from Purdue University, Roberto Colella and Albert Overhauser, carried out one of the pioneering experiments in neutron interferometry at the 2 MW University of Michigan research reactor. It was the famous COW Experiment [Colella et al., Phys. Rev. Lett. 34 (1975) 1472] on gravitationally induced quantum interference. Shortly thereafter he moved to the University of Missouri in Columbia, to set up a program of neutron scattering research, including neutron interferometry. In the 25 years until his retirement a large number of beautiful experiments have been performed by Sam, with his group, his numerous students and many international collaborators. This work and its history are briefly reviewed in this paper.

Host-guest chemistry of dendrimer-drug complexes. 4. An in-depth look into the binding/encapsulation of guanosine monophosphate by dendrimers.

PubMed

Hu, Jingjing; Fang, Min; Cheng, Yiyun; Zhang, Jiahai; Wu, Qinglin; Xu, Tongwen

2010-06-03

In the present study, we investigated the host-guest chemistry of dendrimer/guanosine monophosphate (GMP) and present an in-depth look into the binding/encapsulation of GMP by dendrimers using NMR studies. (1)H NMR spectra showed a significant downfield shift of methylene protons in the outmost layer of the G5 dendrimer, indicating the formation of ion pairs between cationic amine groups of dendrimer and anionic phosphate groups of GMP. Chemical shift titration results showed that the binding constant between G5 dendrimer and GMP is 17,400 M(-1) and each G5 dendrimer has 107 binding sites. The binding of GMP to dendrimers prevents its aggregation in aqueous solutions and thereby enhances its stability. Nuclear Overhauser effect measurements indicated that a GMP binding and encapsulation balance occurs on the surface and in the interior of dendrimer. The binding/encapsulation transitions can be easily tailored by altering the surface and interior charge densities of the dendrimer. All these findings provide a new insight into the host-guest chemistry of dendrimer/guest complexes and may play important roles in the study of dendrimer/DNA aggregates by a "bottom-up" strategy.

Biosynthesis and NMR-studies of a double transmembrane domain from the Y4 receptor, a human GPCR.

PubMed

Zou, Chao; Naider, Fred; Zerbe, Oliver

2008-12-01

The human Y4 receptor, a class A G-protein coupled receptor (GPCR) primarily targeted by the pancreatic polypeptide (PP), is involved in a large number of physiologically important functions. This paper investigates a Y4 receptor fragment (N-TM1-TM2) comprising the N-terminal domain, the first two transmembrane (TM) helices and the first extracellular loop followed by a (His)(6) tag, and addresses synthetic problems encountered when recombinantly producing such fragments from GPCRs in Escherichia coli. Rigorous purification and usage of the optimized detergent mixture 28 mM dodecylphosphocholine (DPC)/118 mM% 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LPPG) resulted in high quality TROSY spectra indicating protein conformational homogeneity. Almost complete assignment of the backbone, including all TM residue resonances was obtained. Data on internal backbone dynamics revealed a high secondary structure content for N-TM1-TM2. Secondary chemical shifts and sequential amide proton nuclear Overhauser effects defined the TM helices. Interestingly, the properties of the N-terminal domain of this large fragment are highly similar to those determined on the isolated N-terminal domain in the presence of DPC micelles.

Field-cycling NMR experiments in an ultra-wide magnetic field range: relaxation and coherent polarization transfer.

PubMed

Zhukov, Ivan V; Kiryutin, Alexey S; Yurkovskaya, Alexandra V; Grishin, Yuri A; Vieth, Hans-Martin; Ivanov, Konstantin L

2018-05-09

An experimental method is described allowing fast field-cycling Nuclear Magnetic Resonance (NMR) experiments over a wide range of magnetic fields from 5 nT to 10 T. The method makes use of a hybrid technique: the high field range is covered by positioning the sample in the inhomogeneous stray field of the NMR spectrometer magnet. For fields below 2 mT a magnetic shield is mounted on top of the spectrometer; inside the shield the magnetic field is controlled by a specially designed coil system. This combination allows us to measure T1-relaxation times and nuclear Overhauser effect parameters over the full range in a routine way. For coupled proton-carbon spin systems relaxation with a common T1 is found at low fields, where the spins are "strongly coupled". In some cases, experiments at ultralow fields provide access to heteronuclear long-lived spin states. Efficient coherent polarization transfer is seen for proton-carbon spin systems at ultralow fields as follows from the observation of quantum oscillations in the polarization evolution. Applications to analysis and the manipulation of heteronuclear spin systems are discussed.

Structure and dynamics of the conserved protein GPI anchor core inserted into detergent micelles.

PubMed

Chevalier, Franck; Lopez-Prados, Javier; Groves, Patrick; Perez, Serge; Martín-Lomas, Manuel; Nieto, Pedro M

2006-10-01

A suitable approach which combines nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations have been used to study the structure and the dynamics of the glycosylphosphatidylinositol (GPI) anchor Manalphal-2Manalpha1-6Manalphal -4GlcNalpha1-6myo-inositol-1-OPO(3)-sn-1,2-dimyristoylglycerol (1) incorporated into dodecylphosphatidylcholine (DPC) micelles. The results have been compared to those previously obtained for the products obtainable from (1) after phospholipase cleavage, in aqueous solution. Relaxation and diffusion NMR experiments were used to establish the formation of stable aggregates and the insertion of (1) into the micelles. MD calculations were performed including explicit water, sodium and chloride ions and using the Particle Mesh Ewald approach for the evaluation of the electrostatic energy term. The MD predicted three dimensional structure and dynamics were substantiated by nuclear overhauser effect (NOE) measurements and relaxation data. The pseudopentasaccharide structure, which was not affected by incorporation of (1) into the micelle, showed a complex dynamic behaviour with a faster relative motion at the terminal mannopyranose unit and decreased mobility close to the micelle. This motion may be better described as an oscillation relative to the membrane rather than a folding event.

Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.

PubMed

Geierhaas, Christian D; Salvatella, Xavier; Clarke, Jane; Vendruscolo, Michele

2008-03-01

It has been suggested that Phi-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Phi-values indicate almost completely folded regions in the TS, intermediate Phi-values regions with a detectable amount of structure and low Phi-values indicate mostly unstructured regions. To explore the extent to which this classification can be used to characterise in detail the structure of TSs for protein folding, we used Phi-values divided into these classes as restraints in molecular dynamics simulations. This type of procedure is related to that used in NMR spectroscopy to define the structure of native proteins from the measurement of inter-proton distances derived from nuclear Overhauser effects. We illustrate this approach by determining the TS ensembles of five proteins and by showing that the results are similar to those obtained by using as restraints the actual numerical Phi-values measured experimentally. Our results indicate that the simultaneous consideration of a set of low-resolution Phi-values can provide sufficient information for characterising the architecture of a TS for folding of a protein.

Characterisation of transition state structures for protein folding using ‘high’, ‘medium’ and ‘low’ Φ-values

PubMed Central

Geierhaas, Christian D.; Salvatella, Xavier; Clarke, Jane; Vendruscolo, Michele

2008-01-01

It has been suggested that Φ-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Φ-values indicate almost completely folded regions in the TS, intermediate Φ-values regions with a detectable amount of structure and low Φ-values indicate mostly unstructured regions. To explore the extent to which this classification can be used to characterise in detail the structure of TSs for protein folding, we used Φ-values divided into these classes as restraints in molecular dynamics simulations. This type of procedure is related to that used in NMR spectroscopy to define the structure of native proteins from the measurement of inter-proton distances derived from nuclear Overhauser effects. We illustrate this approach by determining the TS ensembles of five proteins and by showing that the results are similar to those obtained by using as restraints the actual numerical Φ-values measured experimentally. Our results indicate that the simultaneous consideration of a set of low-resolution Φ-values can provide sufficient information for characterising the architecture of a TS for folding of a protein. PMID:18299294

NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.

PubMed

Ryu, Hyojung; Lim, GyuTae; Sung, Bong Hyun; Lee, Jinhyuk

2016-02-15

Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores. NMRe is available at http://psb.kobic.re.kr/nmre/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Modulators of heterogeneous protein surface water dynamics

NASA Astrophysics Data System (ADS)

Han, Songi

The hydration water that solvates proteins is a major factor in driving or enabling biological events, including protein-protein and protein-ligand interactions. We investigate the role of the protein surface in modulating the hydration water fluctuations on both the picosecond and nanosecond timescale with an emerging experimental NMR technique known as Overhauser Dynamic Nuclear Polarization (ODNP). We carry out site-specific ODNP measurements of the hydration water fluctuations along the surface of Chemotaxis Y (CheY), and correlate the measured fluctuations to hydropathic and topological properties of the CheY surface as derived from molecular dynamics (MD) simulation. Furthermore, we compare hydration water fluctuations measured on the CheY surface to that of other globular proteins, as well as intrinsically disordered proteins, peptides, and liposome surfaces to systematically test characteristic effects of the biomolecular surface on the hydration water dynamics. Our results suggest that the labile (ps) hydration water fluctuations are modulated by the chemical nature of the surface, while the bound (ns) water fluctuations are present on surfaces that feature a rough topology and chemical heterogeneity such as the surface of a folded and structured protein. In collaboration with: Ryan Barnes, Dept of Chemistry and Biochemistry, University of California Santa Barbara

Dynamic interleaved 1H/31P STEAM MRS at 3 Tesla using a pneumatic force-controlled plantar flexion exercise rig

PubMed Central

Meyerspeer, M.; Krššák, M.; Kemp, G.J.; Roden, M.; Moser, E.

2016-01-01

1 Objective To develop a measurement method for interleaved acquisition of 1H and 31P STEAM localised spectra of exercising human calf muscle. 2 Materials and Methods A nonmagnetic exercise rig with a pneumatic piston and sensors for force and pedal angle was constructed to enable plantar flexion measured in the 3 Tesla MR scanner, which holds the dual tuned (1H,31P) surface coil used for signal transmission and reception. 3 Results 31P spectra acquired in interleaved mode benefit from higher SNR (factor of 1.34± 0.06 for PCr) compared to standard acquisition due to the Nuclear Overhauser effect (NOE) and substantial PCr/Pi changes during exercise can be observed in 31P spectra. 1H spectral quality is equal to that in single mode experiments and allows Cr2 changes to be monitored. 4 Conclusion The feasibility of dynamic interleaved localised 1H and 31P spectroscopy during plantar flexion exercise has been demonstrated using a custom-built pneumatic system for muscle activation. This opens the possibility of studying the dynamics of metabolism with multi nuclear MRS in a single run. PMID:16320091

Anomalous nuclear Overhauser effects in carbon-substituted aziridines: scalar cross-relaxation of the first kind.

PubMed

Kuprov, Ilya; Hodgson, David M; Kloesges, Johannes; Pearson, Christopher I; Odell, Barbara; Claridge, Timothy D W

2015-03-16

Anomalous NOESY cross-peaks that cannot be explained by dipolar cross-relaxation or chemical exchange are described for carbon-substituted aziridines. The origin of these is identified as scalar cross-relaxation of the first kind, as demonstrated by a complete theoretical description of this relaxation process and by computational simulation of the NOESY spectra. It is shown that this process relies on the stochastic modulation of J-coupling by conformational transitions, which in the case of aziridines arise from inversion at the nitrogen center. The observation of scalar cross-relaxation between protons does not appear to have been previously reported for NOESY spectra. Conventional analysis would have assigned the cross-peaks as being indicative of a chemical exchange process occurring between correlated spins, were it not for the fact that the pairs of nuclei displaying them cannot undergo such exchange. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Blowpipe Mineralogy for Physics/Environment: Highest-Possible-Tc SC Quest; BOTH PERMANENT FOREVER Carb-IDES SOLID-State Sequestration AND Drought(s)-Elimination

NASA Astrophysics Data System (ADS)

Segler, Kurt; Williams, W.; Siegel, E.

2010-03-01

Detailed are old blowpipe[Kraus,Hunt,Ramsdell, Mineralogy (1936)] new applications:charcoal-block reduction of borates to yield (``N-NW'' of MgB2) Overhauser-[PR 35,1,411(1987); Intl.J.Mod.Phys.1,2 & 4,927(1987)]-``land'' predicted high-EST- POSSIBLE Tc SC ˜ ``LiD2''; very-early: Siegel[Phys.Stat.Sol.(a) 11,45(1972);Semiconductors & Insulators 5: 39,47,62(1979)] carb- IDES SOLID-state phase-TRANSITIONED CHEMICALLY-REDOX"-REACTED STABLE PERMANENT LONG-term STRATEGY, NOT ``CO2" BUT NON-gas Carbon-``ELEMENT"-sequestration: PROFITABLE MARKETABLE SALEABLE VALUABLE USEFUL ``Grab and Sell" TRUMPS ``cap and trade"!!!; Mott alloying/vertical metal-insulator transitions in ``borax-(GLASS)- beads"; and very-early Siegel [3rd Intl.Conf.Alt.Energy,Hemi- sphere/Springer(1980)-vol.5/p.459] ``FLYING-WATER" ``Hindenberg- effect"(H2-UP;H2O-DOWN) via H2-maximal-Archimedes-buoyancy ``chemical-rain-in-piplines", only via Siegel GMR enabled diffusive-magnetoresistance(DMR)enabled Siegel proprietary ``magnetic-H-valve": Renewables-H2-H2O purposely flexible versatile agile scaleable retrofitable integrated operating- system for PERMANENT drought(s)-elimination FOREVER!!!

On the transmit field inhomogeneity correction of relaxation‐compensated amide and NOE CEST effects at 7 T

PubMed Central

Windschuh, Johannes; Siero, Jeroen C.W.; Zaiss, Moritz; Luijten, Peter R.; Klomp, Dennis W.J.; Hoogduin, Hans

2017-01-01

High field MRI is beneficial for chemical exchange saturation transfer (CEST) in terms of high SNR, CNR, and chemical shift dispersion. These advantages may, however, be counter‐balanced by the increased transmit field inhomogeneity normally associated with high field MRI. The relatively high sensitivity of the CEST contrast to B 1 inhomogeneity necessitates the development of correction methods, which is essential for the clinical translation of CEST. In this work, two B 1 correction algorithms for the most studied CEST effects, amide‐CEST and nuclear Overhauser enhancement (NOE), were analyzed. Both methods rely on fitting the multi‐pool Bloch‐McConnell equations to the densely sampled CEST spectra. In the first method, the correction is achieved by using a linear B 1 correction of the calculated amide and NOE CEST effects. The second method uses the Bloch‐McConnell fit parameters and the desired B 1 amplitude to recalculate the CEST spectra, followed by the calculation of B 1‐corrected amide and NOE CEST effects. Both algorithms were systematically studied in Bloch‐McConnell equations and in human data, and compared with the earlier proposed ideal interpolation‐based B 1 correction method. In the low B 1 regime of 0.15–0.50 μT (average power), a simple linear model was sufficient to mitigate B 1 inhomogeneity effects on a par with the interpolation B 1 correction, as demonstrated by a reduced correlation of the CEST contrast with B 1 in both the simulations and the experiments. PMID:28111824

Overhauser shift and dynamic nuclear polarization on carbon fibers

NASA Astrophysics Data System (ADS)

Herb, Konstantin; Denninger, Gert

2018-06-01

We report on the first experimental magnetic resonance determination of the coupling between electrons and nuclear spins (1H, 13C) in carbon fibers. Our results strongly support the assumption that the electronic spins are delocalized on graphene like structures in the fiber. The coupling between these electrons and the nuclei of the lattice results in dynamic nuclear polarization of the nuclei (DNP), enabling very sensitive NMR experiments on these nuclear spins. For possible applications of graphene in spintronics devices the coupling between nuclei and electrons is essential. We were able to determine the interactions down to 30 × 10-9(30 ppb) . We were even able to detect the coupling of the electrons to 13C (in natural abundance). These experiments open the way for a range of new double resonance investigations with possible applications in the field of material science.

Extending the Applicability of Exact Nuclear Overhauser Enhancements to Large Proteins and RNA.

PubMed

Nichols, Parker; Born, Alexandra; Henen, Morkos; Strotz, Dean; Chi, Celestine N; Güntert, Peter; Vögeli, Beat Rolf

2018-06-08

Distance-dependent NOEs are one of the most popular and important experimental restraints for calculating NMR structures. Despite this, they are mostly employed as semi-quantitative upper distance bounds, which discards a wealth of information that is encoded in the cross-relaxation rate constant. Information that is lost includes exact distances between protons and dynamics that occur on the sub-millisecond time-scale. Our recently introduced exact measurement of the NOE (eNOE) requires little additional experimental effort relative to other NMR observables. So far, we have used eNOEs to calculate multi-state ensembles of proteins up to ~150 residues. Here, we briefly revisit the eNOE methodology and present two new directions for the use of eNOEs: Applications to large proteins and RNA. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transient NOE enhancement in solid-state MAS NMR of mobile systems

NASA Astrophysics Data System (ADS)

Cui, Jiangyu; Li, Jun; Peng, Xinhua; Fu, Riqiang

2017-11-01

It has been known that the heteronuclear cross-relaxation affects the dilute S spin magnetization along the longitudinal direction, causing an overshoot phenomenon for those mobile systems in spin-lattice relaxation rate measurements. Here, we analyze the Solomon equations for an I-S system and derive the transient cross relaxation effect as to when an overshoot phenomenon would take place and what the maximum enhancement could be at the time of the overshoot. In order to utilize such a transient nuclear Overhauser effect (NOE), we first time apply it to dynamic solid samples by inverting the 1H magnetization prior to the excitation of the S spin. It is found that the overshoot depends on the ratio of the I and S spin-lattice relaxation rates, i.e. RSS /RII . When RSS /RII ≫ 1 , the maximum enhancement factor for transient NOE could be larger than that obtained in steady-state NOE experiments. Furthermore, transient NOE appears to be more efficient in terms of sensitivity enhancement of dilute spins in solid-state NMR of mobile systems than the traditional cross polarization scheme whose efficiency is greatly compromised by molecular mobility. A sample of natural abundance L-isoleucine amino acid, in which the spin-lattice relaxation rates for the four methyl carbons are different, has been used to demonstrate sensitivity enhancement factors under various experimental schemes.

Determining the Orientation and Localization of Membrane-Bound Peptides

PubMed Central

Hohlweg, Walter; Kosol, Simone; Zangger, Klaus

2012-01-01

Many naturally occurring bioactive peptides bind to biological membranes. Studying and elucidating the mode of interaction is often an essential step to understand their molecular and biological functions. To obtain the complete orientation and immersion depth of such compounds in the membrane or a membrane-mimetic system, a number of methods are available, which are separated in this review into four main classes: solution NMR, solid-state NMR, EPR and other methods. Solution NMR methods include the Nuclear Overhauser Effect (NOE) between peptide and membrane signals, residual dipolar couplings and the use of paramagnetic probes, either within the membrane-mimetic or in the solvent. The vast array of solid state NMR methods to study membrane-bound peptide orientation and localization includes the anisotropic chemical shift, PISA wheels, dipolar waves, the GALA, MAOS and REDOR methods and again the use of paramagnetic additives on relaxation rates. Paramagnetic additives, with their effect on spectral linewidths, have also been used in EPR spectroscopy. Additionally, the orientation of a peptide within a membrane can be obtained by the anisotropic hyperfine tensor of a rigidly attached nitroxide label. Besides these magnetic resonance techniques a series of other methods to probe the orientation of peptides in membranes has been developed, consisting of fluorescence-, infrared- and oriented circular dichroism spectroscopy, colorimetry, interface-sensitive X-ray and neutron scattering and Quartz crystal microbalance. PMID:22044140

High resolution NMR study of T{sub 1} magnetic relaxation dispersion. IV. Proton relaxation in amino acids and Met-enkephalin pentapeptide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pravdivtsev, Andrey N.; Yurkovskaya, Alexandra V.; Ivanov, Konstantin L., E-mail: ivanov@tomo.nsc.ru

2014-10-21

Nuclear Magnetic Relaxation Dispersion (NMRD) of protons was studied in the pentapeptide Met-enkephalin and the amino acids, which constitute it. Experiments were run by using high-resolution Nuclear Magnetic Resonance (NMR) in combination with fast field-cycling, thus enabling measuring NMRD curves for all individual protons. As in earlier works, Papers I–III, pronounced effects of intramolecular scalar spin-spin interactions, J-couplings, on spin relaxation were found. Notably, at low fields J-couplings tend to equalize the apparent relaxation rates within networks of coupled protons. In Met-enkephalin, in contrast to the free amino acids, there is a sharp increase in the proton T{sub 1}-relaxation timesmore » at high fields due to the changes in the regime of molecular motion. The experimental data are in good agreement with theory. From modelling the relaxation experiments we were able to determine motional correlation times of different residues in Met-enkephalin with atomic resolution. This allows us to draw conclusions about preferential conformation of the pentapeptide in solution, which is also in agreement with data from two-dimensional NMR experiments (rotating frame Overhauser effect spectroscopy). Altogether, our study demonstrates that high-resolution NMR studies of magnetic field-dependent relaxation allow one to probe molecular mobility in biomolecules with atomic resolution.« less

Conformational dynamics in fluorophenylcarbamoyl-alpha-chymotrypsins.

PubMed

Kairi, M; Gerig, J T

1990-06-19

A series of fluorine-substituted diphenylcarbamoyl chlorides have been synthesized and used to prepare corresponding diphenylcarbamoylated derivatives of alpha-chymotrypsin. The enzyme is rapidly inactivated by these compounds, as has been previously observed for the unsubstituted chloride, and the derivatives are stable enough to permit extensive studies by fluorine NMR spectroscopy. In combination with previously reported results, these NMR experiments suggest that the aromatic rings of a diphenylcarbamoyl group attached to chymotrypsin may be found in two magnetically and dynamically distinguishable sites, with exchange between these sites taking place by a process that involves rotation about the carbamoyl N-CO bond and localized unfolding of the enzyme. The extent to which a given fluoroaromatic ring is found in one of these sites is dependent on the position of the fluorine substituent and the nature of the partner aromatic ring. It is found that a 2-fluorophenyl ring, when present, dominantly determines site occupation, while a 3-fluorophenyl ring has no effects that are detectably different from those of an unsubstituted phenyl ring. There is evidence for slow aromatic ring rotation within at least one of the phenyl ring interaction sites. Saturation transfer and lineshape methods provide information about the rates of interconversion of the N-phenyl groups between these sites. Line-width, spin-lattice relaxation times and fluorine-proton nuclear Overhauser effects determined at 282 and 470 MHz are reported for each system examined.

A Novel N14Y Mutation in Connexin26 in Keratitis-Ichthyosis-Deafness Syndrome

PubMed Central

Arita, Ken; Akiyama, Masashi; Aizawa, Tomoyasu; Umetsu, Yoshitaka; Segawa, Ikuo; Goto, Maki; Sawamura, Daisuke; Demura, Makoto; Kawano, Keiichi; Shimizu, Hiroshi

2006-01-01

Connexins (Cxs) are transmembranous proteins that connect adjacent cells via channels known as gap junctions. The N-terminal 21 amino acids of Cx26 are located at the cytoplasmic side of the channel pore and are thought to be essential for the regulation of channel selectivity. We have found a novel mutation, N14Y, in the N-terminal domain of Cx26 in a case of keratitis-ichthyosis-deafness syndrome. Reduced gap junctional intercellular communication was observed in the patient’s keratinocytes by the dye transfer assay using scrape-loading methods. The effect of this mutation on molecular structure was investigated using synthetic N-terminal peptides from both wild-type and mutated Cx26. Two-dimensional 1H nuclear magnetic resonance and circular dichroism measurements demonstrated that the secondary structures of these two model peptides are similar to each other. However, several novel nuclear Overhauser effect signals appeared in the N14Y mutant, and the secondary structure of the mutant peptide was more susceptible to induction of 2,2,2-trifluoroethanol than wild type. Thus, it is likely that the N14Y mutation induces a change in local structural flexibility of the N-terminal domain, which is important for exerting the activity of the channel function, resulting in impaired gap junctional intercellular communication. PMID:16877344

The Feasibility of Formation and Kinetics of NMR Signal Amplification by Reversible Exchange (SABRE) at High Magnetic Field (9.4 T)

PubMed Central

2015-01-01

1H NMR signal amplification by reversible exchange (SABRE) was observed for pyridine and pyridine-d5 at 9.4 T, a field that is orders of magnitude higher than what is typically utilized to achieve the conventional low-field SABRE effect. In addition to emissive peaks for the hydrogen spins at the ortho positions of the pyridine substrate (both free and bound to the metal center), absorptive signals are observed from hyperpolarized orthohydrogen and Ir-complex dihydride. Real-time kinetics studies show that the polarization build-up rates for these three species are in close agreement with their respective 1H T1 relaxation rates at 9.4 T. The results suggest that the mechanism of the substrate polarization involves cross-relaxation with hyperpolarized species in a manner similar to the spin-polarization induced nuclear Overhauser effect. Experiments utilizing pyridine-d5 as the substrate exhibited larger enhancements as well as partial H/D exchange for the hydrogen atom in the ortho position of pyridine and concomitant formation of HD molecules. While the mechanism of polarization enhancement does not explicitly require chemical exchange of hydrogen atoms of parahydrogen and the substrate, the partial chemical modification of the substrate via hydrogen exchange means that SABRE under these conditions cannot rigorously be referred to as a non-hydrogenative parahydrogen induced polarization process. PMID:24528143

The feasibility of formation and kinetics of NMR signal amplification by reversible exchange (SABRE) at high magnetic field (9.4 T).

PubMed

Barskiy, Danila A; Kovtunov, Kirill V; Koptyug, Igor V; He, Ping; Groome, Kirsten A; Best, Quinn A; Shi, Fan; Goodson, Boyd M; Shchepin, Roman V; Coffey, Aaron M; Waddell, Kevin W; Chekmenev, Eduard Y

2014-03-05

(1)H NMR signal amplification by reversible exchange (SABRE) was observed for pyridine and pyridine-d5 at 9.4 T, a field that is orders of magnitude higher than what is typically utilized to achieve the conventional low-field SABRE effect. In addition to emissive peaks for the hydrogen spins at the ortho positions of the pyridine substrate (both free and bound to the metal center), absorptive signals are observed from hyperpolarized orthohydrogen and Ir-complex dihydride. Real-time kinetics studies show that the polarization build-up rates for these three species are in close agreement with their respective (1)H T1 relaxation rates at 9.4 T. The results suggest that the mechanism of the substrate polarization involves cross-relaxation with hyperpolarized species in a manner similar to the spin-polarization induced nuclear Overhauser effect. Experiments utilizing pyridine-d5 as the substrate exhibited larger enhancements as well as partial H/D exchange for the hydrogen atom in the ortho position of pyridine and concomitant formation of HD molecules. While the mechanism of polarization enhancement does not explicitly require chemical exchange of hydrogen atoms of parahydrogen and the substrate, the partial chemical modification of the substrate via hydrogen exchange means that SABRE under these conditions cannot rigorously be referred to as a non-hydrogenative parahydrogen induced polarization process.

Pluronic®-bile salt mixed micelles.

PubMed

Patel, Vijay; Ray, Debes; Bahadur, Anita; Ma, Junhe; Aswal, V K; Bahadur, Pratap

2018-06-01

The present study was aimed to examine the interaction of two bile salts viz. sodium cholate (NaC) and sodium deoxycholate (NaDC) with three ethylene polyoxide-polypropylene polyoxide (PEO-PPO-PEO) triblock copolymers with similar PPO but varying PEO micelles with a focus on the effect of pH on mixed micelles. Mixed micelles of moderately hydrophobic Pluronic ® P123 were examined in the presence of two bile salts and compared with those from very hydrophobic L121 and very hydrophilic F127. Both the bile salts increase the cloud point (CP) of copolymer solution and decreased apparent micelle hydrodynamic diameter (D h ). SANS study revealed that P123 forms small spherical micelles showing a decrease in size on progressive addition of bile salts. The negatively charged mixed micelles contained fewer P123 molecules but progressively rich in bile salt. NaDC being more hydrophobic displays more pronounced effect than NaC. Interestingly, NaC shows micellar growth in acidic media which has been attributed to the formation of bile acids by protonation of carboxylate ion and subsequent solubilization. In contrast, NaDC showed phase separation at higher concentration. Nuclear Overhauser effect spectroscopy (NOESY) experiments provided information on interaction and location of bile salts in micelles. Results are discussed in terms of hydrophobicity of bile salts and Pluronics ® and the site of bile salt in polymer micelles. Proposed molecular interactions are useful to understand more about bile salts which play important role in physiological processes. Copyright © 2018 Elsevier B.V. All rights reserved.

On the origins of chemical exchange saturation transfer (CEST) contrast in tumors at 9.4 T.

PubMed

Xu, Junzhong; Zaiss, Moritz; Zu, Zhongliang; Li, Hua; Xie, Jingping; Gochberg, Daniel F; Bachert, Peter; Gore, John C

2014-04-01

Chemical exchange saturation transfer (CEST) provides an indirect means to detect exchangeable protons within tissues through their effects on the water signal. Previous studies have suggested that amide proton transfer (APT) imaging, a specific form of CEST, detects endogenous amide protons with a resonance frequency offset 3.5 ppm downfield from water, and thus may be sensitive to variations in mobile proteins/peptides in tumors. However, as CEST measurements are influenced by various confounding effects, such as spillover saturation, magnetization transfer (MT) and MT asymmetry, the mechanism or degree of increased APT signal in tumors is not certain. In addition to APT, nuclear Overhauser enhancement (NOE) effects upfield from water may also provide distinct information on tissue composition. In the current study, APT, NOE and several other MR parameters were measured and compared comprehensively in order to elucidate the origins of APT and NOE contrasts in tumors at 9.4 T. In addition to conventional CEST methods, a new intrinsic inverse metric was applied to correct for relaxation and other effects. After corrections for spillover, MT and T1 effects, corrected APT in tumors was found not to be significantly different from that in normal tissues, but corrected NOE effects in tumors showed significant decreases compared with those in normal tissues. Biochemical measurements verified that there was no significant enhancement of protein contents in the tumors studied, consistent with the corrected APT measurements and previous literature, whereas quantitative MT data showed decreases in the fractions of immobile macromolecules in tumors. Our results may assist in the better understanding of the contrast depicted by CEST imaging in tumors, and in the development of improved APT and NOE measurements for cancer imaging. Copyright © 2014 John Wiley & Sons, Ltd.

Many-body effects in electron liquids with Rashba spin-orbit coupling

NASA Astrophysics Data System (ADS)

Simion, George E.

The main topic of the present thesis is represented by the many-body effects which characterize the physical behavior of an electron liquid in various realizations. We begin by studying the problem of the response of an otherwise homogeneous electron liquid to the potential of an impurity embedded in its bulk. The most dramatic consequence of this perturbation is the existence of so called Friedel density oscillations. We present calculations of their amplitude valid in two as well as in three dimensions. The second problem we will discuss is that of the correlation effects in a three dimensional electron liquid in the metallic density regime. A number of quasiparticle properties are evaluated: the electron self-energy, the quasiparticle effective mass and the renormalization constant. We also present an analysis of the effective Lande g-factor as well as the compressibility. The effects of the Coulomb interactions beyond the random phase approximation have been treated by means of an approach based on the many-body local field factors theory and by utilizing the latest numerical results of Quantum Monte Carlo numerical simulations. The final chapter includes the results of our extensive work on various aspects regarding the two dimensional Fermi liquid in the presence of linear Rashba spin-orbit coupling. By using a number of many-body techniques, we have studied the interplay between spin-orbit coupling and electron-electron interaction. After proving an extension to the famous Overhauser Hartree-Fock instability theorem, a considerable amount of work will be presented on the problem of the density and spin response functions. For the study of the spin response, we will present the results of extensive numerical calculations based on the time dependent mean field theory approach.

Structure determination of a key intermediate of the enantioselective Pd complex catalyzed allylic substitution reaction

PubMed

Junker; Reif; Steinhagen; Junker; Felli; Reggelin; Griesinger

2000-09-01

The structure of a catalytic intermediate with important implications for the interpretation of the stereochemical outcome of the palladium complex catalyzed allylic substitution with phosphino-oxazoline (PHOX) ligands is determined by liquid state NMR. The complex displays a novel structure that is highly distorted compared with other palladium eta2-olefin complexes known so far. The structure has been determined from nuclear overhauser data (NOE), scalar coupling constants, and long range projection angle restraints derived from dipole dipole cross-correlated relaxation of multiple quantum coherence. The latter restraints have been implemented into a distance geometry protocol. The projection angle restraints yield a higher precision in the determination of the relative orientation of the two molecular moieties and are essential to provide an exact structural definition of the olefinic part of the catalytic intermediate with respect to the ligand.

Discretization of the total magnetic field by the nuclear spin bath in fluorine-doped ZnSe.

PubMed

Zhukov, E A; Kirstein, E; Kopteva, N E; Heisterkamp, F; Yugova, I A; Korenev, V L; Yakovlev, D R; Pawlis, A; Bayer, M; Greilich, A

2018-05-16

The coherent spin dynamics of fluorine donor-bound electrons in ZnSe induced by pulsed optical excitation is studied in a perpendicular applied magnetic field. The Larmor precession frequency serves as a measure for the total magnetic field exerted onto the electron spins and, surprisingly, does not increase linearly with the applied field, but shows a step-like behavior with pronounced plateaus, given by multiples of the laser repetition rate. This discretization occurs by a feedback mechanism in which the electron spins polarize the nuclear spins, which in turn generate a local Overhauser field adjusting the total magnetic field accordingly. Varying the optical excitation power, we can control the plateaus, in agreement with our theoretical model. From this model, we trace the observed discretization to the optically induced Stark field, which causes the dynamic nuclear polarization.

Dynamic nuclear polarization methods in solids and solutions to explore membrane proteins and membrane systems.

PubMed

Cheng, Chi-Yuan; Han, Songi

2013-01-01

Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.

Solubility enhancement of simvastatin by arginine: thermodynamics, solute-solvent interactions, and spectral analysis.

PubMed

Meor Mohd Affandi, M M R; Tripathy, Minaketan; Shah, Syed Adnan Ali; Majeed, A B A

2016-01-01

We examined the solubility of simvastatin in water in 0.01 mol·dm(-3), 0.02 mol·dm(-3), 0.04 mol·dm(-3), 0.09 mol·dm(-3), 0.18 mol·dm(-3), 0.36 mol·dm(-3), and 0.73 mol·dm(-3) arginine (ARG) solutions. The investigated drug is termed the solute, whereas ARG the cosolute. Phase solubility studies illustrated a higher extent of solubility enhancement for simvastatin. The aforementioned system was subjected to conductometric and volumetric measurements at temperatures (T) of 298.15 K, 303.15 K, 308.15 K, and 313.15 K to illustrate the thermodynamics involved and related solute-solvent interactions. The conductance values were used to evaluate the limiting molar conductance and association constants. Thermodynamic parameters (ΔG (0), ΔH (0), ΔS (0), and E s) for the association process of the solute in the aqueous solutions of ARG were calculated. Limiting partial molar volumes and expansibilities were evaluated from the density values. These values are discussed in terms of the solute-solvent and solute-cosolute interactions. Further, these systems were analyzed using ultraviolet-visible analysis, Fourier-transform infrared spectroscopy, and (13)C, (1)H, and two-dimensional nuclear overhauser effect spectroscopy nuclear magnetic resonance to complement thermophysical explanation.

Ionic Liquid-Solute Interactions Studied by 2D NOE NMR Spectroscopy.

PubMed

Khatun, Sufia; Castner, Edward W

2015-07-23

Intermolecular interactions between a Ru(2+)(bpy)3 solute and the anions and cations of four different ionic liquids (ILs) are investigated by 2D NMR nuclear Overhauser effect (NOE) techniques, including {(1)H-(19)F} HOESY and {(1)H-(1)H} ROESY. Four ILs are studied, each having the same bis(trifluoromethylsulfonyl)amide anion in common. Two of the ILs have aliphatic 1-alkyl-1-methylpyrrolidinium cations, while the other two ILs have aromatic 1-alkyl-3-methylimidazolium cations. ILs with both shorter (butyl) and longer (octyl or decyl) cationic alkyl substituents are studied. NOE NMR results suggest that the local environment of IL anions and cations near the Ru(2+)(bpy)3 solute is rather different from the bulk IL structure. The solute-anion and solute-cation interactions are significantly different both for ILs with short vs long alkyl tails and for ILs with aliphatic vs aromatic cation polar head groups. In particular, the solute-anion interactions are observed to be about 3 times stronger for the cations with shorter alkyl tails relative to the ILs with longer alkyl tails. The Ru(2+)(bpy)3 solute interacts with both the polar head and the nonpolar tail groups of the 1-butyl-1-methylpyrrolidinium cation but only with the nonpolar tail groups of the 1-decyl-1-methylpyrrolidinium cation.

Application of NMR Methods to Identify Detection Reagents for Use in the Development of Robust Nanosensors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cosman, M; Krishnan, V V; Balhorn, R

2004-04-29

Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful technique for studying bi-molecular interactions at the atomic scale. Our NMR lab is involved in the identification of small molecules, or ligands that bind to target protein receptors, such as tetanus (TeNT) and botulinum (BoNT) neurotoxins, anthrax proteins and HLA-DR10 receptors on non-Hodgkin's lymphoma cancer cells. Once low affinity binders are identified, they can be linked together to produce multidentate synthetic high affinity ligands (SHALs) that have very high specificity for their target protein receptors. An important nanotechnology application for SHALs is their use in the development of robust chemical sensors ormore » biochips for the detection of pathogen proteins in environmental samples or body fluids. Here, we describe a recently developed NMR competition assay based on transferred nuclear Overhauser effect spectroscopy (trNOESY) that enables the identification of sets of ligands that bind to the same site, or a different site, on the surface of TeNT fragment C (TetC) than a known ''marker'' ligand, doxorubicin. Using this assay, we can identify the optimal pairs of ligands to be linked together for creating detection reagents, as well as estimate the relative binding constants for ligands competing for the same site.« less

Heat-bath algorithmic cooling with correlated qubit-environment interactions

NASA Astrophysics Data System (ADS)

Rodríguez-Briones, Nayeli A.; Li, Jun; Peng, Xinhua; Mor, Tal; Weinstein, Yossi; Laflamme, Raymond

2017-11-01

Cooling techniques are essential to understand fundamental thermodynamic questions of the low-energy states of physical systems, furthermore they are at the core of practical applications of quantum information science. In quantum computing, this controlled preparation of highly pure quantum states is required from the state initialization of most quantum algorithms to a reliable supply of ancilla qubits that satisfy the fault-tolerance threshold for quantum error correction. Heat-bath algorithmic cooling has been shown to purify qubits by controlled redistribution of entropy and multiple contact with a bath, not only for ensemble implementations but also for technologies with strong but imperfect measurements. In this paper, we show that correlated relaxation processes between the system and environment during rethermalization when we reset hot ancilla qubits, can be exploited to enhance purification. We show that a long standing upper bound on the limits of algorithmic cooling Schulman et al (2005 Phys. Rev. Lett. 94, 120501) can be broken by exploiting these correlations. We introduce a new tool for cooling algorithms, which we call ‘state-reset’, obtained when the coupling to the environment is generalized from individual-qubits relaxation to correlated-qubit relaxation. Furthermore, we present explicit improved cooling algorithms which lead to an increase of purity beyond all the previous work, and relate our results to the Nuclear Overhauser Effect.

Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants.

PubMed

Rathner, Petr; Rathner, Adriana; Horničáková, Michaela; Wohlschlager, Christian; Chandra, Kousik; Kohoutová, Jaroslava; Ettrich, Rüdiger; Wimmer, Reinhard; Müller, Norbert

2015-09-01

The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this "missing link", we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1-45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Momentum distribution of the uniform electron gas: Improved parametrization and exact limits of the cumulant expansion

NASA Astrophysics Data System (ADS)

Gori-Giorgi, Paola; Ziesche, Paul

2002-12-01

The momentum distribution of the unpolarized uniform electron gas in its Fermi-liquid regime, n(k,rs), with the momenta k measured in units of the Fermi wave number kF and with the density parameter rs, is constructed with the help of the convex Kulik function G(x). It is assumed that n(0,rs),n(1±,rs), the on-top pair density g(0,rs), and the kinetic energy t(rs) are known (respectively, from accurate calculations for rs=1,…,5, from the solution of the Overhauser model, and from quantum Monte Carlo calculations via the virial theorem). Information from the high- and the low-density limit, corresponding to the random-phase approximation and to the Wigner crystal limit, is used. The result is an accurate parametrization of n(k,rs), which fulfills most of the known exact constraints. It is in agreement with the effective-potential calculations of Takada and Yasuhara [Phys. Rev. B 44, 7879 (1991)], is compatible with quantum Monte Carlo data, and is valid in the density range rs≲12. The corresponding cumulant expansions of the pair density and of the static structure factor are discussed, and some exact limits are derived.

Molecular motions of [Beta]-carotene and a carotenoporphyrin dyad in solution. A carbon-13 NMR spin-lattice relaxation time study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, S.; Swindle, S.L.; Smith, S.K.

1995-03-09

Analysis of [sup 13]C NMR spin-lattice relaxation times (T[sub 1]) yields information concerning both overall tumbling of molecules in solution and internal rotations about single bonds. Relaxation time and nuclear Overhauser effect data have been obtained for [Beta]-carotene and two related molecules, squalane and squalene, for zinc meso-tetraphenylporphyrin, and for a dyad consisting of a porphyrin covalently linked to a carotenoid polyene through a trimethylene bridge. Squalane and squalene, which lack conjugated double bonds, behave essentially as limp string, with internal rotations at least as rapid as overall isotropic tumbling motions. In contrast, [Beta]-carotene reorients as a rigid rod, withmore » internal motions which are too slow to affect relaxation times. Modeling it as an anisotropic rotor yields a rotational diffusion coefficient for motion about the major axis which is 14 times larger than that for rotation about axes perpendicular to that axis. The porphyrin reorients more nearly isotropically and features internal librational motions about the single bonds to the phenyl groups. The relaxation time data for the carotenoporphyrin are consistent with internal motions similar to those of a medieval military flail. 31 refs., 3 figs., 5 tabs.« less

Nuclear magnetic resonance and restrained molecular dynamics studies of the interaction of an epidermal growth factor-derived peptide with protein tyrosine phosphatase 1B.

PubMed

Glover, N R; Tracey, A S

1999-04-20

The epidermal growth factor-derived (EGFR988) fluorophosphonate peptide, DADE(F2Pmp)L, is a potent (30 pM) inhibitor of the protein tyrosine phosphatase PTP1B. Nuclear magnetic resonance (NMR) transferred nuclear Overhauser effect (nOe) experiments have been used to determine the conformation of DADE(F2Pmp)L while bound in the active site of PTP1B. When bound, the peptide adopts an extended beta-strand conformation. Molecular modeling and molecular dynamics simulations allowed the elucidation of the sources of many of the interactions leading to binding of this inhibitor. Electrostatic, hydrophobic, and hydrogen-bonding interactions were all found to contribute significantly to its binding. However, despite the overall tight binding of this inhibitor, the N-terminal and adjacent residue of the peptide were virtually unrestrained in their motion. The major contributions to binding arose from hydrophobic interactions at the leucine and at the aromatic center, hydrogen bonding to the pro-R fluorine of the fluorophosphonomethyl group, and electrostatic interactions involving the carboxylate functionalities of the aspartate and glutamate residues. These latter two residues were found to form tight contacts with surface recognition elements (arginine and lysine) situated near the active-site cleft.

NMR studies of protein-nucleic acid interactions.

PubMed

Varani, Gabriele; Chen, Yu; Leeper, Thomas C

2004-01-01

Protein-DNA and protein-RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein-protein complexes: the interaction surfaces between the molecules must be carefully delineated, the relative orientation of the two species needs to be accurately and precisely determined, and close intermolecular contacts defined by nuclear Overhauser effects (NOEs) must be obtained. However, differences in NMR properties (e.g., chemical shifts) and biosynthetic pathways for sample productions generate important differences. Chemical shift differences between the protein and nucleic acid resonances can aid the NMR structure determination process; however, the relatively limited dispersion of the RNA ribose resonances makes the process of assigning intermolecular NOEs more difficult. The analysis of the resulting structures requires computational tools unique to nucleic acid interactions. This chapter summarizes the most important elements of the structure determination by NMR of protein-nucleic acid complexes and their analysis. The main emphasis is on recent developments (e.g., residual dipolar couplings and new Web-based analysis tools) that have facilitated NMR studies of these complexes and expanded the type of biological problems to which NMR techniques of structural elucidation can now be applied.

Stabilization of a supersaturated solution of mefenamic acid from a solid dispersion with EUDRAGIT(®) EPO.

PubMed

Kojima, Taro; Higashi, Kenjirou; Suzuki, Toyofumi; Tomono, Kazuo; Moribe, Kunikazu; Yamamoto, Keiji

2012-10-01

The stabilization mechanism of a supersaturated solution of mefenamic acid (MFA) from a solid dispersion with EUDRAGIT(®) EPO (EPO) was investigated. The solid dispersions were prepared by cryogenic grinding method. Powder X-ray diffractometry, in vitro dissolution test, in vivo oral absorption study, infrared spectroscopy, and solid- and solution-state NMR spectroscopies were used to characterize the solid dispersions. Dissolution tests in acetate buffer (pH 5.5) revealed that solid dispersion showed > 200-fold higher concentration of MFA. Supersaturated solution was stable over 1 month and exhibited improved oral bioavailability of MFA in rats, with a 7.8-fold higher area under the plasma concentration-versus-time curve. Solid-state (1)H spin-lattice relaxation time (T(1)) measurement showed that MFA was almost monomolecularly dispersed in the EPO polymer matrix. Intermolecular interaction between MFA and EPO was indicated by solid-state infrared and (13)C-T(1) measurements. Solution-state (1)H-NMR measurement demonstrated that MFA existed in monomolecular state in supersaturated solution. (1)H-T(1) and difference nuclear Overhauser effect measurements indicated that cross relaxation occurred between MFA and EPO due to the small distance between them. The formation and high stability of the supersaturated solution were attributable to the specifically formed intermolecular interactions between MFA and EPO.

Intramolecular Hydrogen Bonding in Benzoxazines: When Structural Design Becomes Functional.

PubMed

Froimowicz, Pablo; Zhang, Kan; Ishida, Hatsuo

2016-02-18

The future evolution of benzoxazines and polybenzoxazines as advanced molecular, structural, functional, engineering, and newly commercial materials depends to a great extent on a deeper and more fundamental understanding at the molecular level. In this contribution, the field of benzoxazines is briefly introduced along with a more detailed review of ortho-amide-functional benzoxazines, which are the main subjects of this article. Provided in this article are the detailed and solid scientific evidences of intramolecular five-membered-ring hydrogen bonding, which is supposed to be responsible for the unique and characteristic features exhibited by this ever-growing family of ortho-functionalized benzoxazines. One-dimensional (1D) (1)H NMR spectroscopy was used to study various concentrations of benzoxazines in various solvents with different hydrogen-bonding capability and at various temperatures to investigate in detail the nature of hydrogen bonding in both ortho-amide-functionalized benzoxazine and its para counterpart. These materials were further investigated by two-dimensional (2D) (1)H-(1)H nuclear Overhauser effect spectroscopy (NOESY) to verify and support the conclusions derived during the 1D (1)H NMR experiments. Only highly purified single-crystal benzoxazine samples have been used for this study to avoid additional interactions caused by any impurities. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solubility enhancement of simvastatin by arginine: thermodynamics, solute–solvent interactions, and spectral analysis

PubMed Central

Meor Mohd Affandi, MMR; Tripathy, Minaketan; Shah, Syed Adnan Ali; Majeed, ABA

2016-01-01

We examined the solubility of simvastatin in water in 0.01 mol·dm−3, 0.02 mol·dm−3, 0.04 mol·dm−3, 0.09 mol·dm−3, 0.18 mol·dm−3, 0.36 mol·dm−3, and 0.73 mol·dm−3 arginine (ARG) solutions. The investigated drug is termed the solute, whereas ARG the cosolute. Phase solubility studies illustrated a higher extent of solubility enhancement for simvastatin. The aforementioned system was subjected to conductometric and volumetric measurements at temperatures (T) of 298.15 K, 303.15 K, 308.15 K, and 313.15 K to illustrate the thermodynamics involved and related solute–solvent interactions. The conductance values were used to evaluate the limiting molar conductance and association constants. Thermodynamic parameters (ΔG0, ΔH0, ΔS0, and Es) for the association process of the solute in the aqueous solutions of ARG were calculated. Limiting partial molar volumes and expansibilities were evaluated from the density values. These values are discussed in terms of the solute–solvent and solute–cosolute interactions. Further, these systems were analyzed using ultraviolet–visible analysis, Fourier-transform infrared spectroscopy, and 13C, 1H, and two-dimensional nuclear overhauser effect spectroscopy nuclear magnetic resonance to complement thermophysical explanation. PMID:27041998

Nuclear Overhauser Enhancement Imaging of Glioblastoma at 7 Tesla: Region Specific Correlation with Apparent Diffusion Coefficient and Histology

PubMed Central

Windschuh, Johannes; Meissner, Jan-Eric; Zaiss, Moritz; Eidel, Oliver; Kickingereder, Philipp; Nowosielski, Martha; Wiestler, Benedikt; Sahm, Felix; Floca, Ralf Omar; Neumann, Jan-Oliver; Wick, Wolfgang; Heiland, Sabine; Bendszus, Martin; Schlemmer, Heinz-Peter; Ladd, Mark Edward; Bachert, Peter; Radbruch, Alexander

2015-01-01

Objective To explore the correlation between Nuclear Overhauser Enhancement (NOE)-mediated signals and tumor cellularity in glioblastoma utilizing the apparent diffusion coefficient (ADC) and cell density from histologic specimens. NOE is one type of chemical exchange saturation transfer (CEST) that originates from mobile macromolecules such as proteins and might be associated with tumor cellularity via altered protein synthesis in proliferating cells. Patients and Methods For 15 patients with newly diagnosed glioblastoma, NOE-mediated CEST-contrast was acquired at 7 Tesla (asymmetric magnetization transfer ratio (MTRasym) at 3.3ppm, B1 = 0.7 μT). Contrast enhanced T1 (CE-T1), T2 and diffusion-weighted MRI (DWI) were acquired at 3 Tesla and coregistered. The T2 edema and the CE-T1 tumor were segmented. ADC and MTRasym values within both regions of interest were correlated voxelwise yielding the correlation coefficient rSpearman (rSp). In three patients who underwent stereotactic biopsy, cell density of 12 specimens per patient was correlated with corresponding MTRasym and ADC values of the biopsy site. Results Eight of 15 patients showed a weak or moderate positive correlation of MTRasym and ADC within the T2 edema (0.16≤rSp≤0.53, p<0.05). Seven correlations were statistically insignificant (p>0.05, n = 4) or yielded rSp≈0 (p<0.05, n = 3). No trend towards a correlation between MTRasym and ADC was found in CE-T1 tumor (-0.310.05, n = 6). The biopsy-analysis within CE-T1 tumor revealed a strong positive correlation between tumor cellularity and MTRasym values in two of the three patients (rSp patient3 = 0.69 and rSp patient15 = 0.87, p<0.05), while the correlation of ADC and cellularity was heterogeneous (rSp patient3 = 0.545 (p = 0.067), rSp patient4 = -0.021 (p = 0.948), rSp patient15 = -0.755 (p = 0.005)). Discussion NOE-imaging is a new contrast promising insight into pathophysiologic processes in glioblastoma regarding cell density and protein content, setting itself apart from DWI. Future studies might be based on the assumption that NOE-mediated CEST visualizes cellularity more accurately than ADC, especially in the CE-T1 tumor region. PMID:25789657

Nuclear Overhauser Enhancement imaging of glioblastoma at 7 Tesla: region specific correlation with apparent diffusion coefficient and histology.

PubMed

Paech, Daniel; Burth, Sina; Windschuh, Johannes; Meissner, Jan-Eric; Zaiss, Moritz; Eidel, Oliver; Kickingereder, Philipp; Nowosielski, Martha; Wiestler, Benedikt; Sahm, Felix; Floca, Ralf Omar; Neumann, Jan-Oliver; Wick, Wolfgang; Heiland, Sabine; Bendszus, Martin; Schlemmer, Heinz-Peter; Ladd, Mark Edward; Bachert, Peter; Radbruch, Alexander

2015-01-01

To explore the correlation between Nuclear Overhauser Enhancement (NOE)-mediated signals and tumor cellularity in glioblastoma utilizing the apparent diffusion coefficient (ADC) and cell density from histologic specimens. NOE is one type of chemical exchange saturation transfer (CEST) that originates from mobile macromolecules such as proteins and might be associated with tumor cellularity via altered protein synthesis in proliferating cells. For 15 patients with newly diagnosed glioblastoma, NOE-mediated CEST-contrast was acquired at 7 Tesla (asymmetric magnetization transfer ratio (MTRasym) at 3.3ppm, B1 = 0.7 μT). Contrast enhanced T1 (CE-T1), T2 and diffusion-weighted MRI (DWI) were acquired at 3 Tesla and coregistered. The T2 edema and the CE-T1 tumor were segmented. ADC and MTRasym values within both regions of interest were correlated voxelwise yielding the correlation coefficient rSpearman (rSp). In three patients who underwent stereotactic biopsy, cell density of 12 specimens per patient was correlated with corresponding MTRasym and ADC values of the biopsy site. Eight of 15 patients showed a weak or moderate positive correlation of MTRasym and ADC within the T2 edema (0.16≤rSp≤0.53, p<0.05). Seven correlations were statistically insignificant (p>0.05, n = 4) or yielded rSp≈0 (p<0.05, n = 3). No trend towards a correlation between MTRasym and ADC was found in CE-T1 tumor (-0.310.05, n = 6). The biopsy-analysis within CE-T1 tumor revealed a strong positive correlation between tumor cellularity and MTRasym values in two of the three patients (rSppatient3 = 0.69 and rSppatient15 = 0.87, p<0.05), while the correlation of ADC and cellularity was heterogeneous (rSppatient3 = 0.545 (p = 0.067), rSppatient4 = -0.021 (p = 0.948), rSppatient15 = -0.755 (p = 0.005)). NOE-imaging is a new contrast promising insight into pathophysiologic processes in glioblastoma regarding cell density and protein content, setting itself apart from DWI. Future studies might be based on the assumption that NOE-mediated CEST visualizes cellularity more accurately than ADC, especially in the CE-T1 tumor region.

Inhibitory effect of hydroxypropyl methylcellulose acetate succinate on drug recrystallization from a supersaturated solution assessed using nuclear magnetic resonance measurements.

PubMed

Ueda, Keisuke; Higashi, Kenjirou; Yamamoto, Keiji; Moribe, Kunikazu

2013-10-07

We examined the inhibitory effect of hydroxypropyl methylcellulose acetate succinate (HPMC-AS) on drug recrystallization from a supersaturated solution using carbamazepine (CBZ) and phenytoin (PHT) as model drugs. HPMC-AS HF grade (HF) inhibited the recrystallization of CBZ more strongly than that by HPMC-AS LF grade (LF). 1D-1H NMR measurements showed that the molecular mobility of CBZ was clearly suppressed in the HF solution compared to that in the LF solution. Interaction between CBZ and HF in a supersaturated solution was directly detected using nuclear Overhauser effect spectroscopy (NOESY). The cross-peak intensity obtained using NOESY of HF protons with CBZ aromatic protons was greater than that with the amide proton, which indicated that CBZ had hydrophobic interactions with HF in a supersaturated solution. In contrast, no interaction was observed between CBZ and LF in the LF solution. Saturation transfer difference NMR measurement was used to determine the interaction sites between CBZ and HF. Strong interaction with CBZ was observed with the acetyl substituent of HPMC-AS although the interaction with the succinoyl substituent was quite small. The acetyl groups played an important role in the hydrophobic interaction between HF and CBZ. In addition, HF appeared to be more hydrophobic than LF because of the smaller ratio of the succinoyl substituent. This might be responsible for the strong hydrophobic interaction between HF and CBZ. The intermolecular interactions between CBZ and HPMC-AS shown by using NMR spectroscopy clearly explained the strength of inhibition of HPMC-AS on drug recrystallization.

Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement.

PubMed

Cui, Feng; Jernigan, Robert; Wu, Zhijun

2008-04-01

Nuclear Overhauser effects (NOE) distance constraints and torsion angle constraints are major conformational constraints for nuclear magnetic resonance (NMR) structure refinement. In particular, the number of NOE constraints has been considered as an important determinant for the quality of NMR structures. Of course, the availability of torsion angle constraints is also critical for the formation of correct local conformations. In our recent work, we have shown how a set of knowledge-based short-range distance constraints can also be utilized for NMR structure refinement, as a complementary set of conformational constraints to the NOE and torsion angle constraints. In this paper, we show the results from a series of structure refinement experiments by using different types of conformational constraints--NOE, torsion angle, or knowledge-based constraints--or their combinations, and make a quantitative assessment on how the experimentally acquired constraints contribute to the quality of structural models and whether or not they can be combined with or substituted by the knowledge-based constraints. We have carried out the experiments on a small set of NMR structures. Our preliminary calculations have revealed that the torsion angle constraints contribute substantially to the quality of the structures, but require to be combined with the NOE constraints to be fully effective. The knowledge-based constraints can be functionally as crucial as the torsion angle constraints, although they are statistical constraints after all and are not meant to be able to replace the latter.

Quantification of in vivo pH-weighted amide proton transfer (APT) MRI in acute ischemic stroke

NASA Astrophysics Data System (ADS)

Zhou, Iris Y.; Igarashi, Takahiro; Guo, Yingkun; Sun, Phillip Z.

2015-03-01

Amide proton transfer (APT) imaging is a specific form of chemical exchange saturation transfer (CEST) MRI that probes the pH-dependent amide proton exchange.The endogenous APT MRI is sensitive to tissue acidosis, which may complement the commonly used perfusion and diffusion scans for characterizing heterogeneous ischemic tissue damage. Whereas the saturation transfer asymmetry analysis (MTRasym) may reasonably compensate for direct RF saturation, in vivo MTRasym is however, susceptible to an intrinsically asymmetric shift (MTR'asym). Specifically, the reference scan for the endogenous APT MRI is 7 ppm upfield from that of the label scan, and subjects to concomitant RF irradiation effects, including nuclear overhauser effect (NOE)-mediated saturation transfer and semisolid macromolecular magnetization transfer. As such, the commonly used asymmetry analysis could not fully compensate for such slightly asymmetric concomitant RF irradiation effects, and MTRasym has to be delineated in order to properly characterize the pH-weighted APT MRI contrast. Given that there is very little change in relaxation time immediately after ischemia and the concomitant RF irradiation effects only minimally depends on pH, the APT contrast can be obtained as the difference of MTRasym between the normal and ischemic regions. Thereby, the endogenous amide proton concentration and exchange rate can be solved using a dual 2-pool model, and the in vivo MTR'asym can be calculated by subtracting the solved APT contrast from asymmetry analysis (i.e., MTR'asym =MTRasym-APTR). In addition, MTR'asym can be quantified using the classical 2-pool exchange model. In sum, our study delineated the conventional in vivo pH-sensitive MTRasym contrast so that pHspecific contrast can be obtained for imaging ischemic tissue acidosis.

Analysis of the (Trimethylsilyl)propionic Acid-β(12-28) Peptide Binding Equilibrium with NMR Spectroscopy.

PubMed

Jayawickrama, D A; Larive, C K

1999-06-01

The binding of a small molecule, (trimethylsilyl)propionic acid (TSP), to a 17-residue peptide, β(12-28), is examined using (1)H NMR spectroscopy. β(12-28) (VHHQKLVFFAEDVGSNK) is a central fragment of the 40-42-residue Alzheimer's-associated Aβ peptide. This peptide has been previously shown to form soluble aggregates in low-pH aqueous solution. The TSP resonance is broadened appreciably in solutions containing relatively high concentrations (∼2 mM) of the peptide. The changes in TSP line width measured by titration of a peptide solution with TSP indicate a 1:1 binding stoichiometry. If the concentrations of both the peptide and TSP are reduced by 1 order of magnitude, the resonances of both species are sharp, suggesting that TSP binds predominately to the aggregated peptide. Nuclear Overhauser effect experiments indicate that the TSP interacts predominately with the side chains of the aliphatic peptide residues Leu(17) and Val(18). Pulsed-field gradient NMR measurements of TSP and peptide diffusion coefficients provide a more quantitative picture of the TSP-peptide binding equilibrium. The measured diffusion coefficients were used to calculate the fractions of the free and bound TSP. These results substantiate the conclusion that the stoichiometry of the TSP-peptide binding equilibrium is essentially 1:1 and further indicate anticooperative behavior in solutions containing an excess of TSP resulting in a dissociation of the peptide aggregates.

A one- and two-dimensional NMR study of the B to Z transition of (m5dC-dG)3 in methanolic solution.

PubMed Central

Feigon, J; Wang, A H; van der Marel, G A; Van Boom, J H; Rich, A

1984-01-01

The deoxyribose hexanucleoside pentaphosphate (m5dC-dG)3 has been studied by 500 MHz 1H NMR in D2O (0.1 M NaCl) and in D2O/deuterated methanol mixtures. Two conformations, in slow equilibrium on the NMR time scale, were detected in methanolic solution. Two-dimensional nuclear Overhauser effect (NOE) experiments were used to assign the base and many of the sugar resonances as well as to determine structural features for both conformations. The results were consistent with the an equilibrium in solution between B-DNA and Z-DNA. The majority of the molecules have a B-DNA structure in low-salt D2O and a Z-DNA structure at high methanol concentrations. A cross-strand NOE between methyl groups on adjacent cytosines is observed for Z-DNA but not B-DNA. The B-DNA conformation predominates at low methanol concentrations and is stabilized by increasing temperature, while the Z-DNA conformation predominates at high methanol concentrations and low temperatures. 31P NMR spectra gave results consistent with those obtained by 1H NMR. Comparison of the 31P spectra with those obtained on poly(dG-m5dC) allow assignment of the lower field resonances to GpC in the Z conformation. PMID:6694910

Ionic Liquid–Solute Interactions Studied by 2D NOE NMR Spectroscopy

DOE PAGES

Khatun, Sufia; Castner, Edward W.

2014-11-26

Intermolecular interactions between a Ru²⁺(bpy)₃ solute and the anions and cations of four different ionic liquids (ILs) are investigated by 2D NMR nuclear Overhauser effect (NOE) techniques, including {¹H-¹⁹F} HOESY and {¹H-¹H} ROESY. Four ILs are studied, each having the same bis(trifluoromethylsulfonyl)amide anion in common. Two of the ILs have aliphatic 1-alkyl-1-methylpyrrolidinium cations, while the other two ILs have aromatic 1-alkyl-3-methylimidazolium cations. ILs with both shorter (butyl) and longer (octyl or decyl) cationic alkyl substituents are studied. NOE NMR results suggest that the local environment of IL anions and cations near the Ru²⁺(bpy)₃ solute is rather different from the bulkmore » IL structure. The solute-anion and solute-cation interactions are significantly different both for ILs with short vs long alkyl tails and for ILs with aliphatic vs aromatic cation polar head groups. In particular, the solute-anion interactions are observed to be about 3 times stronger for the cations with shorter alkyl tails relative to the ILs with longer alkyl tails. The Ru²⁺(bpy)₃ solute interacts with both the polar head and the nonpolar tail groups of the 1- butyl-1-methylpyrrolidinium cation but only with the nonpolar tail groups of the 1-decyl-1-methylpyrrolidinium cation.« less

Spiroketalcarminic Acid, a Novel Minor Anthraquinone Pigment in Cochineal Extract Used in Food Additives.

PubMed

Ito, Yusai; Harikai, Naoki; Ishizuki, Kyoko; Shinomiya, Kazufusa; Sugimoto, Naoki; Akiyama, Hiroshi

2017-09-01

Cochineal extract prepared from the scale insect Dactylopus coccus (American cochineal) has been used as a natural red dye for food, cosmetics, and pharmaceuticals. The major pigment in cochineal extract is carminic acid (CA), an anthraquinone glucoside, and several minor pigments have been previously reported. Our investigation aimed at establishing the safety of cochineal dye products using ultra performance liquid chromatography-photo diode array-electrospray ionization-time of flight (UPLC-PDA-ESI-TOF)/MS found an unknown minor pigment, spiroketalcarminic acid (1), in three commercial cochineal extract samples; cochineal extract used in food additives, carmine that is an aluminum salt of cochineal extract used as natural dye, and a research reagent of CA. The purification of 1 from cochineal extract involved sequential chromatographic techniques, including preparative reversed-phase HPLC. Two dimensional (2D)-NMR and mass analyses established the structure of 1 to be a novel anthraquinone with an unusual 6,5-spiroketal system instead of the C-glucosyl moiety of CA. The absolute stereochemistry of the spiroketal moiety in 1 was determined by nuclear Overhauser effect spectroscopy (NOESY) correlations and optical rotation. No data corresponding to 1 had previously been reported for extracts of dried cochineal insects and traditional art products dyed with cochineal extract, indicating that 1 is likely produced during the preparation of commercial cochineal extract.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramelot, Theresa A.; Rossi, Paolo M.; Forouhar, Farhad

The solution nuclear magnetic resonance (NMR) structures and backbone (15)N dynamics of the specialized acyl carrier protein (ACP), RpAcpXL, from Rhodopseudomonas palustris, in both the apo form and holo form modified by covalent attachment of 4'-phosphopantetheine at S37, are virtually identical, monomeric, and correspond to the closed conformation. The structures have an extra α-helix compared to the archetypical ACP from Escherichia coli, which has four helices, resulting in a larger opening to the hydrophobic cavity. Chemical shift differences between apo- and holo-RpAcpXL indicated some differences in the hinge region between α2 and α3 and in the hydrophobic cavity environment, butmore » corresponding changes in nuclear Overhauser effect cross-peak patterns were not detected. In contrast to the NMR structures, apo-RpAcpXL was observed in an open conformation in crystals that diffracted to 2.0 Å resolution, which resulted from movement of α3. On the basis of the crystal structure, the predicted biological assembly is a homodimer. Although the possible biological significance of dimerization is unknown, there is potential that the resulting large shared hydrophobic cavity could accommodate the very long-chain fatty acid (28-30 carbons) that this specialized ACP is known to synthesize and transfer to lipid A. These structures are the first representatives of the AcpXL family and the first to indicate that dimerization may be important for the function of these specialized ACPs.« less

Sucrose in Aqueous Solution Revisited: 2. Adaptively Biased Molecular Dynamics Simulations and Computational Analysis of NMR Relaxation

PubMed Central

Xia, Junchao; Case, David A.

2012-01-01

We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4 M), and in a 7:3 water-DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive-biased simulations along the glycosidic φ and ψ torsion angles. NMR relaxation parameters, including longitudinal (R1) and transverse (R2) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S2) were computed from the resulting time-correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80–90% of the conformations having φ – ψ values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO-water mixtures. PMID:22058066

Conformational diversity in contryphans from Conus venom: cis-trans isomerisation and aromatic/proline interactions in the 23-membered ring of a 7-residue peptide disulfide loop.

PubMed

Sonti, Rajesh; Gowd, Konkallu Hanumae; Rao, K N Shashanka; Ragothama, Srinivasarao; Rodriguez, Alex; Perez, Juan Jesus; Balaram, Padmanabhan

2013-11-04

Conformational diversity or "shapeshifting" in cyclic peptide natural products can, in principle, confer a single molecular entity with the property of binding to multiple receptors. Conformational equilibria have been probed in the contryphans, which are peptides derived from Conus venom possessing a 23-membered cyclic disulfide moiety. The natural sequences derived from Conus inscriptus, GCV(D)LYPWC* (In936) and Conus loroisii, GCP(D)WDPWC* (Lo959) differ in the number of proline residues within the macrocyclic ring. Structural characterisation of distinct conformational states arising from cis-trans equilibria about Xxx-Pro bonds is reported. Isomerisation about the C2-P3 bond is observed in the case of Lo959 and about the Y5-P6 bond in In936. Evidence is presented for as many as four distinct species in the case of the synthetic analogue V3P In936. The Tyr-Pro-Trp segment in In936 is characterised by distinct sidechain orientations as a consequence of aromatic/proline interactions as evidenced by specific sidechain-sidechain nuclear Overhauser effects and ring current shifted proton chemical shifts. Molecular dynamics simulations suggest that Tyr5 and Trp7 sidechain conformations are correlated and depend on the geometry of the Xxx-Pro bond. Thermodynamic parameters are derived for the cis↔trans equilibrium for In936. Studies on synthetic analogues provide insights into the role of sequence effects in modulating isomerisation about Xxx-Pro bonds. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical-exchange-sensitive MRI of amide, amine and NOE at 9.4 T versus 15.2 T.

PubMed

Chung, Julius Juhyun; Choi, Wonmin; Jin, Tao; Lee, Jung Hee; Kim, Seong-Gi

2017-09-01

Chemical exchange (CE)-sensitive MRI benefits greatly from stronger magnetic fields; however, field effects on CE-sensitive imaging have not yet been studied well in vivo. We have compared CE-sensitive Z-spectra and maps obtained at the fields of 9.4 T and 15.2 T in phantoms and rats with off-resonance chemical-exchange-sensitive spin lock (CESL), which is similar to conventional chemical exchange saturation transfer. At higher fields, the background peak at water resonance has less spread and the exchange rate relative to chemical shift decreases, thus CESL intensity is dependent on B 0 . For the in vivo amide and nuclear Overhauser enhancement (NOE) composite resonances of rat brains, intensities were similar for both magnetic fields, but effective amide proton transfer and NOE values obtained with three-point quantification or a curve fitting method were larger at 15.2 T due to the reduced spread of attenuation at the direct water resonance. When using intermediate exchange-sensitive irradiation parameters, the amine proton signal was 65% higher at 15.2 T than at 9.4 T due to a reduced ratio of exchange rate to chemical shift. In summary, increasing magnetic field provides enhancements to CE-sensitive signals in the intermediate exchange regime and reduces contamination from background signals in the slow exchange regime. Consequently, ultrahigh magnetic field is advantageous for CE-sensitive MRI, especially for amine and hydroxyl protons. Copyright © 2017 John Wiley & Sons, Ltd.

Magnetic observations at Geophysical Observatory Paratunka IKIR FEB RAS: tasks, possibilities and future prospects

NASA Astrophysics Data System (ADS)

Khomutov, Sergey Y.

2017-10-01

Continuous magnetic measurements at Geophysical Observatory "Paratunka" (PET) of IKIR FEB RAS are performed since 1967. In the new millennium analogue magnetometers were modernized to digital, the technologies of absolute observations were changed, the data processing was completely transferred to computers, and the status of INTERMAGNET observatory was obtained. Currently, the observatory uses the following magnetometers: (a) for absolute observations - DIflux LEMI-203 (theodolite 3T2KP) and Mag-01 (theodolite Wild-T1), Overhauser magnetometers POS-1 and GSM-19W; (b) for variation measurements - fluxgate magnetometers FGE-DTU, FRG-601 and MAGDAS (installed under international agreements of IKIR), vector magnetometers dIdD GSM-19FD and POS-4 with Overhauser sensors and coil systems, scalar magnetometer GSM-90 and induction magnetometer STELAB. During Spring-Autumn season dIdD also is installed at remote station "Karymshina" at distance of 15 km from Observatory. There is monitoring system for monitoring of conditions in which magnetic observations are performed, including the semi-professional weather stations Davis Vantage Pro2 and WS2000 and a network of digital temperature sensors DS19B20 located at various points in magnetic pavilions and outdoor. All measurements are synchronized with the UTC. The results of observations are collected by the IKIR data server from the recorders and loggers, including in real-time. Specialized software was developed (based on MATLAB and Octave packages), which allows automatic and semi-automatic processing of data, the comparison of the results from different magnetometers and presenting final data in formats, defined by international standards, including INTERMAGNET. Significant efforts of observatory staff are direct to archive (raw) magnetic data, a significant part of which has not been entirely processed, is not presented in international data centers and is still not available to the scientific community. Digital images of analog magnetograms have been obtained, the digitization of which allowed to fill the gaps in the hourly data available in the WDC for 1991, 1996-1997. The state of the set of the instruments and databases shows that the observatory "Paratunka" can solve most of the problems that arise in the geomagnetic field researches, including the provision of data for the development of regional and global field models, ground support of magnetometers located on satellites, support of the surface (sea) and aeromagnetic surveys and drilling, providing the data for researches of processes in the lithosphere, magnetosphere and ionosphere over a wide frequency range, and also for a number of applied problems. ARRAY(0x189e680)

Tertiary structure in N-linked oligosaccharides.

PubMed

Homans, S W; Dwek, R A; Rademacher, T W

1987-10-06

Distance constraints derived from two-dimensional nuclear Overhauser effect measurements have been used to define the orientation of the Man alpha 1-3Man beta linkage in seven different N-linked oligosaccharides, all containing the common pentasaccharide core Man alpha 1-6(Man alpha 1-3)Man beta 1-4GlcNAc beta 1-4GlcNAc. Conformational invariance of the Man alpha 1-3Man beta linkage was found for those structures bearing substitutions on the Man alpha 1-3Man beta antenna. However, the presence of either a GlcNAc residue in the beta 1-4 linkage to Man beta ("bisecting GlcNAc") or a xylose residue in the beta 1-2 linkage to Man beta of the trimannosyl core was found to generate conformational transitions that were similar. These transitions were accompanied by characteristic chemical shift perturbations of proton resonances in the vicinity of the Man alpha 1-3Man beta linkage. Molecular orbital energy calculations suggest that the conformational transition between the unsubstituted and substituted cores arises from energetic constraints in the vicinity of the Man alpha 1-3Man beta linkage, rather than specific long-range interactions. These data taken together with our previous results on the Man alpha 1-6Man beta linkage [Homans, S. W., Dwek R. A., Boyd, J., Mahmoudian, M., Richards, W. G., & Rademacher, T. W. (1986) Biochemistry 25, 6342] allow us to discuss the consequences of the modulation of oligosaccharide solution conformations.

A table-top PXI based low-field spectrometer for solution dynamic nuclear polarization.

PubMed

Biller, Joshua R; Stupic, Karl F; Moreland, J

2018-03-01

We present the development of a portable dynamic nuclear polarization (DNP) instrument based on the PCI eXtensions for Instrumentation platform. The main purpose of the instrument is for study of 1 H polarization enhancements in solution through the Overhauser mechanism at low magnetic fields. A DNP probe set was constructed for use at 6.7 mT, using a modified Alderman-Grant resonator at 241 MHz for saturation of the electron transition. The solenoid for detection of the enhanced 1 H signal at 288 kHz was constructed with Litz wire. The largest observed 1 H enhancements (ε) at 6.7 mT for 14 N-CTPO radical in air saturated aqueous solution was ε~65. A concentration dependence of the enhancement is observed, with maximum ε at 5.5 mM. A low resonator efficiency for saturation of the electron paramagnetic resonance transition results in a decrease in ε for the 10.3 mM sample. At high incident powers (42 W) and long pump times, capacitor heating effects can also decrease the enhancement. The core unit and program described here could be easily adopted for multi-frequency DNP work, depending on available main magnets and selection of the "plug and play" arbitrary waveform generator, digitizer, and radiofrequency synthesizer PCI eXtensions for Instrumentatione cards. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Communication: Contrasting effects of glycerol and DMSO on lipid membrane surface hydration dynamics and forces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schrader, Alex M.; Cheng, Chi-Yuan; Israelachvili, Jacob N.

2016-07-28

Glycerol and dimethyl sulfoxide (DMSO) are commonly used cryoprotectants in cellular systems, but due to the challenges of measuring the properties of surface-bound solvent, fundamental questions remain regarding the concentration, interactions, and conformation of these solutes at lipid membrane surfaces. We measured the surface water diffusivity at gel-phase dipalmitoylphosphatidylcholine (DPPC) bilayer surfaces in aqueous solutions containing ≤7.5 mol. % of DMSO or glycerol using Overhauser dynamic nuclear polarization. We found that glycerol similarly affects the diffusivity of water near the bilayer surface and that in the bulk solution (within 20%), while DMSO substantially increases the diffusivity of surface water relativemore » to bulk water. We compare these measurements of water dynamics with those of equilibrium forces between DPPC bilayers in the same solvent mixtures. DMSO greatly decreases the range and magnitude of the repulsive forces between the bilayers, whereas glycerol increases it. We propose that the differences in hydrogen bonding capability of the two solutes leads DMSO to dehydrate the lipid head groups, while glycerol affects surface hydration only as much as it affects the bulk water properties. The results suggest that the mechanism of the two most common cryoprotectants must be fundamentally different: in the case of DMSO by decoupling the solvent from the lipid surface, and in the case of glycerol by altering the hydrogen bond structure and intermolecular cohesion of the global solvent, as manifested by increased solvent viscosity.« less

A New Sucrase Enzyme Inhibitor from Azadirachta indica

PubMed Central

Abdelhady, Mohamed I. S.; Shaheen, Usama; Bader, Ammar; Youns, Mahmoud A.

2016-01-01

Background: Sucrase enzyme inhibitor considered as an oral anti-diabetic therapy that delays the absorption of eaten carbohydrates, reducing the postprandial glucose and insulin peaks to reach normoglycemia. Materials and Methods: Chromatographic fractionation of the hydroalcoholic extract of leaves of Azadirachta indica growing in KSA, followed by in-vitro assay of sucrase enzyme inhibition activity. Results: This investigation led to the isolation of a new remarkable sucrase enzyme inhibitor; 4’-methyl Quercetin-7-O-β-D-glucuronopyranoside (1) alongside with four known compounds; 2,3-hexahydroxydiphenoyl-(α/β)-D-4C1-glucopyranose (2), Avicularin (3), Castalagin (4) and Quercetin-3-O-glucoside (5). The structure of the new compound (1) was elucidated on the basis of its spectral data, including ESI-MS, UV, 1H NMR, 13C NMR, 1H-1H COSY, HSQC, NOESY and HMBC. Conclusion: Under the assay conditions, hydroalcoholic extract of A. indica and compounds 1-5 exhibited significant sucrase enzyme inhibitory activity. SUMMARY Chromatographic fractionation of the hydroalcoholic extract of leaves of Azadirachta indica, led to the Isolation of a new flavonoid glycoside named 4’-methyl Quercetin-7-O-β-D-glucuronopyranoside, alongside to other 4 known polyphenols. The hydroalcoholic extract as well as the isolated compounds exhibited significant sucrase enzyme inhibitory activity. Abbreviations used: ESI-MS; electrospray ionization-mass spectrometry, UV; ultraviolet, NMR; nuclear magnetic resonance, 1H-1H COSY; 1H-1H correlation spectroscopy, NOESY; nuclear overhauser effect spectroscopy, and HSQC; heteronuclear multiple bond correlation. A. indica; Azadirachta indica. PMID:27563214

A New Sucrase Enzyme Inhibitor from Azadirachta indica.

PubMed

Abdelhady, Mohamed I S; Shaheen, Usama; Bader, Ammar; Youns, Mahmoud A

2016-05-01

Sucrase enzyme inhibitor considered as an oral anti-diabetic therapy that delays the absorption of eaten carbohydrates, reducing the postprandial glucose and insulin peaks to reach normoglycemia. Chromatographic fractionation of the hydroalcoholic extract of leaves of Azadirachta indica growing in KSA, followed by in-vitro assay of sucrase enzyme inhibition activity. This investigation led to the isolation of a new remarkable sucrase enzyme inhibitor; 4'-methyl Quercetin-7-O-β-D-glucuronopyranoside (1) alongside with four known compounds; 2,3-hexahydroxydiphenoyl-(α/β)-D-(4)C1-glucopyranose (2), Avicularin (3), Castalagin (4) and Quercetin-3-O-glucoside (5). The structure of the new compound (1) was elucidated on the basis of its spectral data, including ESI-MS, UV, (1)H NMR, (13)C NMR, (1)H-(1)H COSY, HSQC, NOESY and HMBC. Under the assay conditions, hydroalcoholic extract of A. indica and compounds 1-5 exhibited significant sucrase enzyme inhibitory activity. Chromatographic fractionation of the hydroalcoholic extract of leaves of Azadirachta indica, led to the Isolation of a new flavonoid glycoside named 4'-methyl Quercetin-7-O-β-D-glucuronopyranoside, alongside to other 4 known polyphenols. The hydroalcoholic extract as well as the isolated compounds exhibited significant sucrase enzyme inhibitory activity. Abbreviations used: ESI-MS; electrospray ionization-mass spectrometry, UV; ultraviolet, NMR; nuclear magnetic resonance, 1H-1H COSY; 1H-1H correlation spectroscopy, NOESY; nuclear overhauser effect spectroscopy, and HSQC; heteronuclear multiple bond correlation. A. indica; Azadirachta indica.

Close temporal correspondence between geomagnetic anomalies and earthquakes during the 2002-2003 eruption of Etna volcano

USGS Publications Warehouse

Currenti, G.; Del, Negro C.; Johnston, M.; Sasai, Y.

2007-01-01

The early stages of the 2002-2003 lateral eruption at Mount Etna were accompanied by slow changes (over some hours) and some rapid step offsets in the local magnetic field. At five monitoring locations, the total magnetic field intensity has been measured using continuously operating Overhauser magnetometers at a sampling rate of 10 s. The very unique aspect of these observations is the close temporal correspondence between magnetic field offsets and earthquakes that occurred in the upper northern flank of the volcano on 27 October 2002 prior to a primary eruption. Rapid coseismic changes of the magnetic field were clearly identified for three of the most energetic earthquakes, which were concentrated along the Northeast Rift at a depth of about 1 km below sea level. Coseismic magnetic signals, with amplitudes from 0.5 to 2.5 nT, have been detected for three of the largest seismic events located roughly midway between the magnetic stations. We quantitatively examine possible geophysical mechanisms, which could cause the magnetic anomalies. The comparison between magnetic data, seismicity and surface phenomena implies that piezomagnetic effects are the primary physical mechanism responsible for the observed magnetic anomalies although the detailed cause of the rapid high stress change required is not clear. The modeling of the observed coseismic magnetic changes in terms of piezomagnetic mechanism provides further evidence of the complex interaction between volcanic and tectonic processes during dike propagation along the Northeast Rift. Copyright 2007 by the American Geophysical Union.

Thymosin α1 Interacts with Exposed Phosphatidylserine in Membrane Models and in Cells and Uses Serum Albumin as a Carrier.

PubMed

Mandaliti, Walter; Nepravishta, Ridvan; Sinibaldi Vallebona, Paola; Pica, Francesca; Garaci, Enrico; Paci, Maurizio

2016-03-15

Thymosin α1 is a peptidic hormone with pleiotropic activity and is used in the therapy of several diseases. It is unstructured in water solution and interacts with negative regions of vesicles by assuming two tracts of helical conformation with a structural break between them. This study reports on Thymosin α1's interaction with mixed phospholipids phosphatidylcholine and phosphatidylserine, the negative component of the membranes, by ¹H and natural abundance ¹⁵N nuclear magnetic resonance (NMR). The results indicate that interaction occurs when the membrane is negatively charged by exposing phosphatidylserine. Moreover, the direct interaction of Thymosin α1 with K562 cells with an overexposure of phosphatidylserine as a consequence of resveratrol-induced apoptosis was conducted. Thymosin α1's interaction with human serum albumin was also investigated by NMR spectroscopy. Steady-state saturation transfer, transfer nuclear Overhauser effect spectroscopy, and diffusion-ordered spectroscopy methodologies all reveal that the C-terminal region of Thymosin α1 is involved in the interaction with serum albumin. These results may shed more light on Thymosin α1's mechanism of action by its insertion in negative regions of membranes due to the exposure of phosphatidylserine. Once Thymosin α1's N-terminus has been inserted into the membrane, the rest may interact with nearby proteins and/or receptors acting as effectors and causing a biological signaling cascade, thus exerting thymosin α1's pleiotropy.

Investigating the Interaction Pattern and Structural Elements of a Drug-Polymer Complex at the Molecular Level.

PubMed

Nie, Haichen; Mo, Huaping; Zhang, Mingtao; Song, Yang; Fang, Ke; Taylor, Lynne S; Li, Tonglei; Byrn, Stephen R

2015-07-06

Strong associations between drug and polymeric carriers are expected to contribute to higher drug loading capacities and better physical stability of amorphous solid dispersions. However, molecular details of the interaction patterns and underlying mechanisms are still unclear. In the present study, a series of amorphous solid dispersions of clofazimine (CLF), an antileprosy drug, were prepared with different polymers by applying the solvent evaporation method. When using hypromellose phthalate (HPMCP) as the carrier, the amorphous solid dispersion system exhibits not only superior drug loading capacity (63% w/w) but also color change due to strong drug-polymer association. In order to further explain these experimental observations, the interaction between CLF and HPMCP was investigated in a nonpolar volatile solvent system (chloroform) prior to forming the solid dispersion. We observed significant UV/vis and (1)H NMR spectral changes suggesting the protonation of CLF and formation of ion pairs between CLF and HPMCP in chloroform. Furthermore, nuclear Overhauser effect spectroscopy (NOESY) and diffusion order spectroscopy (DOSY) were employed to evaluate the strength of associations between drug and polymers, as well as the molecular mobility of CLF. Finally, by correlating the experimental values with quantum chemistry calculations, we demonstrate that the protonated CLF is binding to the carboxylate group of HPMCP as an ion pair and propose a possible structural model of the drug-polymer complex. Understanding the drug and carrier interaction patterns from a molecular perspective is critical for the rational design of new amorphous solid dispersions.

Optimized 31P MRS in the human brain at 7 T with a dedicated RF coil setup

PubMed Central

van de Bank, Bart L.; Orzada, Stephan; Smits, Frits; Lagemaat, Miriam W.; Rodgers, Christopher T.; Bitz, Andreas K.

2015-01-01

The design and construction of a dedicated RF coil setup for human brain imaging (1H) and spectroscopy (31P) at ultra‐high magnetic field strength (7 T) is presented. The setup is optimized for signal handling at the resonance frequencies for 1H (297.2 MHz) and 31P (120.3 MHz). It consists of an eight‐channel 1H transmit–receive head coil with multi‐transmit capabilities, and an insertable, actively detunable 31P birdcage (transmit–receive and transmit only), which can be combined with a seven‐channel receive‐only 31P array. The setup enables anatomical imaging and 31P studies without removal of the coil or the patient. By separating transmit and receive channels and by optimized addition of array signals with whitened singular value decomposition we can obtain a sevenfold increase in SNR of 31P signals in the occipital lobe of the human brain compared with the birdcage alone. These signals can be further enhanced by 30 ± 9% using the nuclear Overhauser effect by B 1‐shimmed low‐power irradiation of water protons. Together, these features enable acquisition of 31P MRSI at high spatial resolutions (3.0 cm3 voxel) in the occipital lobe of the human brain in clinically acceptable scan times (~15 min). © 2015 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd. PMID:26492089

Trp-cage: folding free energy landscape in explicit water.

PubMed

Zhou, Ruhong

2003-11-11

Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle-particle particle-mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 A Calpha-RMSD (Calpha-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence.

Trp-cage: Folding free energy landscape in explicit water

NASA Astrophysics Data System (ADS)

Zhou, Ruhong

2003-11-01

Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle-particle particle-mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 Å C-RMSD (C-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence.

Trp-cage: Folding free energy landscape in explicit water

PubMed Central

Zhou, Ruhong

2003-01-01

Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle–particle particle–mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 Å Cα-RMSD (Cα-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence. PMID:14581616

Ion specific effects: decoupling ion-ion and ion-water interactions

PubMed Central

Song, Jinsuk; Kang, Tae Hui; Kim, Mahn Won; Han, Songi

2015-01-01

Ion-specific effects in aqueous solution, known as the Hofmeister effect is prevalent in diverse systems ranging from pure ionic to complex protein solutions. The objective of this paper is to explicitly demonstrate how complex ion-ion and ion-water interactions manifest themselves in the Hofmeister effects, based on a series of recent experimental observation. These effects are not considered in the classical description of ion effects, such as the Deryaguin-Landau-Verwey-Overbeek (DLVO) theory that, likely for that reason, fail to describe the origin of the phenomenological Hofmeister effect. However, given that models considering the basic forces of electrostatic and van der Waals interactions can offer rationalization for the core experimental observations, a universal interaction model stands a chance to be developed. In this perspective, we separately derive the contribution from ion-ion electrostatic interaction and ion-water interaction from second harmonic generation (SHG) data at the air-ion solution interface, which yields an estimate of ion-water interactions in solution. Hofmeister ion effects observed on biological solutes in solution should be similarly influenced by contributions from ion-ion and ion-water interactions, where the same ion-water interaction parameters derived from SHG data at the air-ion solution interface could be applicable. A key experimental data set available from solution systems to probe ion-water interaction is the modulation of water diffusion dynamics near ions in bulk ion solution, as well as near biological liposome surfaces. It is obtained from Overhauser dynamic nuclear polarization (ODNP), a nuclear magnetic resonance (NMR) relaxometry technique. The surface water diffusivity is influenced by the contribution from ion-water interactions, both from localized surface charges and adsorbed ions, although the relative contribution of the former is larger on liposome surfaces. In this perspective, ion-water interaction energy values derived from experimental data for various ions are compared with theoretical values in the literature. Ultimately, quantifying ion-induced changes in surface energy for the purpose of developing valid theoretical models for ion-water interaction, will be critical to rationalizing the Hofmeister effect. PMID:25761273

Comparison of pulsed three-dimensional CEST acquisition schemes at 7 tesla: steady state versus pseudosteady state.

PubMed

Khlebnikov, Vitaliy; Geades, Nicolas; Klomp, Dennis W J; Hoogduin, Hans; Gowland, Penny; Mougin, Olivier

2017-06-01

To compare two pulsed, volumetric chemical exchange saturation transfer (CEST) acquisition schemes: steady state (SS) and pseudosteady state (PS) for the same brain coverage, spatial/spectral resolution and scan time. Both schemes were optimized for maximum sensitivity to amide proton transfer (APT) and nuclear Overhauser enhancement (NOE) effects through Bloch-McConnell simulations, and compared in terms of sensitivity to APT and NOE effects, and to transmit field inhomogeneity. Five consented healthy volunteers were scanned on a 7 Tesla Philips MR-system using the optimized protocols at three nominal B 1 amplitudes: 1 μT, 2 μT, and 3 μT. Region of interest based analysis revealed that PS is more sensitive (P < 0.05) to APT and NOE effects compared with SS at low B 1 amplitudes (0.7-1.0 μT). Also, both sequences have similar dependence on the transmit field inhomogeneity. For the optimum CEST presaturation parameters (1 μT and 2 μT for APT and NOE, respectively), NOE is less sensitive to the inhomogeneity effects (15% signal to noise ratio [SNR] change for a B 1 dropout of 40%) compared with APT (35% SNR change for a B 1 dropout of 40%). For the same brain coverage, spatial/spectral resolution and scan time, at low power levels PS is more sensitive to the slow chemical exchange-mediated processes compared with SS. Magn Reson Med 77:2280-2287, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Clinical NOE 13C MRS for neuropsychiatric disorders of the frontal lobe

NASA Astrophysics Data System (ADS)

Sailasuta, Napapon; Robertson, Larry W.; Harris, Kent C.; Gropman, Andrea L.; Allen, Peter S.; Ross, Brian D.

2008-12-01

In this communication, a scheme is described whereby in vivo 13C MRS can safely be performed in the frontal lobe, a human brain region hitherto precluded on grounds of SAR, but important in being the seat of impaired cognitive function in many neuropsychiatric and developmental disorders. By combining two well known features of 13C NMR—the use of low power NOE and the focus on 13C carbon atoms which are only minimally coupled to protons, we are able to overcome the obstacle of SAR and develop means of monitoring the 13C fluxes of critically important metabolic pathways in frontal brain structures of normal volunteers and patients. Using a combination of low-power WALTZ decoupling, variants of random noise for nuclear overhauser effect enhancement it was possible to reduce power deposition to 20% of the advised maximum specific absorption rate (SAR). In model solutions 13C signal enhancement achieved with this scheme were comparable to that obtained with WALTZ-4. In human brain, the low power procedure effectively determined glutamine, glutamate and bicarbonate in the posterior parietal brain after [1- 13C] glucose infusion. The same 13C enriched metabolites were defined in frontal brain of human volunteers after administration of [1- 13C] acetate, a recognized probe of glial metabolism. Time courses of incorporation of 13C into cerebral glutamate, glutamine and bicarbonate were constructed. The results suggest efficacy for measurement of in vivo cerebral metabolic rates of the glutamate-glutamine and tricarboxylic acid cycles in 20 min MR scans in previously inaccessible brain regions in humans at 1.5T. We predict these will be clinically useful biomarkers in many human neuropsychiatric and genetic conditions.

Function and solution structure of huwentoxin-IV, a potent neuronal tetrodotoxin (TTX)-sensitive sodium channel antagonist from Chinese bird spider Selenocosmia huwena.

PubMed

Peng, Kuan; Shu, Qin; Liu, Zhonghua; Liang, Songping

2002-12-06

We have isolated a highly potent neurotoxin from the venom of the Chinese bird spider, Selenocosmia huwena. This 4.1-kDa toxin, which has been named huwentoxin-IV, contains 35 residues with three disulfide bridges: Cys-2-Cys-17, Cys-9-Cys-24, and Cys-16-Cys-31, assigned by a chemical strategy including partial reduction of the toxin and sequence analysis of the modified intermediates. It specifically inhibits the neuronal tetrodotoxin-sensitive (TTX-S) voltage-gated sodium channel with the IC(50) value of 30 nm in adult rat dorsal root ganglion neurons, while having no significant effect on the tetrodotoxin-resistant (TTX-R) voltage-gated sodium channel. This toxin seems to be a site I toxin affecting the sodium channel through a mechanism quite similar to that of TTX: it suppresses the peak sodium current without altering the activation or inactivation kinetics. The three-dimensional structure of huwentoxin-IV has been determined by two-dimensional (1)H NMR combined with distant geometry and simulated annealing calculation by using 527 nuclear Overhauser effect constraints and 14 dihedral constraints. The resulting structure is composed of a double-stranded antiparallel beta-sheet (Leu-22-Ser-25 and Trp-30-Tyr-33) and four turns (Glu-4-Lys-7, Pro-11-Asp-14, Lys-18-Lys-21 and Arg-26-Arg-29) and belongs to the inhibitor cystine knot structural family. After comparison with other toxins purified from the same species, we are convinced that the positively charged residues of loop IV (residues 25-29), especially residue Arg-26, must be crucial to its binding to the neuronal tetrodotoxin-sensitive voltage-gated sodium channel.

Main-chain optically active riboflavin polymer for asymmetric catalysis and its vapochromic behavior.

PubMed

Iida, Hiroki; Iwahana, Soichiro; Mizoguchi, Tomohisa; Yashima, Eiji

2012-09-12

A novel optically active polymer consisting of riboflavin units as the main chain (poly-1) was prepared from naturally occurring riboflavin (vitamin B(2)) in three steps. The riboflavin residues of poly-1 were converted to 5-ethylriboflavinium cations (giving poly-2), which could be reversibly transformed into the corresponding 4a-hydroxyriboflavins (giving poly-2OH) through hydroxylation/dehydroxylation reactions. This reversible structural change was accompanied by a visible color change along with significant changes in the absorption and circular dichroism (CD) spectra. The nuclear Overhauser effect spectroscopy (NOESY) and CD spectra of poly-2 revealed a supramolecularly twisted helical structure with excess one-handedness through face-to-face stacking of the intermolecular riboflavinium units, as evidenced by the apparent NOE correlations between the interstrand riboflavin units and intense Cotton effects induced in the flavinium chromophore regions. The hydroxylation of poly-2 at the 4a-position proceeded in a diastereoselective fashion via chirality transfer from the induced supramolecular helical chirality assisted by the ribityl pendants, resulting in a 83:17 diastereomeric mixture of poly-2OH. The diastereoselectivity of poly-2 was remarkably higher than that of the corresponding monomeric model (64.5:35.5), indicating amplification of the chirality resulting from the supramolecular chirality induced in the stacked poly-2 backbones. The optically active poly-2 efficiently catalyzed the asymmetric organocatalytic oxidation of sulfides with hydrogen peroxide, yielding optically active sulfoxides with up to 60% enantiomeric excess (ee), whose enantioselectivity was higher than that catalyzed by the monomeric counterpart (30% ee). In addition, upon exposure to primary and secondary amines, poly-2 exhibited unique high-speed vapochromic behavior arising from the formation of 4a-amine adducts in the film.

Unravelling RNA-substrate interactions in a ribozyme-catalysed reaction using fluorescent turn-on probes.

PubMed

Gaffarogullari, Ece Cazibe; Greulich, Peter; Kobitski, Andrei Yu; Nierth, Alexander; Nienhaus, G Ulrich; Jäschke, Andres

2015-04-07

The Diels-Alder reaction is one of the most important C-C bond-forming reactions in organic chemistry, and much effort has been devoted to controlling its enantio- and diastereoselectivity. The Diels-Alderase ribozyme (DAse) catalyses the reaction between anthracene dienes and maleimide dienophiles with multiple-turnover, stereoselectivity, and up to 1100-fold rate acceleration. Here, a new generation of anthracene-BODIPY-based fluorescent probes was developed to monitor catalysis by the DAse. The brightness of these probes increases up to 93-fold upon reaction with N-pentylmaleimide (NPM), making these useful tools for investigating the stereochemistry of the ribozyme-catalysed reaction. With these probes, we observed that the DAse catalyses the reaction with >91% de and >99% ee. The stereochemistry of the major product was determined unambiguously by rotating-frame nuclear Overhauser NMR spectroscopy (ROESY-NMR) and is in agreement with crystallographic structure information. The pronounced fluorescence change of the probes furthermore allowed a complete kinetic analysis, which revealed an ordered bi uni type reaction mechanism, with the dienophile binding first. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fogh, R.H.; Mabbutt, B.C.; Kem, W.R.

Sequence-specific assignments are reported for the 500-MHz H nuclear magnetic resonance (NMR) spectrum of the 48-residue polypeptide neurotoxin I from the sea anemone Stichodactyla helianthus (Sh I). Spin systems were first identified by using two-dimensional relayed or multiple quantum filtered correlation spectroscopy, double quantum spectroscopy, and spin lock experiments. Specific resonance assignments were then obtained from nuclear Overhauser enhancement (NOE) connectivities between protons from residues adjacent in the amino acid sequence. Of a total of 265 potentially observable resonances, 248 (i.e., 94%) were assigned, arising from 39 completely and 9 partially assigned amino acid spin systems. The secondary structure ofmore » Sh I was defined on the basis of the pattern of sequential NOE connectivities. NOEs between protons on separate strands of the polypeptide backbone, and backbone amide exchange rates. Sh I contains a four-stranded antiparallel {beta}-sheet encompassing residues 1-5, 16-24, 30-33, and 40-46, with a {beta}-bulge at residues 17 and 18 and a reverse turn, probably a type II {beta}-turn, involving residues 27-30. No evidence of {alpha}-helical structure was found.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Driscoll, P.C.; Clore, G.M.; Beress, L.

The sequential resonance assignment of the {sup 1}H NMR spectrum of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata is presented. This is carried out with two-dimensional NMR techniques to identify through-bond and through-space (< 5{angstrom}) connectivities. Added spectral complexity arises from the fact that the sample is an approximately 1:1 mixture of two BDS-I isoproteins, (Leu-18)-BDS-I and (Phe-18)-BDS-I. Complete assignments, however, are obtained, largely due to the increased resolution and sensitivity afforded at 600 MHz. In addition, the stereospecific assignment of a large number of {beta}-methylene protons is achieved from an analysis of the patternmore » of {sup 3}J{sub {alpha}{beta}} coupling constants and the relative magnitudes of intraresidue NOEs involving the NH, C{sup {alpha}}H, and C{sup {beta}}H protons. Regular secondary structure elements are deduced from a qualitative interpretation of the nuclear Overhauser enhancement, {sup 3}J{sub HN{alpha}} coupling constant, and amide NH exchange data. A triple-stranded antiparallel {beta}-sheet is found to be related to that found in partially homologous sea anemone polypeptide toxins.« less

NMR of (133)Cs(+) in stretched hydrogels: One-dimensional, z- and NOESY spectra, and probing the ion's environment in erythrocytes.

PubMed

Kuchel, Philip W; Shishmarev, Dmitry; Puckeridge, Max; Levitt, Malcolm H; Naumann, Christoph; Chapman, Bogdan E

2015-12-01

(133)Cs nuclear magnetic resonance (NMR) spectroscopy was conducted on (133)Cs(+) in gelatin hydrogels that were either relaxed or stretched. Stretching generated a septet from this spin-7/2 nucleus, and its nuclear magnetic relaxation was studied via z-spectra, and two-dimensional nuclear Overhauser (NOESY) spectroscopy. Various spectral features were well simulated by using Mathematica and the software package SpinDynamica. Spectra of CsCl in suspensions of human erythrocytes embedded in gelatin gel showed separation of the resonances from the cation inside and outside the cells. Upon stretching the sample, the extracellular (133)Cs(+) signal split into a septet, while the intracellular peak was unchanged, revealing different alignment/ordering properties of the environment inside and around the cells. Differential interference contrast light microscopy confirmed that the cells were stretched when the overall sample was elongated. Analysis of the various spectral features of (133)Cs(+) reported here opens up applications of this K(+) congener for studies of cation-handling by metabolically-active cells and tissues in aligned states. Copyright © 2015 Elsevier Inc. All rights reserved.

NMR studies on the structure and dynamics of lac operator DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, S.C.

Nuclear Magnetic Resonance spectroscopy was used to elucidate the relationships between structure, dynamics and function of the gene regulatory sequence corresponding to the lactose operon operator of Escherichia coli. The length of the DNA fragments examined varied from 13 to 36 base pair, containing all or part of the operator sequence. These DNA fragments are either derived genetically or synthesized chemically. Resonances of the imino protons were assigned by one dimensional inter-base pair nuclear Overhauser enhancement (NOE) measurements. Imino proton exchange rates were measured by saturation recovery methods. Results from the kinetic measurements show an interesting dynamic heterogeneity with amore » maximum opening rate centered about a GTG/CAC sequence which correlates with the biological function of the operator DNA. This particular three base pair sequence occurs frequently and often symmetrically in prokaryotic nd eukaryotic DNA sites where one anticipates specific protein interaction for gene regulation. The observed sequence dependent imino proton exchange rate may be a reflection of variation of the local structure of regulatory DNA. The results also indicate that the observed imino proton exchange rates are length dependent.« less

Characterization of the International Humic Substances Society standard and reference fulvic and humic acids by solution state carbon-13 (13C) and hydrogen-1 (1H) nuclear magnetic resonance spectrometry

USGS Publications Warehouse

Thorn, Kevin A.; Folan, Daniel W.; MacCarthy, Patrick

1989-01-01

Standard and reference samples of the International Humic Substances Society have been characterized by solution state carbon-13 and hydrogen-1 nuclear magnetic resonance (NMR) spectrometry. Samples included the Suwannee River, soil, and peat standard fulvic and humic acids, the Leonardite standard humic acid, the Nordic aquatic reference fulvic and humic acids, and the Summit Hill soil reference humic acid. Aqueous-solution carbon-13 NMR analyses included the measurement of spin-lattice relaxation times, measurement of nuclear Overhauser enhancement factors, measurement of quantitative carbon distributions, recording of attached proton test spectra, and recording of spectra under nonquantitative conditions. Distortionless enhancement by polarization transfer carbon-13 NMR spectra also were recorded on the Suwannee River fulvic acid in deuterated dimethyl sulfoxide. Hydrogen-1 NMR spectra were recorded on sodium salts of the samples in deuterium oxide. The carbon aromaticities of the samples ranged from 0.24 for the Suwannee River fulvic acid to 0.58 for the Leonardite humic acid.

Effect of the Flexible Regions of the Oncoprotein Mouse Double Minute X on Inhibitor Binding Affinity.

PubMed

Qin, Lingyun; Liu, Huili; Chen, Rong; Zhou, Jingjing; Cheng, Xiyao; Chen, Yao; Huang, Yongqi; Su, Zhengding

2017-11-07

The oncoprotein MdmX (mouse double minute X) is highly homologous to Mdm2 (mouse double minute 2) in terms of their amino acid sequences and three-dimensional conformations, but Mdm2 inhibitors exhibit very weak affinity for MdmX, providing an excellent model for exploring how protein conformation distinguishes and alters inhibitor binding. The intrinsic conformation flexibility of proteins plays pivotal roles in determining and predicting the binding properties and the design of inhibitors. Although the molecular dynamics simulation approach enables us to understand protein-ligand interactions, the mechanism underlying how a flexible binding pocket adapts an inhibitor has been less explored experimentally. In this work, we have investigated how the intrinsic flexible regions of the N-terminal domain of MdmX (N-MdmX) affect the affinity of the Mdm2 inhibitor nutlin-3a using protein engineering. Guided by heteronuclear nuclear Overhauser effect measurements, we identified the flexible regions that affect inhibitor binding affinity around the ligand-binding pocket on N-MdmX. A disulfide engineering mutant, N-MdmX C25-C110/C76-C88 , which incorporated two staples to rigidify the ligand-binding pocket, allowed an affinity for nutlin-3a higher than that of wild-type N-MdmX (K d ∼ 0.48 vs K d ∼ 20.3 μM). Therefore, this mutant provides not only an effective protein model for screening and designing of MdmX inhibitors but also a valuable clue for enhancing the intermolecular interactions of the pharmacophores of a ligand with pronounced flexible regions. In addition, our results revealed an allosteric ligand-binding mechanism of N-MdmX in which the ligand initially interacts with a compact core, followed by augmenting intermolecular interactions with intrinsic flexible regions. This strategy should also be applicable to many other protein targets to accelerate drug discovery.

Preparative isolation and purification of seven isoflavones from Belamcanda chinensis.

PubMed

Lee, Yeon Sil; Kim, Seon Ha; Kim, Jin Kyu; Lee, Sanghyun; Jung, Sang Hoon; Lim, Soon Sung

2011-01-01

Isoflavonoids from Belamcanda chinensis are known to have a number of physiological benefits including anti-inflammatory, anti-angiogenic and anti-mutagenic properties. However, there have been no reports on the effective isolation and purification of isoflavonoids from B. chinensis. To develop an efficient method for the preparative isolation and purification of isoflavones from B. chinensis by high-speed counter-current chromatography (HSCCC). A two-step HSCCC isolation method was developed using solvent system of n-hexane-ethyl acetate-2-propanol-methanol-water (5:6:2:3.5:6, v/v) and of ethyl acetate-methanol-water (10:2:9, v/v). FLASH purification system (45% methanol, isocratic) was also used for further purification. The purities and chemical structures of the isolated compounds were determined by high-performance liquid chromatography-photodiode array detection (HPLC-PDA), electrospray ionisation-mass spectrometry (ESI-MS), ¹H- and ¹³C-nuclear magnetic resonance spectrometry (NMR) and nuclear overhauser enhancement (NOE). HSCCC was successfully used for the preparative separation and purification of seven isoflavones, including tectoridin (145.4 mg, 97.5%), iridin (77.9 mg, 94.0%), irilin D (42.0 mg, 92.0%), tectorigenin (294.1 mg, 98.6%), iristectorigenin A (86.8 mg, 93.4%), irigenin (141.8 mg, 95.8%) and irisflorentin (73.4 mg, 94.7%) from the rhizomes of B. chinensis. Two isoflavone glycosides and five isoflavone derivatives were successfully isolated and purified from the crude methanol extract of dried rhizomes of the B. chinensis by HSCCC. Copyright © 2011 John Wiley & Sons, Ltd.

Assignment of the sup 1 H and sup 15 N NMR spectra of Rhodobacter capsulatus ferrocytochrome c sub 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gooley, P.R.; Caffrey, M.S.; Cusanovich, M.A.

1990-03-06

The peptide resonances of the {sup 1}H and {sup 15}N nuclear magnetic resonance spectra of ferrocytochrome c{sub 2} from Rhodobacter capsulatus are sequentially assigned by a combination of 2D {sup 1}H-{sup 1}H and {sup 1}H-{sup 15}N spectroscopy, the latter performed on {sup 15}N-enriched protein. Short-range nuclear Overhauser effect (NOE) data show {alpha}-helices from residues 3-17, 55-65, 69-88, and 103-115. Within the latter two {alpha}-helices, there are three single 3{sub 10} turns, 70-72, 76-78, and 107-109. In addition {alpha}H-NH{sub i+1} and {alpha}H-NH{sub i+2} NOEs indicate that the N-terminal helix (3-17) is distorted. Compared to horse or tuna cytochrome c and cytochromemore » c{sub 2} of Rhodospirillium rubrum, there is a 6-residue insertion at residues 23-29 in R. capsulatus cytochrome c{sub 2}. The NOE data show that this insertion forms a loop, probably an {Omega} loop. {sup 1}H-{sup 15}N heteronuclear multiple quantum correlation experiments are used to follow NH exchange over a period of 40 h. As the 2D spectra are acquired in short time periods (30 min), rates for intermediate exchanging protons can be measured. Comparison of the NH exchange data for the N-terminal helix of cytochrome c{sub 2} of R. capsulatus with the highly homologous horse heart cytochrome c shows that this helix is less stable in cytochrome c{sub 2}.« less

An Introduction to Biological NMR Spectroscopy*

PubMed Central

Marion, Dominique

2013-01-01

NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP). PMID:23831612

The role of alpha-, 3(10)-, and pi-helix in helix-->coil transitions.

PubMed

Armen, Roger; Alonso, Darwin O V; Daggett, Valerie

2003-06-01

The conformational equilibrium between 3(10)- and alpha-helical structure has been studied via high-resolution NMR spectroscopy by Millhauser and coworkers using the MW peptide Ac-AMAAKAWAAKA AAARA-NH2. Their 750-MHz nuclear Overhauser effect spectroscopy (NOESY) spectra were interpreted to reflect appreciable populations of 3(10)-helix throughout the peptide, with the greatest contribution at the N and C termini. The presence of simultaneous alphaN(i,i + 2) and alphaN(i,i + 4) NOE cross-peaks was proposed to represent conformational averaging between 3(10)- and alpha-helical structures. In this study, we describe 25-nsec molecular dynamics simulations of the MW peptide at 298 K, using both an 8 A and a 10 A force-shifted nonbonded cutoff. The ensemble averages of both simulations are in reasonable agreement with the experimental helical content from circular dichroism (CD), the (3)J(HNalpha) coupling constants, and the 57 observed NOEs. Analysis of the structures from both simulations revealed very little formation of contiguous i --> i + 3 hydrogen bonds (3(10)-helix); however, there was a large population of bifurcated i --> i + 3 and i --> i + 4 alpha-helical hydrogen bonds. In addition, both simulations contained considerable populations of pi-helix (i --> i + 5 hydrogen bonds). Individual turns formed over residues 1-9, which we predict contribute to the intensities of the experimentally observed alphaN(i,i + 2) NOEs. Here we show how sampling of both folded and unfolded structures can provide a structural framework for deconvolution of the conformational contributions to experimental ensemble averages.

The role of α-, 310-, and π-helix in helix→coil transitions

PubMed Central

Armen, Roger; Alonso, Darwin O.V.; Daggett, Valerie

2003-01-01

The conformational equilibrium between 310- and α-helical structure has been studied via high-resolution NMR spectroscopy by Millhauser and coworkers using the MW peptide Ac-AMAAKAWAAKA AAARA-NH2. Their 750-MHz nuclear Overhauser effect spectroscopy (NOESY) spectra were interpreted to reflect appreciable populations of 310-helix throughout the peptide, with the greatest contribution at the N and C termini. The presence of simultaneous αN(i,i + 2) and αN(i,i + 4) NOE cross-peaks was proposed to represent conformational averaging between 310- and α-helical structures. In this study, we describe 25-nsec molecular dynamics simulations of the MW peptide at 298 K, using both an 8 Å and a 10 Å force-shifted nonbonded cutoff. The ensemble averages of both simulations are in reasonable agreement with the experimental helical content from circular dichroism (CD), the 3JHNα coupling constants, and the 57 observed NOEs. Analysis of the structures from both simulations revealed very little formation of contiguous i → i + 3 hydrogen bonds (310-helix); however, there was a large population of bifurcated i → i + 3 and i → i + 4 α-helical hydrogen bonds. In addition, both simulations contained considerable populations of π-helix (i → i + 5 hydrogen bonds). Individual turns formed over residues 1–9, which we predict contribute to the intensities of the experimentally observed αN(i,i + 2) NOEs. Here we show how sampling of both folded and unfolded structures can provide a structural framework for deconvolution of the conformational contributions to experimental ensemble averages. PMID:12761385

The proline-rich region of 18.5 kDa myelin basic protein binds to the SH3-domain of Fyn tyrosine kinase with the aid of an upstream segment to form a dynamic complex in vitro

PubMed Central

De Avila, Miguel; Vassall, Kenrick A.; Smith, Graham S. T.; Bamm, Vladimir V.; Harauz, George

2014-01-01

The intrinsically disordered 18.5 kDa classic isoform of MBP (myelin basic protein) interacts with Fyn kinase during oligodendrocyte development and myelination. It does so primarily via a central proline-rich SH3 (Src homology 3) ligand (T92–R104, murine 18.5 kDa MBP sequence numbering) that is part of a molecular switch due to its high degree of conservation and modification by MAP (mitogen-activated protein) and other kinases, especially at residues T92 and T95. Here, we show using co-transfection experiments of an early developmental oligodendroglial cell line (N19) that an MBP segment upstream of the primary ligand is involved in MBP–Fyn–SH3 association in cellula. Using solution NMR spectroscopy in vitro, we define this segment to comprise MBP residues (T62–L68), and demonstrate further that residues (V83–P93) are the predominant SH3-target, assessed by the degree of chemical shift change upon titration. We show by chemical shift index analysis that there is no formation of local poly-proline type II structure in the proline-rich segment upon binding, and by NOE (nuclear Overhauser effect) and relaxation measurements that MBP remains dynamic even while complexed with Fyn–SH3. The association is a new example first of a non-canonical SH3-domain interaction and second of a fuzzy MBP complex. PMID:25343306

Evidence of formation of site-selective inclusion complexation between beta-cyclodextrin and poly(ethylene oxide)-block-poly(propylene oxide)- block-poly(ethylene oxide) copolymers.

PubMed

Tsai, Chi-Chun; Zhang, Wen-Bin; Wang, Chien-Lung; Van Horn, Ryan M; Graham, Matthew J; Huang, Jing; Chen, Yongming; Guo, Mingming; Cheng, Stephen Z D

2010-05-28

A series of inclusion complexes of poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (PEO-b-PPO-b-PEO) with beta-cyclodextrin (beta-CD) was prepared. Their formation, structure, and dynamics were investigated by solution two-dimensional rotating-frame Overhauser effect spectroscopy (2D ROESY) and one-dimensional (1D) and 2D solid-state (13)C NMR. The inclusion complexes between the PEO-b-PPO-b-PEO copolymers and the beta-CDs were formed in aqueous solution and detected by 2D ROESY. The high efficiency of cross polarization and spin diffusion experiments in (13)C solid-state NMR showed that the mobility of the PPO blocks dramatically decreases after beta-CD complexation, indicating that they are selectively incorporated onto the PPO blocks. The hydrophobic cavities of beta-CD restrict the PPO block mobility, which is evidence of the formation of inclusion complexes in the solid state. The 2D wide-line separation NMR experiments suggested that beta-CDs only thread onto the PPO blocks while forming the inclusion complexes. The stoichiometry of inclusion complexes was studied using (1)H NMR, and a 3:1 (PO unit to beta-CD) was found for all inclusion complexes, which indicated that the number of threaded beta-CDs was only dependent on the molecular weight of the PPO blocks. 1D wide angle x-ray diffraction studies demonstrated that the beta-CD in the inclusion complex formed a channel-like structure that is different from the pure beta-CD crystal structure.

Evidence of formation of site-selective inclusion complexation between β-cyclodextrin and poly(ethylene oxide)-block-poly(propylene oxide)- block-poly(ethylene oxide) copolymers

NASA Astrophysics Data System (ADS)

Tsai, Chi-Chun; Zhang, Wen-Bin; Wang, Chien-Lung; Van Horn, Ryan M.; Graham, Matthew J.; Huang, Jing; Chen, Yongming; Guo, Mingming; Cheng, Stephen Z. D.

2010-05-01

A series of inclusion complexes of poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (PEO-b-PPO-b-PEO) with β-cyclodextrin (β-CD) was prepared. Their formation, structure, and dynamics were investigated by solution two-dimensional rotating-frame Overhauser effect spectroscopy (2D ROESY) and one-dimensional (1D) and 2D solid-state C13 NMR. The inclusion complexes between the PEO-b-PPO-b-PEO copolymers and the β-CDs were formed in aqueous solution and detected by 2D ROESY. The high efficiency of cross polarization and spin diffusion experiments in C13 solid-state NMR showed that the mobility of the PPO blocks dramatically decreases after β-CD complexation, indicating that they are selectively incorporated onto the PPO blocks. The hydrophobic cavities of β-CD restrict the PPO block mobility, which is evidence of the formation of inclusion complexes in the solid state. The 2D wide-line separation NMR experiments suggested that β-CDs only thread onto the PPO blocks while forming the inclusion complexes. The stoichiometry of inclusion complexes was studied using H1 NMR, and a 3:1 (PO unit to β-CD) was found for all inclusion complexes, which indicated that the number of threaded β-CDs was only dependent on the molecular weight of the PPO blocks. 1D wide angle x-ray diffraction studies demonstrated that the β-CD in the inclusion complex formed a channel-like structure that is different from the pure β-CD crystal structure.

Application of pulsed field gradient NMR techniques for investigating binding of flavor compounds to macromolecules.

PubMed

Jung, Da-Mi; De Ropp, Jeffrey S; Ebeler, Susan E

2002-07-17

Two diffusion-based NMR techniques are presented and used to investigate the binding of selected flavor compounds to macromolecules. A pulsed field gradient NMR (PFG-NMR) method was applied to measure the apparent diffusion coefficients of four alkanone compounds as they associated with bovine serum albumin (BSA). The change in the apparent diffusion coefficient as a function of the BSA/alkanone ratio was fitted to yield binding constants (K(a)()) and binding stoichiometry (n) for each alkanone. The results showed that the apparent diffusion coefficients of alkanones increased with a decrease in the BSA/alkanone ratios, and the measured values of K(a)() and n were comparable with those obtained with other methods and depended on the alkanone structure. A diffusion-based nuclear Overhauser effect (called diffusion NOE pumping) method was also applied to screen mixtures of flavor compounds and identify those that have a binding affinity to complex macromolecules. Using this technique benzaldehyde and vanillin were observed to bind with bovine serum albumin, whereas 2-phenylethanol was identified as a nonbinding or weakly binding ligand with BSA. The diffusion NOE pumping method was also applied to a hydro alcoholic solution of cacao bean tannin extracts to which a mixture of ethylbenzoate, benzaldehyde, and 2-phenylethanol was added. The diffusion NOE pumping technique clearly indicated that ethylbenzoate had a stronger binding affinity to the polymeric (-)-epicatechin units of the cacao bean tannin extracts than the other two flavor compounds. The results successfully demonstrate the potential applications of diffusion-based NMR techniques for studying flavors and nonvolatile food matrix interactions.

NMR Reveals Double Occupancy of Quinone-type Ligands in the Catalytic Quinone Binding Site of the Na+-translocating NADH:Quinone Oxidoreductase from Vibrio cholerae*

PubMed Central

Nedielkov, Ruslan; Steffen, Wojtek; Steuber, Julia; Möller, Heiko M.

2013-01-01

The sodium ion-translocating NADH:quinone oxidoreductase (Na+-NQR) from the pathogen Vibrio cholerae exploits the free energy liberated during oxidation of NADH with ubiquinone to pump sodium ions across the cytoplasmic membrane. The Na+-NQR consists of four membrane-bound subunits NqrBCDE and the peripheral NqrF and NqrA subunits. NqrA binds ubiquinone-8 as well as quinones with shorter prenyl chains (ubiquinone-1 and ubiquinone-2). Here we show that the quinone derivative 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), a known inhibitor of the bc1 and b6f complexes found in mitochondria and chloroplasts, also inhibits quinone reduction by the Na+-NQR in a mixed inhibition mode. Tryptophan fluorescence quenching and saturation transfer difference NMR experiments in the presence of Na+-NQR inhibitor (DBMIB or 2-n-heptyl-4-hydroxyquinoline N-oxide) indicate that two quinone analog ligands are bound simultaneously by the NqrA subunit with very similar interaction constants as observed with the holoenzyme complex. We conclude that the catalytic site of quinone reduction is located on NqrA. The two ligands bind to an extended binding pocket in direct vicinity to each other as demonstrated by interligand Overhauser effects between ubiquinone-1 and DBMIB or 2-n-heptyl-4-hydroxyquinoline N-oxide, respectively. We propose that a similar spatially close arrangement of the native quinone substrates is also operational in vivo, enhancing the catalytic efficiency during the final electron transfer steps in the Na+-NQR. PMID:24003222

The proline-rich region of 18.5 kDa myelin basic protein binds to the SH3-domain of Fyn tyrosine kinase with the aid of an upstream segment to form a dynamic complex in vitro.

PubMed

De Avila, Miguel; Vassall, Kenrick A; Smith, Graham S T; Bamm, Vladimir V; Harauz, George

2014-12-08

The intrinsically disordered 18.5 kDa classic isoform of MBP (myelin basic protein) interacts with Fyn kinase during oligodendrocyte development and myelination. It does so primarily via a central proline-rich SH3 (Src homology 3) ligand (T92-R104, murine 18.5 kDa MBP sequence numbering) that is part of a molecular switch due to its high degree of conservation and modification by MAP (mitogen-activated protein) and other kinases, especially at residues T92 and T95. Here, we show using co-transfection experiments of an early developmental oligodendroglial cell line (N19) that an MBP segment upstream of the primary ligand is involved in MBP-Fyn-SH3 association in cellula. Using solution NMR spectroscopy in vitro, we define this segment to comprise MBP residues (T62-L68), and demonstrate further that residues (V83-P93) are the predominant SH3-target, assessed by the degree of chemical shift change upon titration. We show by chemical shift index analysis that there is no formation of local poly-proline type II structure in the proline-rich segment upon binding, and by NOE (nuclear Overhauser effect) and relaxation measurements that MBP remains dynamic even while complexed with Fyn-SH3. The association is a new example first of a non-canonical SH3-domain interaction and second of a fuzzy MBP complex.

RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case

NASA Astrophysics Data System (ADS)

Beckman, Robert A.; Moreland, David; Louise-May, Shirley; Humblet, Christine

2006-05-01

Nuclear magnetic resonance (NMR) provides structural and dynamic information reflecting an average, often non-linear, of multiple solution-state conformations. Therefore, a single optimized structure derived from NMR refinement may be misleading if the NMR data actually result from averaging of distinct conformers. It is hypothesized that a conformational ensemble generated by a valid molecular dynamics (MD) simulation should be able to improve agreement with the NMR data set compared with the single optimized starting structure. Using a model system consisting of two sequence-related self-complementary ribonucleotide octamers for which NMR data was available, 0.3 ns particle mesh Ewald MD simulations were performed in the AMBER force field in the presence of explicit water and counterions. Agreement of the averaged properties of the molecular dynamics ensembles with NMR data such as homonuclear proton nuclear Overhauser effect (NOE)-based distance constraints, homonuclear proton and heteronuclear 1H-31P coupling constant ( J) data, and qualitative NMR information on hydrogen bond occupancy, was systematically assessed. Despite the short length of the simulation, the ensemble generated from it agreed with the NMR experimental constraints more completely than the single optimized NMR structure. This suggests that short unrestrained MD simulations may be of utility in interpreting NMR results. As expected, a 0.5 ns simulation utilizing a distance dependent dielectric did not improve agreement with the NMR data, consistent with its inferior exploration of conformational space as assessed by 2-D RMSD plots. Thus, ability to rapidly improve agreement with NMR constraints may be a sensitive diagnostic of the MD methods themselves.

One second vector and scalar magnetic measurements at the low-latitude Choutuppal (CPL) magnetic observatory

NASA Astrophysics Data System (ADS)

Phani Chandrasekhar, Nelapatla; Potharaju, Sai Vijay Kumar; Arora, Kusumita; Shakar Rao Kasuba, Chandra; Rakhlin, Leonid; Tymoshyn, Sergey; Merenyi, Laszlo; Chilukuri, Anusha; Bulusu, Jayashree; Khomutov, Sergey

2017-12-01

One second measurements of the geomagnetic field variations, which meet INTERMAGNET quality and transmission specifications, require very special conditions to be maintained at the observatories over sustained periods of time, which pose serious challenges for the operators, particularly when infrastructural and environmental conditions are far from ideal. This work presents the progressive steps, which led to the successful setup of such measurements at the new magnetic observatory of the Council of Scientific and Industrial Research (CSIR)-National Geophysical Research Institute (NGRI) in the Choutuppal (CPL) campus, Hyderabad (HYB), India. The 1 s magnetic measurements in trial mode commenced in 2015 using the newly developed observatory-grade 1 s fluxgate magnetometer, GEOMAG-02MO, from Research Centre GEOMAGNET (GM), Ukraine, and the Overhauser proton precession magnetometer, GSM-90F1, along with the data acquisition system, Magrec-4B from Mingeo, Hungary. Iterative tuning of the setup led to the generation of good quality data from 2016 onward. The processes of commissioning this setup in low-latitude conditions, with the aim of producing 1 s definitive data, and the characteristics of the data from this new instrument are presented here.

Electrically tunable dynamic nuclear spin polarization in GaAs quantum dots at zero magnetic field

NASA Astrophysics Data System (ADS)

Manca, M.; Wang, G.; Kuroda, T.; Shree, S.; Balocchi, A.; Renucci, P.; Marie, X.; Durnev, M. V.; Glazov, M. M.; Sakoda, K.; Mano, T.; Amand, T.; Urbaszek, B.

2018-04-01

In III-V semiconductor nano-structures, the electron and nuclear spin dynamics are strongly coupled. Both spin systems can be controlled optically. The nuclear spin dynamics are widely studied, but little is known about the initialization mechanisms. Here, we investigate optical pumping of carrier and nuclear spins in charge tunable GaAs dots grown on 111A substrates. We demonstrate dynamic nuclear polarization (DNP) at zero magnetic field in a single quantum dot for the positively charged exciton X+ state transition. We tune the DNP in both amplitude and sign by variation of an applied bias voltage Vg. Variation of ΔVg on the order of 100 mV changes the Overhauser splitting (nuclear spin polarization) from -30 μeV (-22%) to +10 μeV (+7%) although the X+ photoluminescence polarization does not change sign over this voltage range. This indicates that absorption in the structure and energy relaxation towards the X+ ground state might provide favourable scenarios for efficient electron-nuclear spin flip-flops, generating DNP during the first tens of ps of the X+ lifetime which is on the order of hundreds of ps. Voltage control of DNP is further confirmed in Hanle experiments.

Siegel[JMMM 7,312(`78)] FIRST EXPERIMENTAL DISCOVERY of Giant-Magnetoresistance Decade Pre ``Fert'' and ``Gruenberg'' ['88 - `78] = 10-Years = One-Decade Sounds, for Nuclear-Power Naïve ``Panacea'' for Global-Warming/Climate-Chan

NASA Astrophysics Data System (ADS)

Hoffmann, Masterace; Siegel, Edward

Siegel[JMMM 7,312(`78); Monju (12/'95) LMFBR PREDICTION!!!] following: Wigner[JAP 17,857(`46)]-(Alvin)Weinberg(ANL/ORNL/ANS)-(Sidney)Siegel(ANL/ORNL/ANS)-Seitz-Overhauser-Rollnick-Pollard-Lofaro-Markey-Pringle[Nuclear-PowerFrom Physics to Politics(`79)] FIRST EXPERIMENTAL DISCOVERY [Siegel<<<''Fert''-''Gruenberg'':2007-Physics-Nobel/2006:-Wolf/Japan-prizes:[`88 -`78] =10-years =1-decade precedence!!!] of granular giant-magnetoresistance(GMR) [Google: ``EDWARD SIEGEL GIANT-MAGNETORESISTANCE ICMAO 1977 FLICKER''] [Google: ``Ana Mayo If LEAKS`Could' KILL''] in austenitic/FCC Ni/Fe-based (so MIScalled)''super''alloy-182/82 transition-welds GENERIC ENDEMIC EXTANT detrimental (SYNONYMS): Wigner's-disease/Ostwald-ripening/spinodal-decompositio/OVERageing-EMBRITTLEMENT/THERMAL-leading-to-mechanical (TLTM)-INstability/``sensitization'' in: nuclear-reactors/spent-fuel dry-casks/refineries/jet/missile/rocket-engines/...SOUNDS A DIRE WARNING FOR NAIVE Hansen-Sommerville-Holdren-DOE-NRC-OSTP-WNA-NEI-AIP-APS-...calls/media-hype/P.R./spin-doctoring for carbon-``free'' nuclear-power as a SUPPOSED ``panacea'' for climate-change/global-warming: ``TRUST BUT VERIFY!!!'' ; a VERY LOUD CAVEAT EMPTOR!!!

Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers

NASA Astrophysics Data System (ADS)

Pitman, Michael C.; Suits, Frank; Gawrisch, Klaus; Feller, Scott E.

2005-06-01

We describe the dynamic behavior of a 1-stearoyl-2-oleoyl-phosphatidylethanolamine (SOPE) bilayer from a 20ns molecular dynamics simulation. The dynamics of individual molecules are characterized in terms of H2 spin-lattice relaxation rates, nuclear overhauser enhancement spectroscopy (NOESY) cross-relaxation rates, and lateral diffusion coefficients. Additionally, we describe the dynamics of hydrogen bonding through an analysis of hydrogen bond lifetimes and the time evolution of clusters of hydrogen bonded lipids. The simulated trajectory is shown to be consistent with experimental measures of internal, intermolecular, and diffusive motion. Consistent with our analysis of SOPE structure in the companion paper, we see hydrogen bonding dominating the dynamics of the interface region. Comparison of H2 T1 relaxation rates for chain methylene segments in phosphatidylcholine and phosphatidylethanolamine bilayers indicates that slower motion resulting from hydrogen bonding extends at least three carbons into the hydrophobic core. NOESY cross-relaxation rates compare well with experimental values, indicating the observed hydrogen bonding dynamics are realistic. Calculated lateral diffusion rates (4±1×10-8cm2/s) are comparable, though somewhat lower than, those determined by pulsed field gradient NMR methods.

Synthetic Human NOTCH1 EGF Modules Unraveled Molecular Mechanisms for the Structural and Functional Roles of Calcium Ions and O-Glycans in the Ligand-Binding Region.

PubMed

Hayakawa, Shun; Koide, Ryosuke; Hinou, Hiroshi; Nishimura, Shin-Ichiro

2016-02-09

The Notch signaling pathway is an evolutionarily highly conserved mechanism that operates across multicellular organisms and is critical for cell-fate decisions during development and homeostasis in most tissues. Notch signaling is modified by posttranslational glycosylations of the Notch extracellular EGF-like domain. To evaluate the structural and functional roles of various glycoforms at multiple EGF domains in the human Notch transmembrane receptor, we established a universal method for the construction of NOTCH1 EGF modules displaying the desired O-glycans at the designated glycosylation sites. The versatility of this strategy was demonstrated by the rapid and highly efficient synthesis of NOTCH1 EGF12 concurrently having a β-D-glucopyranose-initiated glycan (Xylα1 → 3Xylα1 → 3Glcβ1 →) at Ser458 and α-L-fucopyranose-initiated glycan (Neu5Acα2 → 3Galβ1 → 4GlcNAcβ1 → 3Fucα1 →) at Thr466. The efficiency of the proper folding of the glycosylated EGF12 was markedly enhanced in the presence of 5 mM CaCl2. A nuclear magnetic resonance study revealed the existence of strong nuclear Overhauser effects between key sugar moieties and neighboring amino acid residues, indicating that both O-glycans contribute independently to the intramolecular stabilization of the antiparallel β-sheet structure in the ligand-binding region of EGF12. A preliminary test using synthetic human NOTCH1 EGF modules showed significant inhibitory effects on the proliferation and adhesiveness of human breast cancer cell line MCF-7 and lung adenocarcinoma epithelial cell line A549, demonstrating for the first time evidence that exogenously applied synthetic EGF modules have the ability to interact with intrinsic Notch ligands on the surface of cancer cells.

Quantitative analysis of the z-spectrum using a numerically simulated look-up table: Application to the healthy human brain at 7T.

PubMed

Geades, Nicolas; Hunt, Benjamin A E; Shah, Simon M; Peters, Andrew; Mougin, Olivier E; Gowland, Penny A

2017-08-01

To develop a method that fits a multipool model to z-spectra acquired from non-steady state sequences, taking into account the effects of variations in T1 or B1 amplitude and the results estimating the parameters for a four-pool model to describe the z-spectrum from the healthy brain. We compared measured spectra with a look-up table (LUT) of possible spectra and investigated the potential advantages of simultaneously considering spectra acquired at different saturation powers (coupled spectra) to provide sensitivity to a range of different physicochemical phenomena. The LUT method provided reproducible results in healthy controls. The average values of the macromolecular pool sizes measured in white matter (WM) and gray matter (GM) of 10 healthy volunteers were 8.9% ± 0.3% (intersubject standard deviation) and 4.4% ± 0.4%, respectively, whereas the average nuclear Overhauser effect pool sizes in WM and GM were 5% ± 0.1% and 3% ± 0.1%, respectively, and average amide proton transfer pool sizes in WM and GM were 0.21% ± 0.03% and 0.20% ± 0.02%, respectively. The proposed method demonstrated increased robustness when compared with existing methods (such as Lorentzian fitting and asymmetry analysis) while yielding fully quantitative results. The method can be adjusted to measure other parameters relevant to the z-spectrum. Magn Reson Med 78:645-655, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Impact of aging on cardiac high-energy phosphate metabolism determined by phosphorus-31 2-dimensional chemical shift imaging (31P 2D CSI).

PubMed

Schocke, Michael F H; Metzler, Bernhard; Wolf, Christian; Steinboeck, Peter; Kremser, Christian; Pachinger, Otmar; Jaschke, Werner; Lukas, Peter

2003-06-01

Previous echocardiographic and experimental animal studies have shown that cardiac function, structure, and metabolism change with age. The aim of this study was to evaluate the impact of age on left ventricular high-energy phosphate metabolism. Using a 1.5 Tesla whole-body MR scanner 31P 2D CSI (8 x 8 phase encoding steps, 320 mm field of view) was performed in 76 healthy male volunteers (41.7 +/- 13 years) without any history of coronary heart disease. Fourier interpolation, corrections for T1 saturation effects, the nucleus Overhauser effect, and the blood contamination were applied to the spectroscopic data. The volunteers were divided into two groups, younger (n = 37) and older (n = 39) than 41.7 years. In all volunteers, laboratory specimen were sampled, and transthoracal echocardiography was carried out. Significant differences in left ventricular phosphocreatine (PCr) to beta-adenosine-triphosphate (beta-ATP) ratios (2.16 vs. 1.83, p < 0.001), fasting serum glucose levels (83.3 vs. 98.7 mg/dl, p < 0.001), E/A (1.51 vs. 1.14 p < 0.001), and ejection fraction (EF, 65.3 vs. 59.9%, p = 0.005) were detected between the two groups of volunteers, younger and older than 41.7 years. Moreover, age correlated moderately to well with left ventricular PCr to beta-ATP ratios (r = -0.44), fasting serum glucose levels (r = 0.4), E/A (r = -0.7), left ventricular myocardial mass (r = -0.41), and EF (r = -0.55). In conclusion, our study shows that left ventricular PCr to beta-ATP ratios decrease moderately with age, as suggested by previous experimental animal studies. Additionally, age correlates negatively with E/A, left ventricular myocardial mass, and EF, as reported by previous echocardiography studies. The present study is the first to show the impact of age on left ventricular PCr to beta-ATP values in humans.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Chi-Yuan; Kausik, Ravinath; Han, Songi, E-mail: songi@chem.ucsb.edu

Elucidating the physical effect of cholesterol (Chol) on biological membranes is necessary towards rationalizing their structural and functional role in cell membranes. One of the debated questions is the role of hydration water in Chol-embedding lipid membranes, for which only little direct experimental data are available. Here, we study the hydration dynamics in a series of Chol-rich and depleted bilayer systems using an approach termed {sup 1}H Overhauser dynamic nuclear polarization (ODNP) NMR relaxometry that enables the sensitive and selective determination of water diffusion within 5–10 Å of a nitroxide-based spin label, positioned off the surface of the polar headgroupsmore » or within the nonpolar core of lipid membranes. The Chol-rich membrane systems were prepared from mixtures of Chol, dipalmitoyl phosphatidylcholine and/or dioctadecyl phosphatidylcholine lipid that are known to form liquid-ordered, raft-like, domains. Our data reveal that the translational diffusion of local water on the surface and within the hydrocarbon volume of the bilayer is significantly altered, but in opposite directions: accelerated on the membrane surface and dramatically slowed in the bilayer interior with increasing Chol content. Electron paramagnetic resonance (EPR) lineshape analysis shows looser packing of lipid headgroups and concurrently tighter packing in the bilayer core with increasing Chol content, with the effects peaking at lipid compositions reported to form lipid rafts. The complementary capability of ODNP and EPR to site-specifically probe the hydration dynamics and lipid ordering in lipid membrane systems extends the current understanding of how Chol may regulate biological processes. One possible role of Chol is the facilitation of interactions between biological constituents and the lipid membrane through the weakening or disruption of strong hydrogen-bond networks of the surface hydration layers that otherwise exert stronger repulsive forces, as reflected in faster surface water diffusivity. Another is the concurrent tightening of lipid packing that reduces passive, possibly unwanted, diffusion of ions and water across the bilayer.« less

Solid-state NMR spectroscopy of 18.5 kDa myelin basic protein reconstituted with lipid vesicles: spectroscopic characterisation and spectral assignments of solvent-exposed protein fragments.

PubMed

Zhong, Ligang; Bamm, Vladimir V; Ahmed, Mumdooh A M; Harauz, George; Ladizhansky, Vladimir

2007-12-01

Myelin basic protein (MBP, 18.5 kDa isoform) is a peripheral membrane protein that is essential for maintaining the structural integrity of the multilamellar myelin sheath of the central nervous system. Reconstitution of the most abundant 18.5 kDa MBP isoform with lipid vesicles yields an aggregated assembly mimicking the protein's natural environment, but which is not amenable to standard solution NMR spectroscopy. On the other hand, the mobility of MBP in such a system is variable, depends on the local strength of the protein-lipid interaction, and in general is of such a time scale that the dipolar interactions are averaged out. Here, we used a combination of solution and solid-state NMR (ssNMR) approaches: J-coupling-driven polarization transfers were combined with magic angle spinning and high-power decoupling to yield high-resolution spectra of the mobile fragments of 18.5 kDa murine MBP in membrane-associated form. To partially circumvent the problem of short transverse relaxation, we implemented three-dimensional constant-time correlation experiments (NCOCX, NCACX, CONCACX, and CAN(CO)CX) that were able to provide interresidue and intraresidue backbone correlations. These experiments resulted in partial spectral assignments for mobile fragments of the protein. Additional nuclear Overhauser effect spectroscopy (NOESY)-based experiments revealed that the mobile fragments were exposed to solvent and were likely located outside the lipid bilayer, or in its hydrophilic portion. Chemical shift index analysis showed that the fragments were largely disordered under these conditions. These combined approaches are applicable to ssNMR investigations of other peripheral membrane proteins reconstituted with lipids.

NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.

PubMed

Apaydin, Mehmet Serkan; Çatay, Bülent; Patrick, Nicholas; Donald, Bruce R

2011-05-01

Nuclear magnetic resonance (NMR) spectroscopy is an important experimental technique that allows one to study protein structure and dynamics in solution. An important bottleneck in NMR protein structure determination is the assignment of NMR peaks to the corresponding nuclei. Structure-based assignment (SBA) aims to solve this problem with the help of a template protein which is homologous to the target and has applications in the study of structure-activity relationship, protein-protein and protein-ligand interactions. We formulate SBA as a linear assignment problem with additional nuclear overhauser effect constraints, which can be solved within nuclear vector replacement's (NVR) framework (Langmead, C., Yan, A., Lilien, R., Wang, L. and Donald, B. (2003) A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Proc. the 7th Annual Int. Conf. Research in Computational Molecular Biology (RECOMB) , Berlin, Germany, April 10-13, pp. 176-187. ACM Press, New York, NY. J. Comp. Bio. , (2004), 11, pp. 277-298; Langmead, C. and Donald, B. (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR , 29, 111-138). Our approach uses NVR's scoring function and data types and also gives the option of using CH and NH residual dipolar coupling (RDCs), instead of NH RDCs which NVR requires. We test our technique on NVR's data set as well as on four new proteins. Our results are comparable to NVR's assignment accuracy on NVR's test set, but higher on novel proteins. Our approach allows partial assignments. It is also complete and can return the optimum as well as near-optimum assignments. Furthermore, it allows us to analyze the information content of each data type and is easily extendable to accept new forms of input data, such as additional RDCs.

NMR-NOE and MD simulation study on phospholipid membranes: dependence on membrane diameter and multiple time scale dynamics.

PubMed

Shintani, Megumi; Yoshida, Ken; Sakuraba, Shun; Nakahara, Masaru; Matubayasi, Nobuyuki

2011-07-28

Motional correlation times between the hydrophilic and hydrophobic terminal groups in lipid membranes are studied over a wide range of curvatures using the solution-state (1)H NMR-nuclear Overhauser effect (NOE) and molecular dynamics (MD) simulation. To enable (1)H NMR-NOE measurements for large vesicles, the transient NOE method is combined with the spin-echo method, and is successfully applied to a micelle of 1-palmitoyl-lysophosphatidylcholine (PaLPC) with diameter of 5 nm and to vesicles of dipalmitoylphosphatidylcholine (DPPC) with diameters ranging from 30 to 800 nm. It is found that the NOE intensity increases with the diameter up to ∼100 nm, and the model membrane is considered planar on the molecular level beyond ∼100 nm. While the NOE between the hydrophilic terminal and hydrophobic terminal methyl groups is absent for the micelle, its intensity is comparable to that for the neighboring group for vesicles with larger diameters. The origin of NOE signals between distant sites is analyzed by MD simulations of PaLPC micelles and DPPC planar bilayers. The slow relaxation is shown to yield an observable NOE signal even for the hydrophilic and hydrophobic terminal sites. Since the information on distance and dynamics cannot be separated in the experimental NOE alone, the correlation time in large vesicles is determined by combining the experimental NOE intensity and MD-based distance distribution. For large vesicles, the correlation time is found to vary by 2 orders of magnitude over the proton sites. This study shows that NOE provides dynamic information on large vesicles when combined with MD, which provides structural information. © 2011 American Chemical Society

Backbone dynamics of the antifungal Psd1 pea defensin and its correlation with membrane interaction by NMR spectroscopy.

PubMed

de Medeiros, Luciano Neves; Angeli, Renata; Sarzedas, Carolina G; Barreto-Bergter, Eliana; Valente, Ana Paula; Kurtenbach, Eleonora; Almeida, Fabio C L

2010-02-01

Plant defensins are cysteine-rich cationic peptides, components of the innate immune system. The antifungal sensitivity of certain exemplars was correlated to the level of complex glycosphingolipids in the membrane of fungi strains. Psd1 is a 46 amino acid residue defensin isolated from pea seeds which exhibit antifungal activity. Its structure is characterized by the so-called cysteine-stabilized alpha/beta motif linked by three loops as determined by two-dimensional NMR. In the present work we explored the measurement of heteronuclear Nuclear Overhauser Effects, R1 and R2 (15)N relaxation ratios, and chemical shift to probe the backbone dynamics of Psd1 and its interaction with membrane mimetic systems with phosphatidylcholine (PC) or dodecylphosphocholine (DPC) with glucosylceramide (CMH) isolated from Fusarium solani. The calculated R2 values predicted a slow motion around the highly conserved among Gly12 residue and also in the region of the Turn3 His36-Trp38. The results showed that Psd1 interacts with vesicles of PC or PC:CMH in slightly different forms. The interaction was monitored by chemical shift perturbation and relaxation properties. Using this approach we could map the loops as the binding site of Psd1 with the membrane. The major binding epitope showed conformation exchange properties in the mus-ms timescale supporting the conformation selection as the binding mechanism. Moreover, the peptide corresponding to part of Loop1 (pepLoop1: Gly12 to Ser19) is also able to interact with DPC micelles acquiring a stable structure and in the presence of DPC:CMH the peptide changes to an extended conformation, exhibiting NOE mainly with the carbohydrate and ceramide parts of CMH. Copyright 2009 Elsevier B.V. All rights reserved.

Structural characterization by NMR of the natively unfolded extracellular domain of beta-dystroglycan: toward the identification of the binding epitope for alpha-dystroglycan.

PubMed

Bozzi, Manuela; Bianchi, Marzia; Sciandra, Francesca; Paci, Maurizio; Giardina, Bruno; Brancaccio, Andrea; Cicero, Daniel O

2003-11-25

Dystroglycan (DG) is an adhesion molecule playing a crucial role for tissue stability during both early embriogenesis and adulthood and is composed by two tightly interacting subunits: alpha-DG, membrane-associated and highly glycosylated, and the transmembrane beta-DG. Recently, by solid-phase binding assays and NMR experiments, we have shown that the C-terminal domain of alpha-DG interacts with a recombinant extracellular fragment of beta-DG (positions 654-750) independently from glycosylation and that the linear binding epitope is located between residues 550 and 565 of alpha-DG. In order to elucidate which moieties of beta-DG are specifically involved in the complex with alpha-DG, the ectodomain has been recombinantly expressed and purified in a labeled ((13)C,(15)N) form and studied by multidimensional NMR. Although it represents a natively unfolded protein domain, we obtained an almost complete backbone assignment. Chemical shift index, (1)H-(15)N heteronuclear single-quantum coherence and nuclear Overhauser effect (HSQC-NOESY) spectra and (3)J(HN,H)(alpha) coupling constant values confirm that this protein is highly disordered, but (1)H-(15)N steady-state NOE experiments indicate that the protein presents two regions of different mobility. The first one, between residues 659 and 722, is characterized by a limited degree of mobility, whereas the C-terminal portion, containing about 30 amino acids, is highly flexible. The binding of beta-DG(654-750) to the C-terminal region of the alpha subunit, alpha-DG(485-620), has been investigated, showing that the region of beta-DG(654-750) between residues 691 and 719 is involved in the interaction.

Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding

PubMed Central

Newcomer, Rebecca L.; Fraser, LaTasha C.R.; Teschke, Carolyn M.; Alexandrescu, Andrei T.

2015-01-01

The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining 3JNC’ couplings transmitted through H-bonds, the temperature and urea-concentration dependence of 1HN and 15N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and 3JNC’ H-bond couplings, are identified with an accuracy of 90% by 1HN temperature coefficients. The accuracy is improved to 95% when 15N temperature coefficients are also included. In contrast, the urea dependence of 1HN and 15N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility. PMID:26682823

Dynamics-based selective 2D 1H/1H chemical shift correlation spectroscopy under ultrafast MAS conditions

NASA Astrophysics Data System (ADS)

Zhang, Rongchun; Ramamoorthy, Ayyalusamy

2015-05-01

Dynamics plays important roles in determining the physical, chemical, and functional properties of a variety of chemical and biological materials. However, a material (such as a polymer) generally has mobile and rigid regions in order to have high strength and toughness at the same time. Therefore, it is difficult to measure the role of mobile phase without being affected by the rigid components. Herein, we propose a highly sensitive solid-state NMR approach that utilizes a dipolar-coupling based filter (composed of 12 equally spaced 90° RF pulses) to selectively measure the correlation of 1H chemical shifts from the mobile regions of a material. It is interesting to find that the rotor-synchronized dipolar filter strength decreases with increasing inter-pulse delay between the 90° pulses, whereas the dipolar filter strength increases with increasing inter-pulse delay under static conditions. In this study, we also demonstrate the unique advantages of proton-detection under ultrafast magic-angle-spinning conditions to enhance the spectral resolution and sensitivity for studies on small molecules as well as multi-phase polymers. Our results further demonstrate the use of finite-pulse radio-frequency driven recoupling pulse sequence to efficiently recouple weak proton-proton dipolar couplings in the dynamic regions of a molecule and to facilitate the fast acquisition of 1H/1H correlation spectrum compared to the traditional 2D NOESY (Nuclear Overhauser effect spectroscopy) experiment. We believe that the proposed approach is beneficial to study mobile components in multi-phase systems, such as block copolymers, polymer blends, nanocomposites, heterogeneous amyloid mixture of oligomers and fibers, and other materials.

Two-dimensional sup 1 H nuclear magnetic resonance study of AaH IT, an anti-insect toxin from the scorpion Androctonus australis Hector. Sequential resonance assignments and folding of the polypeptide chain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Darbon, H.; Weber, C.; Braun, W.

1991-02-19

Sequence-specific nuclear magnetic resonance assignments for the polypeptide backbone and for most of the amino acid side-chain protons, as well as the general folding of AaH IT, are described. AaH IT is a neurotoxin purified from the venom of the scorpion Androctonus australis Hector and is specifically active on the insect nervous system. The secondary structure and the hydrogen-bonding patterns in the regular secondary structure elements are deduced from nuclear Overhauser effects and the sequence locations of the slowly exchanging amide protons. The backbone folding is determined by distance geometry calculations with the DISMAN program. The regular secondary structure includesmore » two and a half turns of {alpha}-helix running from residues 21 to 30 and a three-stranded antiparallel {beta}-sheet including peptides 3-5, 34-38, and 41-46. Two tight turns are present, one connecting the end of the {alpha}-helix to an external strand of the {beta}-sheet, i.e., turn 31-34, and another connecting this same strand to the central one, i.e., turn 38-41. The differences in the specificity of these related proteins, which are able to discriminate between mammalian and insect voltage-dependent sodium channels of excitable tissues, are most probably brought about by the position of the C-terminal peptide with regard to a hydrophobic surface common to all scorpion toxins examined thus far. Thus, the interaction of a given scorpion toxin with its receptor might well be governed by the presence of this solvent-exposed hydrophobic surface, whereas adjacent areas modulate the specificity of the interaction.« less

Hybrid MR-PET of brain tumours using amino acid PET and chemical exchange saturation transfer MRI.

PubMed

da Silva, N A; Lohmann, P; Fairney, J; Magill, A W; Oros Peusquens, A-M; Choi, C-H; Stirnberg, R; Stoffels, G; Galldiks, N; Golay, X; Langen, K-J; Jon Shah, N

2018-06-01

PET using radiolabelled amino acids has become a promising tool in the diagnostics of gliomas and brain metastasis. Current research is focused on the evaluation of amide proton transfer (APT) chemical exchange saturation transfer (CEST) MR imaging for brain tumour imaging. In this hybrid MR-PET study, brain tumours were compared using 3D data derived from APT-CEST MRI and amino acid PET using O-(2- 18 F-fluoroethyl)-L-tyrosine ( 18 F-FET). Eight patients with gliomas were investigated simultaneously with 18 F-FET PET and APT-CEST MRI using a 3-T MR-BrainPET scanner. CEST imaging was based on a steady-state approach using a B 1 average power of 1μT. B 0 field inhomogeneities were corrected a Prametric images of magnetisation transfer ratio asymmetry (MTR asym ) and differences to the extrapolated semi-solid magnetisation transfer reference method, APT# and nuclear Overhauser effect (NOE#), were calculated. Statistical analysis of the tumour-to-brain ratio of the CEST data was performed against PET data using the non-parametric Wilcoxon test. A tumour-to-brain ratio derived from APT# and 18 F-FET presented no significant differences, and no correlation was found between APT# and 18 F-FET PET data. The distance between local hot spot APT# and 18 F-FET were different (average 20 ± 13 mm, range 4-45 mm). For the first time, CEST images were compared with 18 F-FET in a simultaneous MR-PET measurement. Imaging findings derived from 18 F-FET PET and APT CEST MRI seem to provide different biological information. The validation of these imaging findings by histological confirmation is necessary, ideally using stereotactic biopsy.

The disorderly conduct of Hsc70 and its interaction with the Alzheimer's related Tau protein.

PubMed

Taylor, Isabelle R; Ahmad, Atta; Wu, Taia; Nordhues, Bryce A; Bhullar, Anup; Gestwicki, Jason E; Zuiderweg, Erik R P

2018-05-15

Hsp70 chaperones bind to various protein substrates for folding, trafficking, and degradation. Considerable structural information is available about how prokaryotic Hsp70 (DnaK) binds substrates, but less is known about mammalian Hsp70s, of which there are 13 isoforms encoded in the human genome. Here, we report the interaction between the human Hsp70 isoform heat shock cognate 71 KDa protein (Hsc70 or HSPA8) and peptides derived from the microtubule-associated protein tau, which is linked to Alzheimer's disease. For structural studies, we used an Hsc70 construct (called BETA) comprising the substrate-binding domain, but lacking the lid. Importantly, we found that truncating the lid does not significantly impair Hsc70's chaperone activity or allostery in vitro. Using NMR, we show that BETA is partially dynamically disordered in the absence of substrate and that binding of the tau sequence GKVQIINKKG (with a KD = 500 nM) causes dramatic rigidification of BETA. Nuclear Overhauser effect distance measurements revealed that tau binds to the canonical substrate-binding cleft, similar to the binding observed with DnaK. To further develop BETA as a tool for studying Hsc70 interactions, we also measured BETA binding in NMR and fluorescent competition assays to peptides derived from huntingtin, insulin, a second tau-recognition sequence, and a KFERQ-like sequence linked to chaperone-mediated autophagy. We found that the insulin C-peptide binds BETA with high affinity (KD < 100 nM), whereas the others do not (KD > 100 μM). Together, our findings reveal several similarities and differences in how prokaryotic and mammalian Hsp70 isoforms interact with different substrate peptides. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

PubMed

Yildirim, Ilyas; Stern, Harry A; Kennedy, Scott D; Tubbs, Jason D; Turner, Douglas H

2010-05-11

A reparameterization of the torsional parameters for the glycosidic dihedral angle, chi, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99chi. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99chi force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99chi force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) (1)H, steady-state 1D (1)H nuclear Overhauser effect (NOE), and transient 1D (1)H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2'-endo sugar puckering of the pyrimidines, while the AMBER99chi force field's predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310 degrees for the base orientation of purines. The AMBER99chi force field prefers anti conformations around 185 degrees , which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99chi force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures.

Contact-assisted protein structure modeling by global optimization in CASP11.

PubMed

Joo, Keehyoung; Joung, InSuk; Cheng, Qianyi; Lee, Sung Jong; Lee, Jooyoung

2016-09-01

We have applied the conformational space annealing method to the contact-assisted protein structure modeling in CASP11. For Tp targets, where predicted residue-residue contact information was provided, the contact energy term in the form of the Lorentzian function was implemented together with the physical energy terms used in our template-free modeling of proteins. Although we observed some structural improvement of Tp models over the models predicted without the Tp information, the improvement was not substantial on average. This is partly due to the inaccuracy of the provided contact information, where only about 18% of it was correct. For Ts targets, where the information of ambiguous NOE (Nuclear Overhauser Effect) restraints was provided, we formulated the modeling in terms of the two-tier optimization problem, which covers: (1) the assignment of NOE peaks and (2) the three-dimensional (3D) model generation based on the assigned NOEs. Although solving the problem in a direct manner appears to be intractable at first glance, we demonstrate through CASP11 that remarkably accurate protein 3D modeling is possible by brute force optimization of a relevant energy function. For 19 Ts targets of the average size of 224 residues, generated protein models were of about 3.6 Å Cα atom accuracy. Even greater structural improvement was observed when additional Tc contact information was provided. For 20 out of the total 24 Tc targets, we were able to generate protein structures which were better than the best model from the rest of the CASP11 groups in terms of GDT-TS. Proteins 2016; 84(Suppl 1):189-199. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Structural features of LC8-induced self-association of swallow.

PubMed

Kidane, Ariam I; Song, Yujuan; Nyarko, Afua; Hall, Justin; Hare, Michael; Löhr, Frank; Barbar, Elisar

2013-09-03

Cell functions depend on the collective activity of protein networks within which a few proteins, called hubs, participate in a large number of interactions. Dynein light chain LC8, first discovered as a subunit of the motor protein dynein, is considered to have a role broader than that of dynein, and its participation in diverse systems fits the description of a hub. Among its partners is Swallow with which LC8 is essential for proper localization of bicoid mRNA at the anterior cortex of Drosophila oocytes. Why LC8 is essential in this process is not clear, but emerging evidence suggests that LC8 functions by promoting self-association and/or structural organization of its diverse binding partners. This work addresses the energetics and structural features of LC8-induced Swallow self-association distant from LC8 binding. Mutational design based on a hypothetical helical wheel, intermonomer nuclear Overhauser effects assigned to residues expected at interface positions, and circular dichroism spectral characteristics indicate that the LC8-promoted dimer of Swallow is a coiled coil. Secondary chemical shifts and (15)N backbone relaxation identify the boundaries and distinguishing structural features of the coiled coil. Thermodynamic analysis of Swallow polypeptides designed to decouple self-association from LC8 binding reveals that the higher binding affinity of the engineered bivalent Swallow is of purely entropic origin and that the linker separating the coiled coil from the LC8 binding site remains disordered. We speculate that the LC8-promoted coiled coil is critical for bicoid mRNA localization because it favors structural organization of Swallow, which except for the central LC8-promoted coiled coil is primarily disordered.

1H NMR spectrum of the native human insulin monomer. Evidence for conformational differences between the monomer and aggregated forms.

PubMed

Roy, M; Lee, R W; Brange, J; Dunn, M F

1990-04-05

The effects of high dilution on the 1H Fourier transform NMR spectrum of native human insulin at pH* 8.0 and 9.3 have been examined at 500 MHz resolution. The dependence of the spectrum on concentration and comparison with the spectrum of a biologically highly potent monomeric insulin mutant (SerB9----Asp) establish that at 36 microM (pH* 9.3) or 18 microM (pH* 8) and no added buffer or salts, human insulin is monomeric. Under these conditions of dilution, ionic strength, and pH*, human insulin and the SerB9----Asp mutant exhibit nearly identical 1H NMR spectra. At higher concentrations (i.e. greater than 36 microM to 0.91 mM), native human insulin dimerizes, and this aggregation causes a change in insulin conformation. Although there are many changes in the spectrum, the TyrB26 ring H3,5 proton signals located at 6.63 ppm and the methyl signal located at 0.105 ppm (characteristics of monomeric insulin) are particularly distinct signatures of the conformation change that accompanies dimerization. Magnetization transfer experiments show that the 0.105 ppm methyl signal shifts downfield to a new position at 0.45 ppm. We conclude that the 0.105 ppm methyl signal is due to a conformation in which a Leu methyl group is centered over and in van der Waals contact with the ring of an aromatic side chain. Dimerization causes a conformation change that alters this interaction, thereby causing the downfield shift. Nuclear Overhauser studies indicate that the methyl group involved is located within a cluster of aromatic side chains and that the closest ring-methyl group interaction is with the ring of PheB24.

High-resolution NMR spectroscopic trends and assignment rules of metal-free, metallated and substituted corroles.

PubMed

Balazs, Yael S; Saltsman, Irena; Mahammed, Atif; Tkachenko, Elena; Golubkov, Galina; Levine, Joshua; Gross, Zeev

2004-07-01

Major advances over the last few years have facilitated the synthesis of a large variety of meso-only substituted corroles that display interesting catalytic, therapeutic and photophysical properties. This work is the first to study extensively the NMR spectral characteristics of both metallated and non-metallated triarylcorroles in various organic solvents and provide guidelines for easy and reliable assignments of 1D 1H spectra from trends of J coupling constants and chemical shifts. An excellent correlation is found between C=C bond lengths derived from 3J(H,H) values and experimental lengths determined by x-ray crystallography of the same molecules. The nuclear Overhauser effect provides a robust 1D 1H NMR tool for determining the selectivity of electrophilic substitutions. Variable-temperature NMR and isotopic labelling reveal a single preferred tautomerization state and unsymmetric ring orientations at -70 degrees C. The beta-pyrrole protons demonstrate long-range heteronuclear couplings with the coordination core (15N) and with the ortho-19F nuclei of the meso-carbon aryl rings. In sum, application of multinuclear magnetic resonance to corroles and their metal complexes, through the compilation of chemical shifts and J couplings and the recognition of trends therein, provides basic information essential to reliable spectral assignments. Additionally, the conclusions drawn about the structures of corroles and the electron densities at various positions of the corrole macrocycle resulting from the application of high-resolution NMR techniques are of importance to an in-depth understanding of the molecular interactions and processes of this relatively new and rapidly expanding class of compounds. Copyright 2004 John Wiley & Sons, Ltd.

Multiple-step relayed correlation spectroscopy: sequential resonance assignments in oligosaccharides.

PubMed Central

Homans, S W; Dwek, R A; Fernandes, D L; Rademacher, T W

1984-01-01

A general property of the high-resolution proton NMR spectra of oligosaccharides is the appearance of low-field well-resolved resonances corresponding to the anomeric (H1) and H2 protons. The remaining skeletal protons resonate in the region 3-4 ppm, giving rise to an envelope of poorly resolved resonances. Assignments can be made from the H1 and H2 protons to their J-coupled neighbors (H2 and H3) within this main envelope by using 1H-1H correlated spectroscopy. However, the tight coupling (J congruent to delta) between further protons results in poor spectral dispersion with consequent assignment ambiguities. We describe here three-step two-dimensional relayed correlation spectroscopy and show how it can be used to correlate the resolved anomeric (H1) and H2 protons with remote (H4, H5) protons directly through a linear network of couplings using sequential magnetization transfer around the oligosaccharide rings. Resonance assignments are then obtained by inspection of cross-peaks that appear in well-resolved regions of the two-dimensional spectrum. This offers a general solution to the assignment problem in oligosaccharides and, importantly, these assignments will subsequently allow for the three-dimensional solution conformation to be determined by using one-dimensional and two-dimensional nuclear Overhauser experiments. PMID:6593701

Nuclear Spin Locking and Extended Two-Electron Spin Decoherence Time in an InAs Quantum Dot Molecule

NASA Astrophysics Data System (ADS)

Chow, Colin; Ross, Aaron; Steel, Duncan; Sham, L. J.; Bracker, Allan; Gammon, Daniel

2015-03-01

The spin eigenstates for two electrons confined in a self-assembled InAs quantum dot molecule (QDM) consist of the spin singlet state, S, with J = 0 and the triplet states T-, T0 and T+, with J = 1. When a transverse magnetic field (Voigt geometry) is applied, the two-electron system can be initialized to the different states with appropriate laser excitation. Under the excitation of a weak probe laser, non-Lorentzian lineshapes are obtained when the system is initialized to either T- or T+, where T- results in a ``resonance locking'' lineshape while T+ gives a ``resonance avoiding '' lineshape: two different manifestations of hysteresis showing the importance of memory in the system. These observations signify dynamic nuclear spin polarization (DNSP) arising from a feedback mechanism involving hyperfine interaction between lattice nuclei and delocalized electron spins, and Overhauser shift due to nuclear spin polarization. Using pump configurations that generate coherent population trapping, the isolation of the electron spin from the optical excitation shows the stabilization of the nuclear spin ensemble. The dark-state lineshape measures the lengthened electron spin decoherence time, from 1 ns to 1 μs. Our detailed spectra highlight the potential of QDM for realizing a two-qubit gate. This work is supported by NSF, ARO, AFOSR, DARPA, and ONR.

Correlation of tryptophan fluorescence intensity decay parameters with sup 1 H NMR-determined rotamer conformations: (tryptophan sup 2 )oxytocin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ross, J.B.A.; Schwartz, G.P.; Laws, W.R.

1992-02-18

While the fluorescence decay kinetics of tyrosine model compounds can be explained in terms of heterogeneity derived from the three ground-state {chi}{sup 1} rotamers, a similar correlation has yet to be directly observed for a tryptophan residue. In addition, the asymmetric indole ring might also lead to heterogeneity from {chi}{sup 2} rotations. In this paper, the time-resolved and steady-state fluorescence properties of (tryptophan{sup 2})oxytocin at pH 3 are presented and compared with {sup 1}H NMR results. According to the unrestricted analyses of individual fluorescence decay curves taken as a function of emission wavelength-independent decay constants, only three exponential terms aremore » required. In addition, the preexponential weighting factors (amplitudes) have the same relative relationship (weights) as the {sup 1}H NMR-determined {chi}{sup 1} rotamer populations of the indole side chain. {sup 15}N was used in heteronuclear coupling experiments to confirm the rotamer assignments. Inclusion of a linked function restricting the decay amplitudes to the {chi}{sup 1} rotamer populations in the individual decay curve analyses and in the global analysis confirms this correlation. According to qualitative nuclear Overhauser data, there are two {chi}{sup 2} populations.« less

A new French-Italian geomagnetic observatory in Dome C, Antarctica

NASA Astrophysics Data System (ADS)

Cafarella, L.; Zirizzotti, A.; di Mauro, D.; Schott, J. J.; Pèrès, A.; Cantin, J. M.

2003-04-01

Concordia is a scientific station located in the inner part of Antarctica (latitude 75° 06' S, longitude 123° 23' E, at about 3,200 m above sea level), about 950 km away from the coast. Near by the station a permanent Base is under construction and is expected to open in the year 2004. All this is the result of a join French Italian Antarctic Programs (IFRTP and PNRA respectively) effort to provide support to a growing number of scientific researches. The station is located 1.200 from Terra Nova Bay (Italy), 560 km away from Vostok Station (Russia), 1.100 Km from Dumont D'Urville (France) and Casey (Australia). During the 1998-1999 and 1999-2000 expeditions in Antarctica, some preliminary tests were carried out in order to evaluate the suitability of Dome C site for a permanent geomagnetic observatory. Two parallel data acquisition systems, each equipped with overhauser and flux-gate magnetometers were installed in two shelters at about 300 m from the Base camp. After some tests and checks, the site was considered a good site for geomagnetic investigations. The instrumentation is now in France and in Italy to prepare the instruments and the acquisition systems for the final installation that will take place during the 2004-2005 expedition.

Novel NMR tools to study structure and dynamics of biomembranes.

PubMed

Gawrisch, Klaus; Eldho, Nadukkudy V; Polozov, Ivan V

2002-06-01

Nuclear magnetic resonance (NMR) studies on biomembranes have benefited greatly from introduction of magic angle spinning (MAS) NMR techniques. Improvements in MAS probe technology, combined with the higher magnetic field strength of modern instruments, enables almost liquid-like resolution of lipid resonances. The cross-relaxation rates measured by nuclear Overhauser enhancement spectroscopy (NOESY) provide new insights into conformation and dynamics of lipids with atomic-scale resolution. The data reflect the tremendous motional disorder in the lipid matrix. Transfer of magnetization by spin diffusion along the proton network of lipids is of secondary relevance, even at a long NOESY mixing time of 300 ms. MAS experiments with re-coupling of anisotropic interactions, like the 13C-(1)H dipolar couplings, benefit from the excellent resolution of 13C shifts that enables assignment of the couplings to specific carbon atoms. The traditional 2H NMR experiments on deuterated lipids have higher sensitivity when conducted on oriented samples at higher magnetic field strength. A very large number of NMR parameters from lipid bilayers is now accessible, providing information about conformation and dynamics for every lipid segment. The NMR methods have the sensitivity and resolution to study lipid-protein interaction, lateral lipid organization, and the location of solvents and drugs in the lipid matrix.

Cyclodextrin Complexes of Reduced Bromonoscapine in Guar Gum Microspheres Enhance Colonic Drug Delivery

PubMed Central

2015-01-01

Here, we report improved solubility and enhanced colonic delivery of reduced bromonoscapine (Red-Br-Nos), a cyclic ether brominated analogue of noscapine, upon encapsulation of its cyclodextrin (CD) complexes in bioresponsive guar gum microspheres (GGM). Phase–solubility analysis suggested that Red-Br-Nos complexed with β-CD and methyl-β-CD in a 1:1 stoichiometry, with a stability constant (Kc) of 2.29 × 103 M–1 and 4.27 × 103 M–1. Fourier transforms infrared spectroscopy indicated entrance of an O–CH2 or OCH3–C6H4–OCH3 moiety of Red-Br-Nos in the β-CD or methyl-β-CD cavity. Furthermore, the cage complex of Red-Br-Nos with β-CD and methyl-β-CD was validated by several spectral techniques. Rotating frame Overhauser enhancement spectroscopy revealed that the Ha proton of the OCH3–C6H4–OCH3 moiety was closer to the H5 proton of β-CD and the H3 proton of the methyl-β-CD cavity. The solubility of Red-Br-Nos in phosphate buffer saline (PBS, pH ∼ 7.4) was improved by ∼10.7-fold and ∼21.2-fold when mixed with β-CD and methyl-β-CD, respectively. This increase in solubility led to a favorable decline in the IC50 by ∼2-fold and ∼3-fold for Red-Br-Nos−β-CD-GGM and Red-Br-Nos–methyl-β-CD-GGM formulations respectively, compared to free Red-Br-Nos−β-CD and Red-Br-Nos–methyl-β-CD in human colon HT-29 cells. GGM-bearing drug complex formulations were found to be highly cytotoxic to the HT-29 cell line and further effective with simultaneous continuous release of Red-Br-Nos from microspheres. This is the first study to showing the preparation of drug-complex loaded GGMS for colon delivery of Red-Br-Nos that warrants preclinical assessment for the effective management of colon cancer. PMID:25350222

Glioblastoma (GBM) effects on quantitative MRI of contralateral normal appearing white matter.

PubMed

Mehrabian, Hatef; Lam, Wilfred W; Myrehaug, Sten; Sahgal, Arjun; Stanisz, Greg J

2018-03-28

The objective was to investigate (with quantitative MRI) whether the normal appearing white matter (NAWM) of glioblastoma (GBM) patients on the contralateral side (cNAWM) was different from NAWM of healthy controls. Thirteen patients with newly diagnosed GBM and nine healthy age-matched controls were MRI-scanned with quantitative magnetization transfer (qMT), chemical exchange saturation transfer (CEST), and transverse relaxation time (T 2 )-mapping. MRI scans were performed after surgery and before chemo-radiation treatment. Comprehensive qMT, CEST, T 2 data were acquired. A two-pool MT model was fit to qMT data in transient state, to calculate MT model parameters [Formula: see text]. CEST signal was isolated by removing the contributions from the MT and direct water saturation, and CEST signal was calculated for Amide (CEST Amide ), Amine (CEST Amine ) and nuclear overhauser effect, NOE (CEST NOE ). There was no difference between GBM patients and normal controls in the qMT properties of the macromolecular pool [Formula: see text]. However, their free water pool spectrum was different (1/R a T 2a , patient  = 28.1 ± 3.9, 1/R a T 2a , control  = 25.0 ± 1.1, p = 0.03). This difference could be attributed to the difference in their T 2 time ([Formula: see text] = 83 ± 4, [Formula: see text] = 88 ± 1, p = 0.004). CEST signals were statistically significantly different with the CEST Amide having the largest difference between the two cohorts (CEST Amide,patient  = 2.8 ± 0.4, CEST Amide,control  = 3.4 ± 0.5, p = 0.009). CEST in cNAWM of GBM patients was lower than healthy controls which could be caused by modified brain metabolism due to tumor cell infiltration. There was no difference in MT properties of the patients and controls, however, the differences in free water pool properties were mainly due to reduced T 2 in cNAWM of the patients (resulting from structural changes and increased cellularity).

Solution structure and stability of the DNA undecamer duplexes containing oxanine mismatch

PubMed Central

Pack, Seung Pil; Morimoto, Hirohisa; Makino, Keisuke; Tajima, Kunihiko; Kanaori, Kenji

2012-01-01

Solution structures of DNA duplexes containing oxanine (Oxa, O) opposite a cytosine (O:C duplex) and opposite a thymine (O:T duplex) have been solved by the combined use of 1H NMR and restrained molecular dynamics calculation. One mismatch pair was introduced into the center of the 11-mer duplex of [d(GTGACO6CACTG)/d(CAGTGX17GTCAC), X = C or T]. 1H NMR chemical shifts and nuclear Overhauser enhancement (NOE) intensities indicate that both the duplexes adopt an overall right-handed B-type conformation. Exchangeable resonances of C17 4-amino proton of the O:C duplex and of T17 imino proton of O:T duplex showed unusual chemical shifts, and disappeared with temperature increasing up to 30°C, although the melting temperatures were >50°C. The O:C mismatch takes a wobble geometry with positive shear parameter where the Oxa ring shifted toward the major groove and the paired C17 toward the minor groove, while, in the O:T mismatch pair with the negative shear, the Oxa ring slightly shifted toward the minor groove and the paired T17 toward the major groove. The Oxa mismatch pairs can be wobbled largely because of no hydrogen bond to the O1 position of the Oxa base, and may occupy positions in the strands that optimize the stacking with adjacent bases. PMID:22039100

Small molecule PZL318: forming fluorescent nanoparticles capable of tracing their interactions with cancer cells and activated platelets, slowing tumor growth and inhibiting thrombosis

PubMed Central

Li, Shan; Wang, Yuji; Wang, Feng; Wang, Yaonan; Zhang, Xiaoyi; Zhao, Ming; Feng, Qiqi; Wu, Jianhui; Zhao, Shurui; Wu, Wei; Peng, Shiqi

2015-01-01

Low selectivity of chemotherapy correlates with poor outcomes of cancer patients. To improve this issue, a novel agent, N-(1-[3-methoxycarbonyl-4-hydroxyphenyl]-β-carboline-3-carbonyl)-Trp-Lys-OBzl (PZL318), was reported here. The transmission electron microscopy, scanning electron microscopy, and atomic force microscopy images demonstrated that PZL318 can form nanoparticles. Fluorescent and confocal images visualized that PZL318 formed fluorescent nanoparticles capable of targeting cancer cells and tracing their interactions with cancer cells. In vitro, 40 μM of PZL318 inhibited the proliferation of tumorigenic cells, but not nontumorigenic cells. In vivo, 10 nmol/kg of PZL318 slowed the tumor growth of S180 mice and alleviated the thrombosis of ferric chloride-treated ICR mice, while 100 μmol/kg of PZL318 did not injure healthy mice and they exhibited no liver toxicity. By analyzing Fourier transform–mass spectrometry and rotating-frame Overhauser spectroscopy (ROESY) two-dimensional nuclear magnetic resonance spectra, the chemical mechanism of PZL318-forming trimers and nanoparticles was explored. By using mesoscale simulation, a nanoparticle of 3.01 nm in diameter was predicted containing 13 trimers. Scavenging free radicals, downregulating sP-selectin expression and intercalating toward DNA were correlated with the antitumor mechanism of PZL318. PMID:26345234

Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes.

PubMed

Eichmann, Cédric; Orts, Julien; Tzitzilonis, Christos; Vögeli, Beat; Smrt, Sean; Lorieau, Justin; Riek, Roland

2014-12-11

The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.

PICKY: a novel SVD-based NMR spectra peak picking method.

PubMed

Alipanahi, Babak; Gao, Xin; Karakoc, Emre; Donaldson, Logan; Li, Ming

2009-06-15

Picking peaks from experimental NMR spectra is a key unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite for resonance assignment, nuclear overhauser enhancement (NOE) distance restraint assignment, and structure calculation tasks. Manual or semi-automatic peak picking, which is currently the prominent way used in NMR labs, is tedious, time consuming and costly. We introduce new ideas, including noise-level estimation, component forming and sub-division, singular value decomposition (SVD)-based peak picking and peak pruning and refinement. PICKY is developed as an automated peak picking method. Different from the previous research on peak picking, we provide a systematic study of the proposed method. PICKY is tested on 32 real 2D and 3D spectra of eight target proteins, and achieves an average of 88% recall and 74% precision. PICKY is efficient. It takes PICKY on average 15.7 s to process an NMR spectrum. More important than these numbers, PICKY actually works in practice. We feed peak lists generated by PICKY to IPASS for resonance assignment, feed IPASS assignment to SPARTA for fragments generation, and feed SPARTA fragments to FALCON for structure calculation. This results in high-resolution structures of several proteins, for example, TM1112, at 1.25 A. PICKY is available upon request. The peak lists of PICKY can be easily loaded by SPARKY to enable a better interactive strategy for rapid peak picking.

Structural Insights into the Calcium-Mediated Allosteric Transition in the C-Terminal Domain of Calmodulin from Nuclear Magnetic Resonance Measurements.

PubMed

Kukic, Predrag; Lundström, Patrik; Camilloni, Carlo; Evenäs, Johan; Akke, Mikael; Vendruscolo, Michele

2016-01-12

Calmodulin is a two-domain signaling protein that becomes activated upon binding cooperatively two pairs of calcium ions, leading to large-scale conformational changes that expose its binding site. Despite significant advances in understanding the structural biology of calmodulin functions, the mechanistic details of the conformational transition between closed and open states have remained unclear. To investigate this transition, we used a combination of molecular dynamics simulations and nuclear magnetic resonance (NMR) experiments on the Ca(2+)-saturated E140Q C-terminal domain variant. Using chemical shift restraints in replica-averaged metadynamics simulations, we obtained a high-resolution structural ensemble consisting of two conformational states and validated such an ensemble against three independent experimental data sets, namely, interproton nuclear Overhauser enhancements, (15)N order parameters, and chemical shift differences between the exchanging states. Through a detailed analysis of this structural ensemble and of the corresponding statistical weights, we characterized a calcium-mediated conformational transition whereby the coordination of Ca(2+) by just one oxygen of the bidentate ligand E140 triggers a concerted movement of the two EF-hands that exposes the target binding site. This analysis provides atomistic insights into a possible Ca(2+)-mediated activation mechanism of calmodulin that cannot be achieved from static structures alone or from ensemble NMR measurements of the transition between conformations.

An efficient randomized algorithm for contact-based NMR backbone resonance assignment.

PubMed

Kamisetty, Hetunandan; Bailey-Kellogg, Chris; Pandurangan, Gopal

2006-01-15

Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance (NMR) spectroscopy. A minimalist approach to assignment, which we call 'contact-based', seeks to dramatically reduce experimental time and expense by replacing the standard suite of through-bond experiments with the through-space (nuclear Overhauser enhancement spectroscopy, NOESY) experiment. In the contact-based approach, spectral data are represented in a graph with vertices for putative residues (of unknown relation to the primary sequence) and edges for hypothesized NOESY interactions, such that observed spectral peaks could be explained if the residues were 'close enough'. Due to experimental ambiguity, several incorrect edges can be hypothesized for each spectral peak. An assignment is derived by identifying consistent patterns of edges (e.g. for alpha-helices and beta-sheets) within a graph and by mapping the vertices to the primary sequence. The key algorithmic challenge is to be able to uncover these patterns even when they are obscured by significant noise. This paper develops, analyzes and applies a novel algorithm for the identification of polytopes representing consistent patterns of edges in a corrupted NOESY graph. Our randomized algorithm aggregates simplices into polytopes and fixes inconsistencies with simple local modifications, called rotations, that maintain most of the structure already uncovered. In characterizing the effects of experimental noise, we employ an NMR-specific random graph model in proving that our algorithm gives optimal performance in expected polynomial time, even when the input graph is significantly corrupted. We confirm this analysis in simulation studies with graphs corrupted by up to 500% noise. Finally, we demonstrate the practical application of the algorithm on several experimental beta-sheet datasets. Our approach is able to eliminate a large majority of noise edges and to uncover large consistent sets of interactions. Our algorithm has been implemented in the platform-independent Python code. The software can be freely obtained for academic use by request from the authors.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, X.; Patel, D.J.

The authors report on two-dimensional proton NMR studies of echinomycin complexes with the self-complementary d(A1-C2-G3-Tr) and d(T1-C2-G3-A4) duplexes in aqueous solution. The exchangeable and nonexchangeable antibiotic and nucleic acid protons in the 1 echinomycin per tetranucleotide duplex complexes have been assigned from analyses of scalar coupling and distance connectivities in two-dimensional data sets records in H/sub 2/O and D/sub 2/O solution. An analysis of the intermolecular NOE patterns for both complexes combined with large upfield imino proton and large downfield phosphorus complexation chemical shift changes demonstrates that the two quinoxaline chromophores of echinomycin bisintercalate into the minor groove surrounding themore » dC-dG step of each tetranucleotide duplex. Further, the quinoxaline rings selectively stack between A1 and C2 bases in the d(ACGT) complex and between T1 and C2 bases in the d(TCGA) complex. The intermolecular NOE patterns and the base and sugar proton chemical shifts for residues C2 and G3 are virtually identical for the d(ACGT) and d(TCGA) complexes. A large set of intermolecular contacts established from nuclear Overhauser effects (NOEs) between antibiotic and nucleic acid protons in the echinomycin-tetranucleotide complexes in solution are consistent with corresponding contacts reported for echinomycin-oligonucleotide complexes in the crystalline state. The authors demonstrate that the G x G base pairs adopt Watson-Crick pairing in both d(ACGT) and d(TCGA) complexes in solution. By contrast, the A1 x T4 base pairs adopt Hoogsteen pairing for the echinomycin-d(A1-C2-G3-Tr) complex while the T1 x A4 base pairs adopt Watson-Crick pairing for the echinomycin-d(T1-C2-G3-A4) complex in aqueous solution. These results emphasize the role of sequence in discriminating between Watson-Crick and Hoogsteen pairs at base pairs flanking the echinomycin bisintercalation site in solution.« less

Beta-hairpin formation in aqueous solution and in the presence of trifluoroethanol: a (1)H and (13)C nuclear magnetic resonance conformational study of designed peptides.

PubMed

Santiveri, Clara M; Pantoja-Uceda, David; Rico, Manuel; Jiménez, M Angeles

2005-10-15

In order to check our current knowledge on the principles involved in beta-hairpin formation, we have modified the sequence of a 3:5 beta-hairpin forming peptide with two different purposes, first to increase the stability of the formed 3:5 beta-hairpin, and second to convert the 3:5 beta-hairpin into a 2:2 beta-hairpin. The conformational behavior of the designed peptides was investigated in aqueous solution and in 30% trifluoroethanol (TFE) by analysis of the following nuclear magnetic resonance (NMR) parameters: nuclear Overhauser effect (NOE) data, and C(alpha)H, (13)C(alpha), and (13)C(beta) conformational shifts. From the differences in the ability to adopt beta-hairpin structures in these peptides, we have arrived to the following conclusions: (i) beta-Hairpin population increases with the statistical propensity of residues to occupy each turn position. (ii) The loop length, and in turn, the beta-hairpin type, can be modified as a function of the type of turn favored by the loop sequence. These two conclusions reinforce previous results about the importance of beta-turn sequence in beta-hairpin folding. (iii) Side-chain packing on each face of the beta-sheet may play a major role in beta-hairpin stability; hence simplified analysis in terms of isolated pair interactions and intrinsic beta-sheet propensities is insufficient. (iv) Contributions to beta-hairpin stability of turn and strand sequences are not completely independent. (v) The burial of hydrophobic surface upon beta-hairpin formation that, in turn, depends on side-chain packing also contributes to beta-hairpin stability. (vi) As previously observed, TFE stabilizes beta-hairpin structures, but the extent of the contribution of different factors to beta-hairpin formation is sometimes different in aqueous solution and in 30% TFE. (c) 2005 Wiley Periodicals, Inc. Biopolymers 79: 150-162, 2005.

a Study on SODIUM(110) and Other Nearly Free Electron Metals Using Angle Resolved Photoemission Spectroscopy.

NASA Astrophysics Data System (ADS)

Lyo, In-Whan

Electronic properties of the epitaxially grown Na(110) film have been studied using angle resolved ultraviolet photoemission spectroscopy with synchrotron radiation as the light source. Na provides an ideal ground to study the fundamental aspects of the electron-electron interactions in metals, because of its simple Fermi surface and small pseudopotential. The absolute band structure of Na(110) using angle resolved photoemission spectroscopy has been mapped out using the extrema searching method. The advantage of this approach is that the usual assumption of the unoccupied state dispersion is not required. We have found that the dispersion of Na(1l0) is very close to the parabolic band with the effective mass 1.21 M_{rm e} at 90 K. Self-consistent calculations of the self-energy for the homogeneous electron gas have been performed using the Green's function technique within the framework of the GW approximation, in the hope of understanding the narrowing mechanism of the bandwidth observed for all the nearly-free-electron (NFE) metals. Good agreements between the experimental data and our calculated self-energy were obtained not only for our data on k-dependency from Na(l10), but also for the total bandwidth corrections for other NFE metals, only if dielectric functions beyond the random phase approximation were used. Our findings emphasize the importance of the screening by long wavelength plasmons. Off-normal spectra of angle resolved photoemission from Na(110) show strong asymmetry of the bulk peak intensity for the wide range of photon energies. Using a simple analysis, we show this asymmetry has an origin in the interference of the surface Umklapp electrons with the normal electrons. We have also performed the detailed experimental studies of the anomalous Fermi level structure observed in the forbidden gap region of Na. This was claimed by A. W. Overhauser as the evidence of the charge density wave in the alkali metal. The possibility of this hypothesis is critically discussed against other explanations.

Novel nuclear magnetic resonance techniques for studying biological molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laws, David Douglas

2000-06-01

Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. Inmore » this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone (Φ/Ψ) dihedral angles by comparing experimentally determined 13C a, chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of α-helical and β-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly β-sheet.« less

Binding of peptides with basic and aromatic residues to bilayer membranes: phenylalanine in the myristoylated alanine-rich C kinase substrate effector domain penetrates into the hydrophobic core of the bilayer.

PubMed

Zhang, Wenyi; Crocker, Evan; McLaughlin, Stuart; Smith, Steven O

2003-06-13

Electrostatic interactions with positively charged regions of membrane-associated proteins such as myristoylated alanine-rich C kinase substrate (MARCKS) may have a role in regulating the level of free phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) in plasma membranes. Both the MARCKS protein and a peptide corresponding to the effector domain (an unstructured region that contains 13 basic residues and 5 phenylalanines), MARCKS-(151-175), laterally sequester the polyvalent lipid PI(4,5)P2 in the plane of a bilayer membrane with high affinity. We used high resolution magic angle spinning NMR to establish the location of MARCKS-(151-175) in membrane bilayers, which is necessary to understand the sequestration mechanism. Measurements of cross-relaxation rates in two-dimensional nuclear Overhauser enhancement spectroscopy NMR experiments show that the five Phe rings of MARCKS-(151-175) penetrate into the acyl chain region of phosphatidylcholine bilayers containing phosphatidylglycerol or PI(4,5)P2. Specifically, we observed strong cross-peaks between the aromatic protons of the Phe rings and the acyl chain protons of the lipids, even for very short (50 ms) mixing times. The position of the Phe rings implies that the adjacent positively charged amino acids in the peptide are close to the level of the negatively charged lipid phosphates. The deep location of the MARCKS peptide in the polar head group region should enhance its electrostatic sequestration of PI(4,5)P2 by an "image charge" mechanism. Moreover, this location has interesting implications for membrane curvature and local surface pressure effects and may be relevant to a wide variety of other proteins with basic-aromatic clusters, such as phospholipase D, GAP43, SCAMP2, and the N-methyl-d-aspartate receptor.

Acyclic peptides incorporating the d-Phe-2-Abz turn motif: Investigations on antimicrobial activity and propensity to adopt β-hairpin conformations.

PubMed

Cameron, Alan J; Varnava, Kyriakos G; Edwards, Patrick J B; Harjes, Elena; Sarojini, Vijayalekshmi

2018-06-14

Three linear peptides incorporating d-Phe-2-Abz as the turn motif are reported. Peptide 1, a hydrophobic β-hairpin, served as a proof of principle for the design strategy with both NMR and CD spectra strongly suggesting a β-hairpin conformation. Peptides 2 and 3, designed as amphipathic antimicrobials, exhibited broad spectrum antimicrobial activity, with potency in the nanomolar range against Staphylococcus aureus. Both compounds possess a high degree of selectivity, proving non-haemolytic at concentrations 500 to 800 times higher than their respective minimal inhibitory concentrations (MICs) against S. aureus. Peptide 2 induced cell membrane and cell wall disintegration in both S. aureus and Pseudomonas aeruginosa as observed by transmission electron microscopy. Peptide 2 also demonstrated moderate antifungal activity against Candida albicans with an MIC of 50 μM. Synergism was observed with sub-MIC levels of amphotericin B (AmB), leading to nanomolar MICs against C. albicans for peptide 2. Based on circular dichroism spectra, both peptides 2 and 3 appear to exist as a mixture of conformers with the β-hairpin as a minor conformer in aqueous solution, and a slight increase in hairpin population in 50% trifluoroethanol, which was more pronounced for peptide 3. NMR spectra of peptide 2 in a 1:1 CD 3 CN/H 2 O mixture and 30 mM deuterated sodium dodecyl sulfate showed evidence of an extended backbone conformation of the β-strand residues. However, inter-strand rotating frame Overhauser effects (ROE) could not be detected and a loosely defined divergent hairpin structure resulted from ROE structure calculation in CD 3 CN/H 2 O. The loosely defined hairpin conformation is most likely a result of the electrostatic repulsions between cationic strand residues which also probably contribute towards maintaining low haemolytic activity. Copyright © 2018 European Peptide Society and John Wiley & Sons, Ltd.

Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding.

PubMed

Newcomer, Rebecca L; Fraser, LaTasha C R; Teschke, Carolyn M; Alexandrescu, Andrei T

2015-12-15

The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining (3)JNC' couplings transmitted through H-bonds, the temperature and urea-concentration dependence of (1)HN and (15)N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and (3)JNC' H-bond couplings, are identified with an accuracy of 90% by (1)HN temperature coefficients. The accuracy is improved to 95% when (15)N temperature coefficients are also included. In contrast, the urea dependence of (1)HN and (15)N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Assessing the predictability of IDH mutation and MGMT methylation status in glioma patients using relaxation-compensated multi-pool CEST MRI at 7.0 Tesla.

PubMed

Paech, Daniel; Windschuh, Johannes; Oberhollenzer, Johanna; Dreher, Constantin; Sahm, Felix; Meissner, Jan-Eric; Goerke, Steffen; Schuenke, Patrick; Zaiss, Moritz; Regnery, Sebastian; Bickelhaupt, Sebastian; Bäumer, Philipp; Bendszus, Martin; Wick, Wolfgang; Unterberg, Andreas; Bachert, Peter; Ladd, Mark Edward; Schlemmer, Heinz-Peter; Radbruch, Alexander

2018-05-04

Early identification of prognostic superior characteristics in glioma patients such as Isocitrate dehydrogenase(IDH)-mutation and O6-methylguanine-DNA-methyltransferase (MGMT) promotor methylation status is of great clinical importance. The study purpose was to investigate the non-invasive predictability of IDH-mutation status, MGMT promotor methylation, and differentiation of lower versus higher grade glioma (LGG vs. HGG) in newly-diagnosed patients employing relaxation-compensated multi-pool Chemical Exchange Saturation Transfer (CEST) magnetic resonance imaging (MRI) at 7.0 Tesla (7T). Thirty-one newly-diagnosed glioma patients were included in this prospective study. CEST MRI was performed at a 7T whole-body scanner. Nuclear Overhauser Effect (NOE) and isolated amide proton transfer (APT, downfield NOE-suppressed APT=dns-APT) CEST signals (mean value and 90th signal percentile) were quantitatively investigated in the whole tumor area with regard to predictability of IDH-mutation, MGMT promotor methylation status, and differentiation of LGG vs. HGG. Statistics were performed using receiver operating characteristic (ROC) and area under the curve (AUC) analysis. Results were compared to advanced MRI methods (apparent diffusion coefficient (ADC) and relative cerebral blood volume (rCBV) ROC/AUC analysis) obtained at 3T. dns-APT CEST contrasts yielded highest AUCs in IDH-mutation status prediction (dns-APTmean=91.84%, p<0.01; dns-APT90=97.96%, p<0.001). Furthermore, dns-APT metrics enabled significant differentiation of LGG vs. HGG (AUC: dns-APTmean=0.78, p<0.05; dns-APT90=0.83, p<0.05). There was no significant difference regarding MGMT promotor methylation status at any contrast (p>0.05). Relaxation-compensated multi-pool CEST MRI, particularly dns-APT imaging, enabled prediction of IDH-mutation status and differentiation of LGG vs. HGG and should therefore be considered as non-invasive MR biomarker in the diagnostic workup.

NMR analyses of the conformations of L-isoleucine and L-valine bound to Escherichia coli isoleucyl-tRNA synthetase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kohda, D.; Kawai, G.; Yokoyama, S.

1987-10-06

The 400-MHz /sup 1/H NMR spectra of L-isoleucine and L-valine were measured in the presence of Escherichia coli isoleucyl-tRNA synthetase (IleRS). Because of chemical exchange of L-isoleucine or L-valine between the free state and the IleRS-bound state, a transferred nuclear Overhauser effect (TRNOE) was observed among proton resonances of L-isoleucine or L-valine. However, in the presence of isoleucyl adenylate tightly bound to the amino acid activation site of IleRS, no TRNOE for L-isoleucine or L-valine was observed. This indicates that the observed TRNOE is due to the interaction of L-isoleucine or L-valine with the amino acid activation site of IleRS.more » The conformations of these amino acids in the amino acid activation site of IleRS were determined by the analyses of time dependences of TRNOEs and TRNOE action spectra. The IleRS-bound L-isoleucine takes the gauche/sup +/ form about the C/sub ..cap alpha../-C/sub ..beta../ bond and the trans form about the C/sub ..beta../-C/sub ..gamma../sub 1// bond. The IleRS-bound L-valine takes the guache/sup -/ form about the C/sub ..cap alpha../-C/sub ..beta../ bond. Thus, the conformation of the IleRS-bound L-valine is the same as that of IleRS-bound L-isoleucine except for the delta-methyl group. The side chain of L-isoleucine or L-valine lies in an aliphatic hydrophobic pocket of the active site of IleRS. Such hydrophobic interaction with IleRS is more significant for L-isoleucine than for L-valine. The TRNOE analysis is useful for studying the amino acid discrimination mechanism of aminoacyl-tRNA synthetases.« less

Studies of phospholipid hydration by high-resolution magic-angle spinning nuclear magnetic resonance.

PubMed Central

Zhou, Z; Sayer, B G; Hughes, D W; Stark, R E; Epand, R M

1999-01-01

A sample preparation method using spherical glass ampoules has been used to achieve 1.5-Hz resolution in 1H magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of aqueous multilamellar dispersions of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), serving to differentiate between slowly exchanging interlamellar and bulk water and to reveal new molecular-level information about hydration phenomena in these model biological membranes. The average numbers of interlamellar water molecules in multilamellar vesicles (MLVs) of DOPC and POPC were found to be 37.5 +/- 1 and 37.2 +/- 1, respectively, at a spinning speed of 3 kHz. Even at speeds as high as 9 kHz, the number of interlamellar waters remained as high as 31, arguing against dehydration effects for DOPC and POPC. Both homonuclear and heteronuclear nuclear Overhauser enhancement spectroscopy (NOESY and HOESY) were used to establish the location of water near the headgroup of a PC bilayer. 1H NMR comparisons of DOPC with a lipid that can hydrogen bond (monomethyldioleoylphosphatidylethanolamine, MeDOPE) showed the following trends: 1) the interlamellar water resonance was shifted to lower frequency for DOPC but to higher frequency for MeDOPE, 2) the chemical shift variation with temperature for interlamellar water was less than that of bulk water for MeDOPE MLVs, 3) water exchange between the two lipids was rapid on the NMR time scale if they were mixed in the same bilayer, 4) water exchange was slow if they were present in separate MLVs, and 5) exchange between bulk and interlamellar water was found by two-dimensional exchange experiments to be slow, and the exchange rate should be less than 157 Hz. These results illustrate the utility of ultra-high-resolution 1H MAS NMR for determining the nature and extent of lipid hydration as well as the arrangement of nuclei at the membrane/water interface. PMID:9876150

Human cytochrome P450scc (CYP11A1) catalyzes epoxide formation with ergosterol.

PubMed

Tuckey, Robert C; Nguyen, Minh N; Chen, Jianjun; Slominski, Andrzej T; Baldisseri, Donna M; Tieu, Elaine W; Zjawiony, Jordan K; Li, Wei

2012-03-01

Cytochrome P450scc (P450scc) catalyzes the cleavage of the side chain of both cholesterol and the vitamin D(3) precursor, 7-dehydrocholesterol. The aim of this study was to test the ability of human P450scc to metabolize ergosterol, the vitamin D(2) precursor, and define the structure of the major products. P450scc incorporated into the bilayer of phospholipid vesicles converted ergosterol to two major and four minor products with a k(cat) of 53 mol · min(-1) · mol P450scc(-1) and a K(m) of 0.18 mol ergosterol/mol phospholipid, similar to the values observed for cholesterol metabolism. The reaction of ergosterol with P450scc was scaled up to make enough of the two major products for structural analysis. From mass spectrometry, NMR, and comparison of the NMR data to that for similar molecules, we determined the structures of the two major products as 20-hydroxy-22,23-epoxy-22,23-dihydroergosterol and 22-keto-23-hydroxy-22,23-dihydroergosterol. Molecular modeling and nuclear Overhauser effect (or enhancement) spectroscopy spectra analysis helped to establish the configurations at C20, C22, and C23 and determine the final structures of major products as 22R,23S-epoxyergosta-5,7-diene-3β,20α-diol and 3β,23S-dihydroxyergosta-5,7-dien-22-one. It is likely that the formation of the second product is through a 22,23-epoxy (oxirane) intermediate followed by C22 hydroxylation with the formation of strained 22-hydroxy-22,23-epoxide (oxiranol), which is immediately transformed to the more stable α-hydroxyketone. Molecular modeling of ergosterol into the P450scc crystal structure positioned the ergosterol side chain consistent with formation of the above products. Thus, we have shown that P450scc efficiently catalyzes epoxide formation with ergosterol giving rise to novel epoxy, hydroxy, and keto derivatives, without causing cleavage of the side chain.

Correction of spin diffusion during iterative automated NOE assignment

NASA Astrophysics Data System (ADS)

Linge, Jens P.; Habeck, Michael; Rieping, Wolfgang; Nilges, Michael

2004-04-01

Indirect magnetization transfer increases the observed nuclear Overhauser enhancement (NOE) between two protons in many cases, leading to an underestimation of target distances. Wider distance bounds are necessary to account for this error. However, this leads to a loss of information and may reduce the quality of the structures generated from the inter-proton distances. Although several methods for spin diffusion correction have been published, they are often not employed to derive distance restraints. This prompted us to write a user-friendly and CPU-efficient method to correct for spin diffusion that is fully integrated in our program ambiguous restraints for iterative assignment (ARIA). ARIA thus allows automated iterative NOE assignment and structure calculation with spin diffusion corrected distances. The method relies on numerical integration of the coupled differential equations which govern relaxation by matrix squaring and sparse matrix techniques. We derive a correction factor for the distance restraints from calculated NOE volumes and inter-proton distances. To evaluate the impact of our spin diffusion correction, we tested the new calibration process extensively with data from the Pleckstrin homology (PH) domain of Mus musculus β-spectrin. By comparing structures refined with and without spin diffusion correction, we show that spin diffusion corrected distance restraints give rise to structures of higher quality (notably fewer NOE violations and a more regular Ramachandran map). Furthermore, spin diffusion correction permits the use of tighter error bounds which improves the distinction between signal and noise in an automated NOE assignment scheme.

PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

PubMed

Lee, Woonghee; Stark, Jaime L; Markley, John L

2014-11-01

Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days.

Integrating gravity and magnetic field data to delineate structurally controlled gold mineralization in the Sefwi Belt of Ghana

NASA Astrophysics Data System (ADS)

Konadu Amoah, Bernard; Dadzie, Isaac; Takyi-Kyeremeh, Kwaku

2018-08-01

Gravity and magnetic surveys were used to delineate potential gold mineralization zones in the Sefwi belt of Ghana. The study area is an intrusive dominated area that hosts pockets of small scale mining operations locally referred to as Galamsey. These Galamsey operations are not guided by a scientific approach to back the trend of gold mineralization which is conventionally mined. The study aimed at mapping lithological units, structural setting and relating Galamsey sites to delineate potential zones of gold mineralization. A Scintrex CG5 gravimeter and GEM’s Overhauser magnetometer were used for gravity and magnetic data acquisition respectively. The magnetic data were corrected and enhancing filters such as reduction to the pole (RTP), analytical signal and first vertical derivative were applied using Oasis montaj 7.1. Gravity data were also reduced to the geoid using the Oasis montaj software to produce a complete Bouguer anomaly map. The regional/residual separation technique produced a residual gravity map. The RTP and analytical signal filters from the magnetic data and residual gravity anomaly map from the gravity data helped in mapping belt type (Dixcove) Birimian granitoids and mafic intrusive unit, interpreted as gabbro. The first vertical derivative filter was useful in mapping NE/SW minor faults and crosscutting dykes largely concentrated in the belt type Birimian granitoids. All the three mapped Galamsey sites fell on a minor fault and are associated with the belt type granitoids which were used in delineating four potential zones of gold mineralization.

PICKY: a novel SVD-based NMR spectra peak picking method

PubMed Central

Alipanahi, Babak; Gao, Xin; Karakoc, Emre; Donaldson, Logan; Li, Ming

2009-01-01

Motivation: Picking peaks from experimental NMR spectra is a key unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite for resonance assignment, nuclear overhauser enhancement (NOE) distance restraint assignment, and structure calculation tasks. Manual or semi-automatic peak picking, which is currently the prominent way used in NMR labs, is tedious, time consuming and costly. Results: We introduce new ideas, including noise-level estimation, component forming and sub-division, singular value decomposition (SVD)-based peak picking and peak pruning and refinement. PICKY is developed as an automated peak picking method. Different from the previous research on peak picking, we provide a systematic study of the proposed method. PICKY is tested on 32 real 2D and 3D spectra of eight target proteins, and achieves an average of 88% recall and 74% precision. PICKY is efficient. It takes PICKY on average 15.7 s to process an NMR spectrum. More important than these numbers, PICKY actually works in practice. We feed peak lists generated by PICKY to IPASS for resonance assignment, feed IPASS assignment to SPARTA for fragments generation, and feed SPARTA fragments to FALCON for structure calculation. This results in high-resolution structures of several proteins, for example, TM1112, at 1.25 Å. Availability: PICKY is available upon request. The peak lists of PICKY can be easily loaded by SPARKY to enable a better interactive strategy for rapid peak picking. Contact: mli@uwaterloo.ca PMID:19477998

In Vivo Proton–Electron Double-Resonance Imaging of Extracellular Tumor pH Using an Advanced Nitroxide Probe

PubMed Central

Samouilov, Alexandre; Efimova, Olga V.; Bobko, Andrey A.; Sun, Ziqi; Petryakov, Sergey; Eubank, Timothy D.; Trofimov, Dmitrii G.; Kirilyuk, Igor A.; Grigor’ev, Igor A.; Takahashi, Wataru; Zweier, Jay L.; Khramtsov, Valery V.

2014-01-01

A variable radio frequency proton–electron double-resonance imaging (VRF PEDRI) approach for pH mapping of aqueous samples has been recently developed (Efimova et al. J. Magn. Reson. 2011, 209, 227–232). A pH map is extracted from two PEDRI acquisitions performed at electron paramagnetic resonance (EPR) frequencies of protonated and unprotonated forms of a pH-sensitive probe. To translate VRF PEDRI to an in vivo setting, an advanced pH probe was synthesized. Probe deuteration resulted in a narrow spectral line of 1.2 G compared to a nondeuterated analogue line width of 2.1 G allowing for an increase of Overhauser enhancements and reduction in rf power deposition. Binding of the probe to the cell-impermeable tripeptide, glutathione (GSH), allows for targeting to extracellular tissue space for monitoring extracellular tumor acidosis, a prognostic factor in tumor pathophysiology. The probe demonstrated pH sensitivity in the 5.8–7.8 range, optimum for measurement of acidic extracellular tumor pH (pHe). In vivo VRF PEDRI was performed on Met-1 tumor-bearing mice. Compared to normal mammary glands with a neutral mean pHe (7.1 ± 0.1), we observed broader pH distribution with acidic mean pHe (6.8 ± 0.1) in tumor tissue. In summary, VRF PEDRI in combination with a newly developed pH probe provides an analytical approach for spatially resolved noninvasive pHe monitoring, in vivo. PMID:24372284

Structural studies on Desulfovibrio gigas cytochrome c3 by two-dimensional 1H-nuclear-magnetic-resonance spectroscopy.

PubMed Central

Piçarra-Pereira, M A; Turner, D L; LeGall, J; Xavier, A V

1993-01-01

Several aromatic amino acid residues and haem resonances in the fully reduced form of Desulfovibrio gigas cytochrome c3 are assigned, using two-dimensional 1H n.m.r., on the basis of the interactions between the protons of the aromatic amino acids and the haem protons as well as the intrahaem distances known from the X-ray structure [Kissinger (1989) Ph.D. Thesis, Washington State University]. The interhaem interactions observed in the n.m.r. spectra are in full agreement with the D. gigas X-ray structure and also with the n.m.r. data from Desulfovibrio vulgaris (Hildenborough) [Turner, Salgueiro, LeGall and Xavier (1992) Eur. J. Biochem. 210, 931-936]. The good correlation between the calculated ring-current shifts and the observed chemical shifts strongly supports the present assignments. Observation of the two-dimensional nuclear-Overhauser-enhancement spectra of the protein in the reduced, intermediate and fully oxidized stages led to the ordering of the haems in terms of their midpoint redox potentials and their identification in the X-ray structure. The first haem to oxidize is haem I, followed by haems II, III and IV, numbered according to the Cys ligand positions in the amino acid sequences [Mathews (1985) Prog. Biophys. Mol. Biol. 54, 1-56]. Although the haem core architecture is the same for the different Desulfovibrio cytochromes c3, the order of redox potentials is different. PMID:8397514

Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix.

PubMed

Kaplan, Anne R; Brady, Megan R; Maciejewski, Mark W; Kammerer, Richard A; Alexandrescu, Andrei T

2017-03-21

To understand the roles ion pairs play in stabilizing coiled coils, we determined nuclear magnetic resonance structures of GCN4p at three pH values. At pH 6.6, all acidic residues are fully charged; at pH 4.4, they are half-charged, and at pH 1.5, they are protonated and uncharged. The α-helix monomer and coiled coil structures of GCN4p are largely conserved, except for a loosening of the coiled coil quaternary structure with a decrease in pH. Differences going from neutral to acidic pH include (i) an unwinding of the coiled coil superhelix caused by the loss of interchain ion pair contacts, (ii) a small increase in the separation of the monomers in the dimer, (iii) a loosening of the knobs-into-holes packing motifs, and (iv) an increased separation between oppositely charged residues that participate in ion pairs at neutral pH. Chemical shifts (HN, N, C', Cα, and Cβ) of GCN4p display a seven-residue periodicity that is consistent with α-helical structure and is invariant with pH. By contrast, periodicity in hydrogen exchange rates at neutral pH is lost at acidic pH as the exchange mechanism moves into the EX1 regime. On the basis of 1 H- 15 N nuclear Overhauser effect relaxation measurements, the α-helix monomers experience only small increases in picosecond to nanosecond backbone dynamics at acidic pH. By contrast, 13 C rotating frame T 1 relaxation (T 1ρ ) data evince an increase in picosecond to nanosecond side-chain dynamics at lower pH, particularly for residues that stabilize the coiled coil dimerization interface through ion pairs. The results on the structure and dynamics of GCNp4 over a range of pH values help rationalize why a single structure at neutral pH poorly predicts the pH dependence of the unfolding stability of the coiled coil.

Structural and Biophysical Characterization of the Mycobacterium tuberculosis Protein Rv0577, a Protein Associated with Neutral Red Staining of Virulent Tuberculosis Strains and Homologue of the Streptomyces coelicolor Protein KbpA [Structural and Biophysical Characterization of Rv0577, a Protein Associated with Neutral Red Staining of Virulent Strains of Mycobacterium tuberculosis and homolog of the Streptomyces coelicolor protein KbpA

DOE PAGES

Buchko, Garry W.; Echols, Nathaniel; Flynn, E. Megan; ...

2017-07-10

Mycobacterium tuberculosis protein Rv0577 is a prominent antigen in tuberculosis patients, the component responsible for neutral red staining of virulent strains of M. tuberculosis, a putative component in a methylglyoxal detoxification pathway, and an agonist of toll-like receptor 2. It also has an amino acid sequence that is 36% identical to that of Streptomyces coelicolor AfsK-binding protein A (KbpA), a component in the complex secondary metabolite pathways in the Streptomyces genus. To gain insight into the biological function of Rv0577 and the family of KpbA kinase regulators, the crystal structure for Rv0577 was determined to a resolution of 1.75 Å,more » binding properties with neutral red and deoxyadenosine were surveyed, backbone dynamics were measured, and thermal stability was assayed by circular dichroism spectroscopy. The protein is composed of four approximate repeats with a βαβββ topology arranged radially in consecutive pairs to form two continuous eight-strand β-sheets capped on both ends with an α-helix. The two β-sheets intersect in the center at roughly a right angle and form two asymmetric deep “saddles” that may serve to bind ligands. Nuclear magnetic resonance chemical shift perturbation experiments show that neutral red and deoxyadenosine bind to Rv0577. Binding to deoxyadenosine is weaker with an estimated dissociation constants of 4.1 ± 0.3 mM for saddle 1. Heteronuclear steady-state { 1H}– 15N nuclear Overhauser effect, T 1, and T 2 values were generally uniform throughout the sequence with only a few modest pockets of differences. As a result, circular dichroism spectroscopy characterization of the thermal stability of Rv0577 indicated irreversible unfolding upon heating with an estimated melting temperature of 56 °C.« less

Structural and Biophysical Characterization of the Mycobacterium tuberculosis Protein Rv0577, a Protein Associated with Neutral Red Staining of Virulent Tuberculosis Strains and Homologue of the Streptomyces coelicolor Protein KbpA [Structural and Biophysical Characterization of Rv0577, a Protein Associated with Neutral Red Staining of Virulent Strains of Mycobacterium tuberculosis and homolog of the Streptomyces coelicolor protein KbpA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buchko, Garry W.; Echols, Nathaniel; Flynn, E. Megan

Mycobacterium tuberculosis protein Rv0577 is a prominent antigen in tuberculosis patients, the component responsible for neutral red staining of virulent strains of M. tuberculosis, a putative component in a methylglyoxal detoxification pathway, and an agonist of toll-like receptor 2. It also has an amino acid sequence that is 36% identical to that of Streptomyces coelicolor AfsK-binding protein A (KbpA), a component in the complex secondary metabolite pathways in the Streptomyces genus. To gain insight into the biological function of Rv0577 and the family of KpbA kinase regulators, the crystal structure for Rv0577 was determined to a resolution of 1.75 Å,more » binding properties with neutral red and deoxyadenosine were surveyed, backbone dynamics were measured, and thermal stability was assayed by circular dichroism spectroscopy. The protein is composed of four approximate repeats with a βαβββ topology arranged radially in consecutive pairs to form two continuous eight-strand β-sheets capped on both ends with an α-helix. The two β-sheets intersect in the center at roughly a right angle and form two asymmetric deep “saddles” that may serve to bind ligands. Nuclear magnetic resonance chemical shift perturbation experiments show that neutral red and deoxyadenosine bind to Rv0577. Binding to deoxyadenosine is weaker with an estimated dissociation constants of 4.1 ± 0.3 mM for saddle 1. Heteronuclear steady-state { 1H}– 15N nuclear Overhauser effect, T 1, and T 2 values were generally uniform throughout the sequence with only a few modest pockets of differences. As a result, circular dichroism spectroscopy characterization of the thermal stability of Rv0577 indicated irreversible unfolding upon heating with an estimated melting temperature of 56 °C.« less

Molecular basis for methoxyamine initiated mutagenesis. 1H nuclear magnetic resonance studies of base-modified oligodeoxynucleotides.

PubMed

Stone, M J; Nedderman, A N; Williams, D H; Lin, P K; Brown, D M

1991-12-05

In order to reach a more detailed understanding of the mechanism of the mutagenic action of methoxyamine and of N4-methoxycytidine and its 2'-deoxyribo-analogue, the solution structures of the self-complementary octanucleotide, d(CGAATTCG) and its analogues, d(CGAATCCG), d(CGAATMCG) and d(CGAATPCG) (designated 8mer-AT, 8mer-AC, 8mer-AM, and 8mer-AP, respectively), were investigated by 1H nuclear magnetic resonance spectroscopy; M is N4-methoxycytosine (mo4C) and P is an analogue, the bicyclic dihydropyrimido[4,5-c][1,2]oxazin-7-one, in which the N-O bond is held in the anti configuration with respect to N3 of the cytosine ring. Correlated spectroscopy and nuclear Overhauser spectroscopy allowed assignment of the base, anomeric and H2'/H2" protons in 8mers-AT, -AM and -AP, and showed that all three had features consistent with a regular B-DNA duplex structure. Duplex-to-coil transition temperatures were determined to be 52(+/- 2) degrees C (8mer-AT), 51(+/- 2) degrees C (8mer-AP), 32(+/- 2) degrees C (8mer-AM); on the chemical shift timescale, the melting transition was fast for 8mer-AT and 8mer-AP, but slow for 8mer-AM. Imino proton spectra were indicative of Watson-Crick base-pairing in 8mers-AT, -AP and -AM. The 8mer-AP duplex had a structure and melting characteristics virtually identical with those of the 8mer-AT duplex. The preferred syn configuration of the methoxyl group in M had a destabilising effect on the 8mer-AM duplex. At low temperatures, the A.M base-pair was in fast equilibrium between Watson-Crick and wobble configurations, with the methoxyl function anti-oriented, but the melting transition was accompanied by isomerization of the methoxyl group to the syn conformation. This syn-anti isomerization was the rate-determining step in the duplex-to-coil transition. The 8mer-AC oligomer did not form a stable duplex.

Solution structure of a lipid transfer protein extracted from rice seeds. Comparison with homologous proteins.

PubMed

Poznanski, J; Sodano, P; Suh, S W; Lee, J Y; Ptak, M; Vovelle, F

1999-02-01

Nuclear magnetic resonance (NMR) spectroscopy was used to determine the three dimensional structure of rice nonspecific lipid transfer protein (ns-LTP), a 91 amino acid residue protein belonging to the broad family of plant ns-LTP. Sequence specific assignment was obtained for all but three HN backbone 1H resonances and for more than 95% of the 1H side-chain resonances using a combination of 1H 2D NOESY; TOCSY and COSY experiments at 293 K. The structure was calculated on the basis of four disulfide bridge restraints, 1259 distance constraints derived from 1H-1H Overhauser effects, 72 phi angle restraints and 32 hydrogen-bond restraints. The final solution structure involves four helices (H1: Cys3-Arg18, H2: Ala25-Ala37, H3: Thr41-Ala54 and H4: Ala66-Cys73) followed by a long C-terminal tail (T) with no observable regular structure. N-capping residues (Thr2, Ser24, Thr40), whose side-chain oxygen atoms are involved in hydrogen bonds with i + 3 amide proton additionally stabilize the N termini of the first three helices. The fourth helix involving Pro residues display a mixture of alpha and 3(10) conformation. The rms deviation of 14 final structures with respect to the average structure is 1.14 +/- 0.16 A for all heavy atoms (C, N, O and S) and 0.72 +/- 0.01 A for the backbone atoms. The global fold of rice ns-LTP is close to the previously published structures of wheat, barley and maize ns-LTPs exhibiting nearly identical pattern of the numerous sequence specific interactions. As reported previously for different four-helix topology proteins, hydrophobic, hydrogen bonding and electrostatic mechanisms of fold stabilization were found for the rice ns-LTP. The sequential alignment of 36 ns-LTP primary structures strongly suggests that there is a uniform pattern of specific long-range interactions (in terms of sequence), which stabilize the fold of all plant ns-LTPs.

Metabolomic does not predict response to cardiac resynchronization therapy in patients with heart failure.

PubMed

Padeletti, Luigi; Modesti, Pietro A; Cartei, Stella; Checchi, Luca; Ricciardi, Giuseppe; Pieragnolia, Paolo; Sacchi, Stefania; Padeletti, Margherita; Alterini, Brunetto; Pantaleo, Pietro; Hu, Xiaoyu; Tenori, Leonardo; Luchinat, Claudio

2014-04-01

Metabolomic, a systematic study of metabolites, may be a useful tool in understanding the pathological processes that underlie the occurrence and progression of a disease. We hypothesized that metabolomic would be helpful in assessing a specific pattern in heart failure patients, also according to the underlining causes and in defining, prior to device implantation, the responder and nonresponder patient to cardiac resynchronization therapy (CRT). In this prospective study, blood and urine samples were collected from 32 heart failure patients who underwent CRT. Clinical, electrocardiography and echocardiographic evaluation was performed in each patient before CRT and after 6 months of follow-up. Thirty-nine age and sex-matched healthy individuals were chosen as control group. For each sample, 1H-NMR spectra, Nuclear Overhauser Enhancement Spectroscopy, Carr-Purcell-Meiboom-Gill and diffusion edited spectra were measured. A different metabolomic fingerprint was demonstrated in heart failure patients compared to healthy controls with high accuracy level. Metabolomics fingerprint was similar between patients with ischemic and nonischemic dilated cardiomyopathy. At 6-month follow-up, metabolomic fingerprint was different from baseline. At follow-up, heart failure patients’ metabolomic fingerprint remained significantly different from that of healthy controls, and accuracy of cause discrimination remained low. Responders and nonresponders had a similar metabolic fingerprint at baseline and after 6 months of CRT. It is possible to identify a metabolomic fingerprint characterizing heart failure patients candidate to CRT, it is independent of the different causes of the disease and it is not predictive of the response to CRT.

Fairy-Tale Physics Farewell to Reality Bankrupting Physics: Baggott-Unzicker-Jones Critiques Shame Physics' Shameless Media-Hype P.R. Spin-Doctoring Touting Sci-Fi Veracity-Abandonment ``Show-Biz'' Spectacle: Caveat Emptor!!!

NASA Astrophysics Data System (ADS)

Siegel, Edward

2014-03-01

Baggott[Farewell to Reality: How Fairy-Tale Physics Betrayed Search For Scientific Truth]-Unzicker [Bankrupting Physics: How Top Scientists Are Gambling Away Credibility] shame physics shameless rock-star media-hype P.R. spin-doctoring veracity-abandoning touting sci-fi show-biz aided by online proliferation of uncritical pop-sci science-writers verbal diarrhea, all spectacle vs little truth, lacking Kant-Popper skepticism/ falsification, lemming-like stampedes to truth abandonment, qualified by vague adverbs: might, could, should, may,...vs factual is! Physics, motivated by financial greed, swept up in its very own hype, touts whatever next big thing/cutting-edge bombast ad infinitum/ad nauseum, turning it into mere trendy carney sideshow, full of fury(FOF) but signifying absolutely nothing! Witness: GIGO claims string-theory holographic-universe causes cuprates optical conductivity; failed Anderson RVB cuprates theory vs. Keimer discovery all cuprates ``paramagnons'' bosons aka Overhauser SDWs; Overbye NYT holographic-universe jargonial-obfuscation comments including one from APS journals editor-in-chief re. its unintelligibility, FOF but signifying absolutely nothing INTELLIGIBLE!; Bak/BNL SOC tad late rediscovery of F =ma mere renaming of Siegel acoustic-emission!; 2007 physics Nobel-prize Fert-Gruenberg rediscovery of Siegel[JMMM 7,312(78); https://www.flickr.com/search/?q = GIANT-MAGNETORESISTANCE] GMR. Each trendy latest big thing modulo lack of prior attribution aka out and out bombastic chicanery! Siegel caveat emptor ``Buzzwordism, Bandwagonism, Sloganeering for Fun Profit Survival Ego'' sociological-dysfunctionality thrives!

Fairy-Tale Physics Farewell to Reality Bankrupting Physics: Baggott-Unzicker-Jones Critiques Shame Physics' Shameless Media-Hype P.R. Spin-Doctoring Touting Sci-Fi Veracity-Abandonment ``Show-Biz'' Spectacle: Caveat Emptor!!!

NASA Astrophysics Data System (ADS)

Siegel, Edward

2014-03-01

Baggott[Farewell to Reality: How Fairy-Tale Physics Betrayed Search For Scientific Truth]-Unzicker [Bankrupting Physics: How Top Scientists Are Gambling Away Credibility] shame physics shameless rock-star media-hype P.R. spin-doctoring veracity-abandoning touting sci-fi show-biz aided by online proliferation of uncritical pop-sci science-writers verbal diarrhea, all spectacle vs little truth, lacking Kant-Popper skepticism/falsification, lemming-like stampedes to truth abandonment, qualified by vague adverbs: might, could, should, may,...vs factual is! Physics, motivated by financial greed, swept up in its very own hype, touts whatever next big thing/cutting-edge bombast ad infinitum/ad nauseum, turning it into mere trendy carney sideshow, full of fury(FOF) but signifying absolutely nothing! Witness: GIGO claims string-theory holographic-universe causes cuprates optical conductivity; failed Anderson RVB cuprates theory vs. Keimer discovery all cuprates ``paramagnons'' bosons aka Overhauser SDWs; Overbye NYT holographic-universe jargonial-obfuscation comments including one from APS journals editor-in-chief re. its unintelligibility, FOF but signifying absolutely nothing INTELLIGIBLE!; Bak/BNL SOC tad late rediscovery of F =ma mere renaming of Siegel acoustic-emission!; 2007 physics Nobel-prize Fert-Gruenberg rediscovery of Siegel[JMMM 7,312(78); https://www.flickr.com/search/?q=GIANT-MAGNETORESISTANCE] GMR. Each trendy latest big thing modulo lack of prior attribution aka out and out bombastic chicanery! Siegel caveat emptor ``Buzzwordism, Bandwagonism, Sloganeering for Fun Profit Survival Ego'' sociological-dysfunctionality thrives!

Chemical exchange rotation transfer (CERT) on human brain at 3 Tesla.

PubMed

Lin, Eugene C; Li, Hua; Zu, Zhongliang; Louie, Elizabeth A; Lankford, Christopher L; Dortch, Richard D; Does, Mark D; Gore, John C; Gochberg, Daniel F

2018-05-25

To test the ability of a novel pulse sequence applied in vivo at 3 Tesla to separate the contributions to the water signal from amide proton transfer (APT) and relayed nuclear Overhauser enhancement (rNOE) from background direct water saturation and semisolid magnetization transfer (MT). The lack of such signal source isolation has confounded conventional chemical exchange saturation transfer (CEST) imaging. We quantified APT and rNOE signals using a chemical exchange rotation transfer (CERT) metric, MTR double . A range of duty cycles and average irradiation powers were applied, and results were compared with conventional CEST analyses using asymmetry (MTR asym ) and extrapolated magnetization transfer (EMR). Our results indicate that MTR double is more specific than MTR asym and, because it requires as few as 3 data points, is more rapid than methods requiring a complete Z-spectrum, such as EMR. In white matter, APT (1.5 ± 0.5%) and rNOE (2.1 ± 0.7%) were quantified by using MTR double with a 30% duty cycle and a 0.5-µT average power. In addition, our results suggest that MTR double is insensitive to B 0 inhomogeneity, further magnifying its speed advantage over CEST metrics that require a separate B 0 measurement. However, MTR double still has nontrivial sensitivity to B 1 inhomogeneities. We demonstrated that MTR double is an alternative metric to evaluate APT and rNOE, which is fast, robust to B 0 inhomogeneity, and easy to process. © 2018 International Society for Magnetic Resonance in Medicine.

Sequential /sup 1/H NMR assignments and secondary structure of hen egg white lysozyme in solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Redfield, C.; Dobson, C.M.

Assignments of /sup 1/H NMR resonances of 121 of the 129 residues of hen egg white lysozyme have been obtained by sequence-specific methods. Spin systems were identified with phase-sensitive two-dimensional (2-D) correlated spectroscopy and single and double relayed coherence transfer spectroscopy. For key types of amino acid residues, particularly alanine, threonine, valine, and glycine, complete spin systems were identified. For other residues a less complete definition of the spin system was found to be adequate for the purpose of sequential assignment. Sequence-specific assignments were achieved by phase-sensitive 2-D nuclear Overhauser enhancement spectroscopy (NOESY). Exploitation of the wide range of hydrogenmore » exchange rates found in lysozyme was a useful approach to overcoming the problem of spectral overlap. The sequential assignment was built up from 21 peptide segments ranging in length from 2 to 13 residues. The NOESY spectra were also used to provide information about the secondary structure of the protein in solution. Three helical regions and two regions of ..beta..-sheet were identified from the NOESY data; these regions are identical with those found in the X-ray structure of hen lysozyme. Slowly exchanging amides are generally correlated with hydrogen bonding identified in the X-ray structure; a number of exceptions to this general trend were, however, found. The results presented in this paper indicate that highly detailed information can be obtained from 2-D NMR spectra of a protein that is significantly larger than those studies previously.« less

Low-frequency ESR studies on permeable and impermeable deuterated nitroxyl radicals in corn oil solution.

PubMed

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

2018-04-01

Low-frequency electron spin resonance studies were performed for 2 mM concentration of deuterated permeable and impermeable nitroxyl spin probes, 3-methoxycarbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl and 3-carboxy-2,2,5,5,-tetramethyl-1-pyrrolidinyloxy in pure water and various concentrations of corn oil solution. The electron spin resonance parameters such as the line width, hyperfine coupling constant, g factor, rotational correlation time, permeability, and partition parameter were estimated. The broadening of line width was observed for nitroxyl radicals in corn oil mixture. The rotational correlation time increases with increasing concentration of corn oil, which indicates the less mobile nature of spin probe in corn oil mixture. The membrane permeability and partition parameter values were estimated as a function of corn oil concentration, which reveals that the nitroxyl radicals permeate equally into the aqueous phase and oil phase at the corn oil concentration of 50%. The electron spin resonance spectra demonstrate the permeable and impermeable nature of nitroxyl spin probes. From these results, the corn oil concentration was optimized as 50% for phantom studies. In this work, the corn oil and pure water mixture phantom models with various viscosities correspond to plasma membrane, and whole blood membrane with different hematocrit levels was studied for monitoring the biological characteristics and their interactions with permeable nitroxyl spin probe. These results will be useful for the development of electron spin resonance and Overhauser-enhanced magnetic resonance imaging modalities in biomedical applications. Copyright © 2017 John Wiley & Sons, Ltd.

Complexation of adamantyl compounds by beta-cyclodextrin and monoaminoderivatives.

PubMed

Carrazana, Jorge; Jover, Aida; Meijide, Francisco; Soto, Victor H; Vazquez Tato, José

2005-05-19

Since the beta-cyclodextrin cavity is not a smooth cone but has constrictions in the neighborhoods of the H3 and H5 atoms, the hypothesis that bulky hydrophobic guests can form two isomeric inclusion complexes (one of them, c(p), is formed by the entrance of the guest by the primary side of the cavity, and the other one, c(s), results from the entrance by the secondary side) is checked. Thus, the inclusion processes of two 1-substituted adamantyl derivatives (rimantidine and adamantylmethanol) with beta-cyclodextrin and its two monoamino derivatives at positions 6 (6-NH2beta-CD) and 3 (3-NH2beta-CD) were studied. From rotating-frame Overhauser enhancement spectroscopy experiments, it was deduced that both guests form c(s) complexes with beta-CD and 6-NH2beta-CD but c(p) complexes with 3-NH2beta-CD. In all cases, the hydrophilic group attached to the adamantyl residue protrudes toward the bulk solvent outside the cyclodextrin cavity. The thermodynamic parameters (free energy, equilibrium constant, enthalpy, and entropy) associated with the inclusion phenomena were measured by isothermal titration calorimetry experiments. From these results, the difference in the free energy for the formation of the two complexes, c(s) and c(p), for the same host/guest system has been estimated as being 11.5 +/- 0.8 kJ mol(-1). This large difference explains why under normal experimental conditions only one of the two complexes (c(s)) is detected. It is also concluded that a hyperboloid of revolution can be a better schematic picture to represent the actual geometry of the cyclodextrin cavities than the usual smooth cone or trapezium.

NMR analysis of a kinetically trapped intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.

PubMed

Sugimoto, Hayuki; Noda, Yasuo; Segawa, Shin-ichi

2011-09-16

A thermally unfolded disulfide-deficient mutant of the starch-binding domain of glucoamylase refolds into a kinetically trapped metastable intermediate when subjected to a rapid lowering of temperature. We attempted to characterise this intermediate using multidimensional NMR spectroscopy. The (1)H-(15)N heteronuclear single quantum coherence spectrum after a rapid temperature decrease (the spectrum of the intermediate) showed good chemical shift dispersion but was significantly different from that of the native state, suggesting that the intermediate adopts a nonnative but well-structured conformation. Large chemical shift changes for the backbone amide protons between the native and the intermediate states were observed for residues in the β-sheet consisting of strands 2, 3, 5, 6, and 7 as well as in the C-terminal region. These residues were found to be in close proximity to aromatic residues, suggesting that the chemical shift changes are mainly due to ring current shifts caused by the aromatic residues. The two-dimensional nuclear Overhauser enhancement (NOE) spectroscopy experiments showed that the intermediate contained substantial, native-like NOE connectivities, although there were fewer cross peaks in the spectrum of the intermediate compared with that of the native state. It was also shown that there were native-like interresidue NOEs for residues buried in the protein, whereas many of the NOE cross peaks were lost for the residues involved in a surface-exposed aromatic cluster. These results suggest that, in the intermediate, the aromatic cluster at the surface is structurally less organised, whereas the interior of the protein has relatively rigid, native-like side-chain packing. Copyright © 2011 Elsevier Ltd. All rights reserved.

Solution NMR characterization of magnetic/electronic properties of azide and cyanide-inhibited substrate complexes of human heme oxygenase: implications for steric ligand tilt.

PubMed

Peng, Dungeng; Ogura, Hiroshi; Ma, Li-Hua; Evans, John P; de Montellano, Paul R Ortiz; La Mar, Gerd N

2013-04-01

Solution 2D (1)H NMR was carried out on the azide-ligated substrate complex of human heme oxygenase, hHO, to provide information on the active site molecular structure, chromophore electronic/magnetic properties, and the distal H-bond network linked to the exogenous ligand by catalytically relevant oriented water molecules. While 2D NMR exhibited very similar patterns of two-dimensional nuclear Overhauser spectroscopy cross peaks of residues with substrate and among residues as the previously characterized cyanide complex, significant, broadly distributed chemical shift differences were observed for both labile and non-labile protons. The anisotropy and orientation of the paramagnetic susceptibility tensor, χ, were determined for both the azide and cyanide complexes. The most significant difference observed is the tilt of the major magnetic axes from the heme normal, which is only half as large for the azide than cyanide ligand, with each ligand tilted toward the catalytically cleaved α-meso position. The difference in chemical shifts is quantitatively correlated with differences in dipolar shifts in the respective complexes for all but the distal helix. The necessity of considering dipolar shifts, and hence determination of the orientation/anisotropy of χ, in comparing chemical shifts involving paramagnetic complexes, is emphasized. The analysis shows that the H-bond network cannot detect significant differences in H-bond acceptor properties of cyanide versus azide ligands. Lastly, significant retardation of distal helix labile proton exchange upon replacing cyanide with azide indicates that the dynamic stability of the distal helix is increased upon decreasing the steric interaction of the ligand with the distal helix. Copyright © 2013. Published by Elsevier Inc.

Solution structure of Syrian hamster prion protein rPrP(90-231).

PubMed

Liu, H; Farr-Jones, S; Ulyanov, N B; Llinas, M; Marqusee, S; Groth, D; Cohen, F E; Prusiner, S B; James, T L

1999-04-27

NMR has been used to refine the structure of Syrian hamster (SHa) prion protein rPrP(90-231), which is commensurate with the infectious protease-resistant core of the scrapie prion protein PrPSc. The structure of rPrP(90-231), refolded to resemble the normal cellular isoform PrPC spectroscopically and immunologically, has been studied using multidimensional NMR; initial results were published [James et al. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 10086-10091]. We now report refinement with better definition revealing important structural and dynamic features which can be related to biological observations pertinent to prion diseases. Structure refinement was based on 2778 unambiguously assigned nuclear Overhauser effect (NOE) connectivities, 297 ambiguous NOE restraints, and 63 scalar coupling constants (3JHNHa). The structure is represented by an ensemble of 25 best-scoring structures from 100 structures calculated using ARIA/X-PLOR and further refined with restrained molecular dynamics using the AMBER 4.1 force field with an explicit shell of water molecules. The rPrP(90-231) structure features a core domain (residues 125-228), with a backbone atomic root-mean-square deviation (RMSD) of 0.67 A, consisting of three alpha-helices (residues 144-154, 172-193, and 200-227) and two short antiparallel beta-strands (residues 129-131 and 161-163). The N-terminus (residues 90-119) is largely unstructured despite some sparse and weak medium-range NOEs implying the existence of bends or turns. The transition region between the core domain and flexible N-terminus, i.e., residues 113-128, consists of hydrophobic residues or glycines and does not adopt any regular secondary structure in aqueous solution. There are about 30 medium- and long-range NOEs within this hydrophobic cluster, so it clearly manifests structure. Multiple discrete conformations are evident, implying the possible existence of one or more metastable states, which may feature in conversion of PrPC to PrPSc. To obtain a more comprehensive picture of rPrP(90-231), dynamics have been studied using amide hydrogen-deuterium exchange and 15N NMR relaxation times (T1 and T2) and 15N{1H} NOE measurements. Comparison of the structure with previous reports suggests sequence-dependent features that may be reflected in a species barrier to prion disease transmission.

Three-dimensional structure of the human immunodeficiency virus type 1 matrix protein.

PubMed

Massiah, M A; Starich, M R; Paschall, C; Summers, M F; Christensen, A M; Sundquist, W I

1994-11-25

The HIV-1 matrix protein forms an icosahedral shell associated with the inner membrane of the mature virus. Genetic analyses have indicated that the protein performs important functions throughout the viral life-cycle, including anchoring the transmembrane envelope protein on the surface of the virus, assisting in viral penetration, transporting the proviral integration complex across the nuclear envelope, and localizing the assembling virion to the cell membrane. We now report the three-dimensional structure of recombinant HIV-1 matrix protein, determined at high resolution by nuclear magnetic resonance (NMR) methods. The HIV-1 matrix protein is the first retroviral matrix protein to be characterized structurally and only the fourth HIV-1 protein of known structure. NMR signal assignments required recently developed triple-resonance (1H, 13C, 15N) NMR methodologies because signals for 91% of 132 assigned H alpha protons and 74% of the 129 assignable backbone amide protons resonate within chemical shift ranges of 0.8 p.p.m. and 1 p.p.m., respectively. A total of 636 nuclear Overhauser effect-derived distance restraints were employed for distance geometry-based structure calculations, affording an average of 13.0 NMR-derived distance restraints per residue for the experimentally constrained amino acids. An ensemble of 25 refined distance geometry structures with penalties (sum of the squares of the distance violations) of 0.32 A2 or less and individual distance violations under 0.06 A was generated; best-fit superposition of ordered backbone heavy atoms relative to mean atom positions afforded root-mean-square deviations of 0.50 (+/- 0.08) A. The folded HIV-1 matrix protein structure is composed of five alpha-helices, a short 3(10) helical stretch, and a three-strand mixed beta-sheet. Helices I to III and the 3(10) helix pack about a central helix (IV) to form a compact globular domain that is capped by the beta-sheet. The C-terminal helix (helix V) projects away from the beta-sheet to expose carboxyl-terminal residues essential for early steps in the HIV-1 infectious cycle. Basic residues implicated in membrane binding and nuclear localization functions cluster about an extruded cationic loop that connects beta-strands 1 and 2. The structure suggests that both membrane binding and nuclear localization may be mediated by complex tertiary structures rather than simple linear determinants.

Amide proton spin-lattice relaxation in polypeptides. A field-dependence study of the proton and nitrogen dipolar interactions in alumichrome.

PubMed

Llinás, M; Klein, M P; Wüthrich, K

1978-12-01

The proton nuclear magnetic resonance (NMR) spin-lattice relaxation of all six amides of deferriferrichrome and of various alumichromes dissolved in hexadeutero-dimethylsulfoxide have been investigated at 100, 220, and 360 MHz. We find that, depending on the type of residue (glycyl or ornithyl), the amide proton relaxation rates are rather uniform in the metal-free cyclohexapeptide. In contrast, the (1)H spinlattice relaxation times (T(1)'s) are distinct in the Al(3+)-coordination derivative. Similar patterns are observed in a number of isomorphic alumichrome homologues that differ in single-site residue substitutions, indicating that the spin-lattice relaxation rate is mainly determined by dipole-dipole interactions within a rigid molecular framework rather than by the specific primary structures. Analysis of the data in terms of (1)H-(1)H distances (r) calculated from X-ray coordinates yields a satisfactory linear fit between T(1) (-1) and Sigmar(-6) at the three magnetic fields. Considering the very sensitive r-dependence of T(1), the agreement gives confidence, at a quantitative level, both on the fitness of the crystallographic model to represent the alumichromes' solution conformation and on the validity of assuming isotropic rotational motion for the globular metallopeptides. An extra contribution to the amide proton T(1) (-1) is proposed to mainly originate from the (1)H-(14)N dipolar interaction: this was supported by comparison with measurements on an (15)N-enriched peptide. The nitrogen dipolar contribution to the peptide proton relaxation is discussed in the context of {(1)H}-(1)H nuclear Overhauser enhancement (NOE) studies because, especially at high fields, it can be dominant in determining the amide proton relaxation rates and hence result in a decreased effectiveness for the (1)H-(1)H dipolar mechanism to cause NOE's. From the slope and intersect values of T(1) (-1) vs. Sigmar(-6) linear plots, a number of independent estimates of tau(r), the rotational correlation time, were derived. These and the field-dependence of the T(1)'s yield a best estimate approximately 0.37 ns, in good agreement with 0.38 ns [unk] [unk] 0.41 ns, previously determined from (13)C and (15)N spin-lattice relaxation data.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Topping, R.J.; Stone, M.P.; Brush, C.K.

The {sup 1}H NMR spectrum of the tetradeoxynucleotide d(TpCpGpA) was examined as a function of temperature, pH, and concentration. At pH 7 and above the solution conformation for this oligodeoxynucleotide appears to be a mixture of random coil and Watson-Crick duplex. At 25{degree}C, a pH titration of d(TpCpGaA) shown that distinct conformational changes occur as the pH is lowered below 7.0. These conformational changes are reversible upon readjusting the pH to neutrality, indicating the presence of a pH-dependent set of conformational equilibria. At 25{degree}C, the various conformational state in the mixture are in rapid exchange on the NMR time scale.more » Examination of the titration curve shown the presence of distinct conformational states at pH greater than 7, and between pH 4 and pH 5. When the pH titration is repeated at 5{degree}C, the conformational equilibria are in slow exchange on the NMR time scale; distinct signals from each conformational state are observable. The stable conformational state present between pH 4 and pH 5 represents an ordered conformation of d(TpCpGpA) which dissociates to a less ordered structure upon raising the temperature. The ordered conformation differs from the Watson-Crick helix, as is shown from nuclear Overhauser enhancement experiments, as well as chemical shift data. These results indicate that their ordered conformation is similar to the conformation of d(TpCpGpA) observed between pH 4 and pH 5. In the present case it is likely that stabilization of an ordered duplex conformation for d(TpCpGpA) is achieved by protonation of cytosine. A possible model which could explain the data involves formation of Hoogsteen C{sup +}:G base pairs.« less

Solution Structure of the N-Terminal Domain of Mediator Subunit MED26 and Molecular Characterization of Its Interaction with EAF1 and TAF7.

PubMed

Lens, Zoé; Cantrelle, François-Xavier; Peruzzini, Riccardo; Hanoulle, Xavier; Dewitte, Frédérique; Ferreira, Elisabeth; Baert, Jean-Luc; Monté, Didier; Aumercier, Marc; Villeret, Vincent; Verger, Alexis; Landrieu, Isabelle

2017-10-13

MED26 is a subunit of Mediator, a large complex central to the regulation of gene transcription by RNA Polymerase II. MED26 plays a role in the switch between the initiation and elongation phases of RNA Polymerase II-mediated transcription process. Regulation of these steps requires successive binding of MED26 N-terminal domain (NTD) to TATA-binding protein-associated factor 7 (TAF7) and Eleven-nineteen lysine-rich in leukemia-Associated Factor 1 (EAF1). In order to investigate the mechanism of regulation by MED26, MED26-NTD structure was solved by NMR, revealing a 4-helix bundle. EAF1 (239-268) and TAF7 (205-235) peptide interactions were both mapped to the same groove formed by H3 and H4 helices of MED26-NTD. Both interactions are characterized by dissociation constants in the 10-μM range. Further experiments revealed a folding-upon-binding mechanism that leads to the formation of EAF1 (N247-S260) and TAF7 (L214-S227) helices. Chemical shift perturbations and nuclear Overhauser enhancement contacts support the involvement of residues I222/F223 in anchoring TAF7 helix to a hydrophobic pocket of MED26-NTD, including residues L48, W80 and I84. In addition, Ala mutations of charged residues located in the C-terminal disordered part of TAF7 and EAF1 peptides affected the binding, with a loss of affinity characterized by a 10-time increase of dissociation constants. A structural model of MED26-NTD/TAF7 complex shows bi-partite components, combining ordered and disordered segments, as well as hydrophobic and electrostatic contributions to the binding. This study provides molecular detail that will help to decipher the mechanistic basis for the initiation to elongation switch-function mediated by MED26-NTD. Copyright © 2017 Elsevier Ltd. All rights reserved.

NMR structures of anti-HIV D-peptides derived from the N-terminus of viral chemokine vMIP-II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mori, Mayuko; Liu Dongxiang; Kumar, Santosh

2005-09-30

The viral macrophage inflammatory protein-II (vMIP-II) encoded by Kaposi's sarcoma-associated herpesvirus has unique biological activities in that it blocks the cell entry by several different human immunodeficiency virus type 1 (HIV-1) strains via chemokine receptors including CXCR4 and CCR5. In this paper, we report the solution structure of all-D-amino acid peptides derived from the N-terminus of vMIP-II, which have been shown to have strong CXCR4 binding activity and potently inhibit HIV-1 entry via CXCR4, by using long mixing time two-dimensional nuclear Overhauser enhancement spectroscopy experiments. Both of all-D-peptides vMIP-II (1-10) and vMIP-II (1-21), which are designated as DV3 and DV1,more » respectively, have higher CXCR4 binding ability than their L-peptide counterparts. They are partially structured in aqueous solution, displaying a turn-like structure over residues 5-8. The small temperature coefficients of His-6 amide proton for both peptides also suggest the formation of a small hydrophobic pocket centered on His-6. The structural features of DV3 are very similar to the reported solution structure of all-L-peptide vMIP-II (1-10) [M.P. Crump, E. Elisseeva, J. Gong, I. Clark-Lewis, B.D. Sykes, Structure/function of human herpesvirus-8 MIP-II (1-71) and the antagonist N-terminal segment (1-10), FEBS Lett. 489 (2001) 171], which is consistent with the notion that D- and L-enantiomeric peptides can adopt mirror image conformations. The NMR structures of the D-peptides provide a structural basis to understand their mechanism of action and design new peptidomimetic analogs to further explore the structure-activity relationship of D-peptide ligand binding to CXCR4.« less

The stereochemistry of chlorophyll-c₃ from the haptophyte Emiliania huxleyi: the (13²R)-enantiomers of chlorophylls-c are exclusively selected as the photosynthetically active pigments in chromophyte algae.

PubMed

Mizoguchi, Tadashi; Kimura, Yuki; Yoshitomi, Taichi; Tamiaki, Hitoshi

2011-11-01

Chlorophyll(Chl)-c pigments in algae, diatoms and some prokaryotes are characterized by the fully conjugated porphyrin π-system as well as the acrylate residue at the 17-position. The precise structural characterization of Chl-c(3) from the haptophyte Emiliania huxleyi was performed. The conformations of the π-conjugated peripheral substituents, the 3-/8-vinyl, 7-methoxycarbonyl and 17-acrylate moieties were evaluated, in a solution, using nuclear Overhauser enhancement correlations and molecular modeling calculations. The rotation of the 17-acrylate residue was considerably restricted, whereas the other three substituents readily rotated at ambient temperature. Moreover, the stereochemistry at the 13²-position was determined by combination of chiral high-performance liquid chromatography (HPLC) with circular dichroism (CD) spectroscopy. Compared with the CD spectra of the structurally related, synthetic (13²R)- and (13²S)-protochlorophyllide(PChlide)-a, naturally occurring Chl-c₃ had exclusively the (13²R)-configuration. To elucidate this natural selection of a single enantiomer, we analyzed the three major Chl-c pigments (Chl-c₁, c₂ and c₃) in four phylogenetically distinct classes of Chl-c containing algae, i.e., heterokontophyta, dinophyta, cryptophyta and haptophyta using chiral HPLC. All the photosynthetic organisms contained only the (13²R)-enantiomerically pure Chls-c, and lacked the corresponding enantiomeric (13²S)-forms. Additionally, Chl-c₂ was found in all the organisms as the common Chl-c. These results throw a light on the biosynthesis as well as photosynthetic function of Chl-c pigments: Chl-c₂ is derived from 8-vinyl-PChlide-a by dehydrogenation of the 17-propionate to acrylate residues as generally proposed, and the (13²R)-enantiomers of Chls-c function as photosynthetically active, light-harvesting pigments together with the principal Chl-a and carotenoids. 2011 Elsevier B.V. All rights reserved.

Solution 1H NMR determination of secondary structure for the three-iron form of ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus.

PubMed

Teng, Q; Zhou, Z H; Smith, E T; Busse, S C; Howard, J B; Adams, M W; La Mar, G N

1994-05-24

Two-dimensional 1H NMR data have been used to make sequence-specific assignments and define the secondary structure of the three-iron form of the oxidized ferredoxin, Fd, from the hyperthermophilic archaeon Pyrococcus furiosus, Pf. Signals for at least some protons were located for 65 of the 66 amino acids in the sequence, in spite of the paramagnetic (S = 1/2) ground state, but not all could be assigned. Unassigned and missing signals could be qualitatively correlated with the expected proximity of the protons to the paramagnetic cluster. The secondary structure was deduced from qualitative analysis of the 2D nuclear Overhauser effect, which identified two antiparallel beta-sheets, one triple-stranded including Ala1-Ser5, Val39-Glu41, and Thr62-Ala66, and one double-stranded consisting of Glu26-Asn28 and Lys32-Glu34, as well as an alpha-helix involving Glu43-Glu54. Three tight type I turns are located at residues Asp7-Thr10, Pro22-Phe25, and Asp29-Gly31. Comparison with the crystal structure of Desulfovibrio gigas, Dg, Fd (Kissinger et al., 1991) reveals a very similar folding topology, although several secondary structural elements are extended in Pf relative to Dg Fd. Thus the beta-sheet involving the two termini is expanded to include the two terminal residues and incorporates a third strand from the internal loop that is lengthened by several insertions in Pf relative to Dg Fd. The double-stranded beta-sheet in the interior of Pf Fd is lengthened slightly due to a much tighter type I turn between the two strands. The helix near the C-terminus is three residues longer in Pf than in Dg Fd, as well as being shifted toward the N-terminus. The disulfide link between the two nonligating Cys residues (Cys21 and Cys48) is conserved in Pf Fd, but the link near the C-terminus is in the middle of the long alpha-helix in Pf Fd, instead of at the N-terminus of the helix as in Dg Fd. The extensions of the beta-sheets and alpha-helix increase the number of main-chain hydrogen bonds in Pf Fd by approximately 8 relative to those in Dg Fd and likely contribute to its remarkable thermostability (it is unaffected by anaerobic incubation at 95 degrees C for 24 h).(ABSTRACT TRUNCATED AT 400 WORDS)

Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability.

PubMed

Nonin, S; Phan, A T; Leroy, J L

1997-09-15

Repetitive cytosine-rich DNA sequences have been identified in telomeres and centromeres of eukaryotic chromosomes. These sequences play a role in maintaining chromosome stability during replication and may be involved in chromosome pairing during meiosis. The C-rich repeats can fold into an 'i-motif' structure, in which two parallel-stranded duplexes with hemiprotonated C.C+ pairs are intercalated. Previous NMR studies of naturally occurring repeats have produced poor NMR spectra. This led us to investigate oligonucleotides, based on natural sequences, to produce higher quality spectra and thus provide further information as to the structure and possible biological function of the i-motif. NMR spectroscopy has shown that d(5mCCTTTACC) forms an i-motif dimer of symmetry-related and intercalated folded strands. The high-definition structure is computed on the basis of the build-up rates of 29 intraresidue and 35 interresidue nuclear Overhauser effect (NOE) connectivities. The i-motif core includes intercalated interstrand C.C+ pairs stacked in the order 2*.8/1.7*/1*.7/2.8* (where one strand is distinguished by an asterisk and the numbers relate to the base positions within the repeat). The TTTA sequences form two loops which span the two wide grooves on opposite sides of the i-motif core; the i-motif core is extended at both ends by the stacking of A6 onto C2.C8+. The lifetimes of pairs C2.C8+ and 5mC1.C7+ are 1 ms and 1 s, respectively, at 15 degrees C. Anomalous exchange properties of the T3 imino proton indicate hydrogen bonding to A6 N7 via a water bridge. The d(5mCCTTTTCC) deoxyoligonucleotide, in which position 6 is occupied by a thymidine instead of an adenine, also forms a symmetric i-motif dimer. However, in this structure the two TTTT loops are located on the same side of the i-motif core and the C.C+ pairs are formed by equivalent cytidines stacked in the order 8*.8/1.1*/7*.7/2.2*. Oligodeoxynucleotides containing two C-rich repeats can fold and dimerize into an i-motif. The change of folding topology resulting from the substitution of a single nucleoside emphasizes the influence of the loop residues on the i-motif structure formed by two folded strands.

Near Surface Geophysical Exploration at The Archaeological Site of San Miguel Tocuila, Basin of Mexico.

NASA Astrophysics Data System (ADS)

Arciniega, A.; Hernandez, E.; Cabral-Cano, E.; Diaz-Molina, O.; Morett, L.; Soler, A.

2008-12-01

The village of Tocuila is located on the western margin of Lake Texcoco in central Mexico. Volcanic activity during the Late Pleistocene and Early Holocene closed the basin's drainage and facilitated the development of a lacustrine environment and subsequent deposition of volcano-sedimentary sequences with abundant archaeological and paleontological record. Tocuila was one of the most prominent suburbs of the main civic ceremonial complex of the Aztecs. The rapid expansion of Mexico City's Metropolitan areas in the last three decades strongly influenced Tocuila's environment and has compromised several of its archaeological and ancient human settlements. A near surface geophysical survey including magnetometry, seismic refraction tomography and Ground Penetrating Radar (GPR) techniques was conducted to investigate pre-Hispanic structures. The magnetometric survey was performed using an Overhauser magnetometer with an omnidirectional, 0.015 nT/Hz sensor and 1Hz sampling rate over a 80x100 m area, yielding 990 measurements of total intensity magnetic field at 1.0m height above the ground surface. Thirty seismic refraction profiles were obtained with a 48-channel 24 bits Geometrics StrataVisor NZ seismograph, 14 Hz natural frequency vertical geophones with a 2m separation array and an impact source of 5 kg. The GPR survey consisted of 15 cross sections at two different resolutions with a GSSI SIR-3000 instrument, using a GSSI 200 MHz and a RadarTeam 70 MHz antennas. All surveys were georeferenced with a dual frequency GPS local station and a GPS rover attached to the surveying geophysical instruments. Seismic refraction tomography and GPR radargrams show a platform structure of approx. 80x60 m which can be subdivided in three distinctive layers with a total height of ~10m. Based on the history of ancient settlements in the area surrounding Lake Texcoco and considering the characteristics of shape and height of the surveyed structure, we interpreted that the resulting subsurface images correspond to a buried mound also known as a Tlatel in Nahuatl language. This structure is most likely a buried ceremonial-civic center of Late Aztec times.

Rearranged hopanes in sediments and petroleum

NASA Astrophysics Data System (ADS)

Moldowan, J. Michael; Fago, Frederick J.; Carlson, Robert M. K.; Young, Donald C.; an Duvne, Greg; Clardy, Jon; Schoell, Martin; Pillinger, Colin T.; Watt, David S.

1991-11-01

Two new rearranged hopanoid hydrocarbons have been isolated from a Prudhoe Bay crude, Alaska. 17α(H)-15α-methyl-27-norhopane was determined by X-ray crystallography. It is the first identified member of a new series of rearranged hopanes we propose to call "17α(H)-diahopanes." Analysis by gas chromatography-mass spectrometry - mass spectrometry (GC-MS-MS) of the parents of m/z 191 in several crudes suggests that this compound is a member of a C 29-C 34 series of 17α(H)-diahopanes common to many crude oils and sediments. In addition, a new member of the 18α(H)-neohopane series has also been elucidated. Determination of 18α(H)-17α-methyl-28,30-dinorhopane [18α(H)-30-norneohopane ], which we propose to nickname "C 29Ts," hinged upon advanced nuclear magnetic resonance (NMR) techniques (at 500 and 600 MHz) such as proton-detected 1H- 13C correlated spectra for the C-skeleton and Rotating-frame Overhauser Enhancement Spectroscopy (ROESY) for stereochemistry, as well as several other two-dimensional (2D) NMR techniques. This compound is the second known pseudohomolog of the neohopane series (together with 18α(H),22,29,30-trisnorneohopane, Ts), but the existence of additional pseudohomologs is still not clear. The structures of these rearranged hopanes are consistent with an origin by catalytic rearrangement from hopenes during early diagenesis. Carbon isotopic data collected on Ts, 17α(H)-diahopane, C 29Ts, 17α(H)-22,29,30-trisnorhopane (Tm), 17α(H)-30-norhopane, and 17α(H)-hopane isolated from the Prudhoe Bay oil are in the -27 to -28%o δ 13C range supporting mechanistic arguments based on structures that all are derived from common precursors. These δ 13C values are slightly more positive than the whole Prudhoe Bay oil (-30.1%), suggesting that these hopanes may have been derived from heterotrophic or cyanobacteria in the paleoecosystem during deposition of its source rock. Molecular mechanics calculations predict relative thermal stabilities in the order 17α(H)-diahopanes > 18α(H)-neohopanes > 17α(H)-hopanes, suggesting new maturity parameters that may be useful into the late oil window.

Geophysical survey at Tell Barri (Syria)

NASA Astrophysics Data System (ADS)

Florio, Giovanni; Cella, Federico; Pierobon, Raffaella; Castaldo, Raffaele; Castiello, Gabriella; Fedi, Maurizio

2010-05-01

A geophysical survey at the archaeological site of Tell Barri (Northeasterm Syria) was carried out. The Tell (Arab word for "hill") is 32 m high with a whole covered area of 37 hectares. The Tell, with its huge dimensions and with a great amount of pottery on the surface, is a precious area to study the regional history from IV mill. BC to Islamic and Medieval period. The geophysical study consisted in magnetic and electromagnetic measurements in the lower town area. The aim of this survey was to provide evidence of the presence of buried archaeological structures around an already excavated area. The wall structures in the Tell Barri are made by backed or crude clay bricks. The instrument used for the magnetic survey was an Overhauser-effect proton magnetometer (Gem GSM-19GF), in gradiometric configuration. The electromagnetic instrument used, Geonics Ltd. EM31, implements a Frequency Domain Electromagnetic Method (FDEM). It was used in vertical coils configuration, and this choice should grant a maximum theoretical investigation depth of about 6 m. Before starting the measurements on a larger scale, we conducted a magnetic and EM test profile on some already excavated, outcropping, baked bricks walls. Results were encouraging, because clear and strong magnetic and EM anomalies were recorded over the outcropping walls. However, in the survey area these structures are covered by 3 to 4 meters of clay material and the increased sensors-structures distance will reduce the anomalies amplitude. Moreover, the cover material is disseminated with bricks, basalt blocks and ceramics, all of which have relevant magnetic properties. After magnetic surveying some 50 m side square areas, we verified that unfortunately their effect resulted to be dominant with respect to the deeper wall structures, degrading too much the signal-to-noise ratio. The processing and analysis of magnetic data is however currently underway and will determine decisions about further use of this method in future surveys. These disturbances were much lower in the EM data, thus, these data were acquired in 7 squares having 50 m long sides, along profiles spaced 0.5 m. The acquisition rate, combined with the operator speed, resulted in an average sampling step of 0.2-0.25 m along each profile. First, the quadrature and inphase data were interpolated at a regular step of 0.5 m and visualized in false colour maps representing the spatial variation of conductivity and magnetic susceptibility, respectively. Then, corrections for zig-zag effect and heading error were applied. In both maps many elongated anomalies are visible, often crossing each other perpendicularly and arranged with a meaningful orientation with respect to the topography. This suggest a possible archaeological meaning for these anomalies. Quadrature data were processed by AGC filter to obtain an amplitude-normalized map. Data were further processed with algorithms based on spatial derivatives that can define the position of the source bodies with higher definition. Some hypothesis about the meaning of these linear anomalies include the presence of an urbanization area, with edifices and roads. The orientation of many structures in directions parallel or perpendicular to the altitude isolines may also suggest the presence of ancient defensive structures. Thus, the main result of the geophysical investigation was to highlight that the urbanized area extent is wider than known before. The fine stratification of the archaeological remains at Tell Barri site represents a major difficulty to the interpretation. During the next mission some anomalies will be the target of excavations to improve our understanding of the conductivity pattern and its interpretation.

Screening Mixtures of Small Molecules for Binding to Multiple Sites on the Surface Tetanus Toxin C Fragment by Bioaffinity NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cosman, M; Zeller, L; Lightstone, F C

2002-01-01

The clostridial neurotoxins include the closely related tetanus (TeNT) and botulinum (BoNT) toxins. Botulinum toxin is used to treat severe muscle disorders and as a cosmetic wrinkle reducer. Large quantities of botulinum toxin have also been produced by terrorists for use as a biological weapon. Because there are no known antidotes for these toxins, they thus pose a potential threat to human health whether by an accidental overdose or by a hostile deployment. Thus, the discovery of high specificity and affinity compounds that can inhibit their binding to neural cells can be used as antidotes or in the design ofmore » chemical detectors. Using the crystal structure of the C fragment of the tetanus toxin (TetC), which is the cell recognition and cell surface binding domain, and the computational program DOCK, sets of small molecules have been predicted to bind to two different sites located on the surface of this protein. While Site-1 is common to the TeNT and BoNTs, Site-2 is unique to TeNT. Pairs of these molecules from each site can then be linked together synthetically to thereby increase the specificity and affinity for this toxin. Electrospray ionization mass spectroscopy was used to experimentally screen each compound for binding. Mixtures containing binders were further screened for activity under biologically relevant conditions using nuclear magnetic resonance (NMR) methods. The screening of mixtures of compounds offers increased efficiency and throughput as compared to testing single compounds and can also evaluate how possible structural changes induced by the binding of one ligand can influence the binding of the second ligand. In addition, competitive binding experiments with mixtures containing ligands predicted to bind the same site could identify the best binder for that site. NMR transfer nuclear Overhauser effect (trNOE) confirm that TetC binds doxorubicin but that this molecule is displaced by N-acetylneuraminic acid (sialic acid) in a mixture that also contains 3-sialyllactose (another predicted site 1 binder) and bisbenzimide 33342 (non-binder). A series of five predicted Site-2 binders were then screened sequentially in the presence of the Site-1 binder doxorubicin. These experiments showed that the compounds lavendustin A and naphthofluorescein-di-({beta}-D-galactopyranoside) binds along with doxorubicin to TetC. Further experiments indicate that doxorubicin and lavendustin are potential candidates to use in preparing a bidendate inhibitor specific for TetC. The simultaneous binding of two different predicted Site-2 ligands to TetC suggests that they may bind multiple sites. Another possibility is that the conformations of the binding sites are dynamic and can bind multiple diverse ligands at a single site depending on the pre-existing conformation of the protein, especially when doxorubicin is already bound.« less

Formation of Annular Protofibrillar Assembly by Cysteine Tripeptide: Unraveling the Interactions with NMR, FTIR, and Molecular Dynamics.

PubMed

Banerji, Biswadip; Chatterjee, Moumita; Pal, Uttam; Maiti, Nakul C

2017-07-06

Both hydrogen-bonding and hydrophobic interactions play a significant role in molecular assembly, including self-assembly of proteins and peptides. In this study, we report the formation of annular protofibrillar structure (diameter ∼500 nm) made of a newly synthesized s-benzyl-protected cysteine tripeptide, which was primarily stabilized by hydrogen-bonding and hydrophobic interactions. Atomic force microscopy and field emission scanning electron microscopy analyses found small oligomers (diameter ∼60 nm) to bigger annular (outer diameter ∼300 nm; inner diameter, 100 nm) and protofibrillar structures after 1-2 days of incubation. Rotating-frame Overhauser spectroscopic (ROESY) analysis revealed the presence of several nonbonded proton-proton interactions among the residues, such as amide protons with methylene group, aromatic protons with tertiary butyl group, and methylene protons with tertiary butyl group. These added significant stability to bring the peptides closer to form a well-ordered assembled structure. Hydrogen-deuterium exchange NMR measurement further suggested that two individual amide protons among the three amide groups were strongly engaged with the adjacent tripeptide via H-bond interaction. However, the remaining amide proton was found to be exposed to solvent and remained noninteracting with other tripeptide molecules. In addition to chemical shift values, a significant change in amide bond vibrations of the tripeptide was found due to the formation of the self-assembled structure. The amide I mode of vibrations involving two amide linkages appeared at 1641 and 1695 cm -1 in the solid state. However, in the assembled state, the stretching band at 1695 cm -1 became broad and slightly shifted to ∼1689 cm -1 . On the contrary, the band at 1641 cm -1 shifted to 1659 cm -1 and indicated that the -C═O bond associated with this vibration became stronger in the assembled state. These changes in Fourier transform infrared spectroscopy frequency clearly indicated changes in the amide backbone conformation and the associated hydrogen-bonding pattern due to the formation of the assembled structure. In addition to hydrogen bonding, molecular dynamics simulation indicated that the number of π-π interactions also increased with increasing number of tripeptides participated in the self-assembly process. Combined results envisaged a cross β-sheet assembly unit consisting of four intermolecular hydrogen bonds. Such noncovalent peptide assemblies glued by hydrogen-bonding and other weak forces may be useful in developing nanocapsule and related materials.

NMR structural studies of the ionizing radiation adduct 7-hydro-8-oxodeoxyguanosine (8-oxo-7H-dG) opposite deoxyadenosine in a DNA duplex. 8-oxo-7H-dG(syn)ter dot dA(anti) alignment at lesion site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kouchakdjian, M.; Patel, D.J.; Bodepudi, V.

1991-02-05

Proton NMR studies are reported on the complementary d(C1-C2-A3-C4-T5-A6-oxo-G7-T8-C9-A10-C11-C12){center dot}d(G13-G14-T15-G16-A17-A18-T19-A20-G21-T22-G23-G24) dodecanucleotide duplex (designated 8-oxo-7H-dG{center dot}dA 12-mer), which contains a centrally located 7-hydro-8-oxodeoxyguanosine (8-oxo-7H-dG) residue, a group commonly found in DNA that has been exposed to ionizing radiation or oxidizing free radicals. From the NMR spectra it can be deduced that this moiety exists as two tautomers, or gives rise to two DNA conformations, that are in equilibrium and that exchange slowly. The present study focuses on the major component of the equilibrium that originates in the 6,8-dioxo tautomer of 8-oxo-7H-dG. The authors have assigned the exchangeable NH1, NH7, and NH{submore » 2}-2 base protons located on the Watson-Crick and Hoogsteen edges of 8-oxo-7H-dG7 in the 8-oxo-7H-dG{center dot}dA 12-mer duplex, using an analysis of one- and two-dimensional nuclear Overhauser enhancement (NOE) data in H{sub 2}O solution. They were able to detect a set of intra- and interstrand NOEs between protons (exchangeable and nonexchangeable) on adjacent residues in the d(A6-oxo-G7-T8){center dot}d(A17-A18-T19) trinucleotide segment centered about the lesion site that establishes stacking of the oxo-dG7(syn){center dot}dA(anti) pair between stable Watson-Crick dA6{center dot}dT19 and dT8{center dot}A17 base pairs with minimal perturbation of the helix. The structural studies demonstrate that 8-oxo-7H-dG(syn){center dot}dA(anti) forms a stable pair in the interior of the helix, providing a basis for the observed incorporation of dA opposite 8-oxo-7H-dG when readthrough occurs past this oxidized nucleoside base.« less

Mapping of the total magnetic field in the area of Lake Balaton

NASA Astrophysics Data System (ADS)

Visnovitz, Ferenc; Hegyi, Betti; Raveloson, Andrea; Rozman, Gábor; Lenkey, László; Kovács, Péter; Csontos, András; Heilig, Balázs; Horváth, Ferenc

2017-04-01

The Lake Balaton with 600 km2 area represents the largest lake in Central Europe and a blank spot on the magnetic anomaly map of Hungary. It is because the construction of the Hungarian magnetic anomaly map dates back to the 1960s and relied mainly on classical vertical-field balance surveys. To fill the gap, we initiated a systematic mapping using modern magnetometers and positioning system in the framework of a complex geophysical study of Lake Balaton (National Research Project 109255 K). The main goal of this study has been to identify subvolcanic bodies and tectonic structures below the lake and correlate them with well-known features mapped onshore in the vicinity of Balaton. During the magnetic survey an Overhauser field magnetometer (GEM System, GSM-19) was mounted on a plastic boat and towed behind a motorboat in a distance of 20 m with a speed of 6 to 16 km/h depending on weather conditions. Tests measurements showed that at this distance the magnetic noise generated by the motorboat was negligible. We measured total field values with a sampling interval of 1 to 2 s. As a result, the whole lake has been covered by magnetic profiles in an orthogonal grid with spacing of 1 km. During data interpretation we applied for correction of temporal variation of magnetic field registered in the Tihany Geophysical Observatory and normal field correction from a regional model. The final anomaly map in the western part of the lake shows anomalies with amplitudes of 20 to 60 nT and a half wavelength of 0.5 to 1 km. A larger feature was recognized related to the Badacsony Hill a major basaltic bute at the northern shore of the lake. In the middle part of the lake the total field is rather smooth, no significant anomaly has been revealed. However, slight disturbances can be noticed in the proximity of a neotectonic fault zone mapped by high resolution seismic data. In the eastern part of the lake few low amplitude (5-20 nT) anomalies have been observed that are associated also with seismically mapped strike-slip faults. As an interesting by-product a map was created showing short wavelength anomalies that are most probably caused by artificial metal objects sank and stuck in the lake mud. Some of these anomalies can be caused by parts of fallen warplanes and sunken tanks from military activities during the II. World War.

High Frequency Dynamic Nuclear Polarization

PubMed Central

Ni, Qing Zhe; Daviso, Eugenio; Can, Thach V.; Markhasin, Evgeny; Jawla, Sudheer K.; Swager, Timothy M.; Temkin, Richard J.; Herzfeld, Judith; Griffin, Robert G.

2013-01-01

Conspectus During the three decades 1980–2010, magic angle spinning (MAS) NMR developed into the method of choice to examine many chemical, physical and biological problems. In particular, a variety of dipolar recoupling methods to measure distances and torsion angles can now constrain molecular structures to high resolution. However, applications are often limited by the low sensitivity of the experiments, due in large part to the necessity of observing spectra of low-γ nuclei such as the I = ½ species 13C or 15N. The difficulty is still greater when quadrupolar nuclei, like 17O or 27Al, are involved. This problem has stimulated efforts to increase the sensitivity of MAS experiments. A particularly powerful approach is dynamic nuclear polarization (DNP) which takes advantage of the higher equilibrium polarization of electrons (which conventionally manifests in the great sensitivity advantage of EPR over NMR). In DNP, the sample is doped with a stable paramagnetic polarizing agent and irradiated with microwaves to transfer the high polarization in the electron spin reservoir to the nuclei of interest. The idea was first explored by Overhauser and Slichter in 1953. However, these experiments were carried out on static samples, at magnetic fields that are low by current standards. To be implemented in contemporary MAS NMR experiments, DNP requires microwave sources operating in the subterahertz regime — roughly 150–660 GHz — and cryogenic MAS probes. In addition, improvements were required in the polarizing agents, because the high concentrations of conventional radicals that are required to produce significant enhancements compromise spectral resolution. In the last two decades scientific and technical advances have addressed these problems and brought DNP to the point where it is achieving wide applicability. These advances include the development of high frequency gyrotron microwave sources operating in the subterahertz frequency range. In addition, low temperature MAS probes were developed that permit in-situ microwave irradiation of the samples. And, finally, biradical polarizing agents were developed that increased the efficiency of DNP experiments by factors of ~4 at considerably lower paramagnet concentrations. Collectively these developments have made it possible to apply DNP on a routine basis to a number of different scientific endeavors, most prominently in the biological and material sciences. This Account reviews these developments, including the primary mechanisms used to transfer polarization in high frequency DNP, and the current choice of microwave sources and biradical polarizing agents. In addition, we illustrate the utility of the technique with a description of applications to membrane and amyloid proteins that emphasizes the unique structural information that is available in these two cases. PMID:23597038

Dynamic properties of biologically active synthetic heparin-like hexasaccharides.

PubMed

Angulo, Jesús; Hricovíni, Milos; Gairi, Margarida; Guerrini, Marco; de Paz, José Luis; Ojeda, Rafael; Martín-Lomas, Manuel; Nieto, Pedro M

2005-10-01

A complete study of the dynamics of two synthetic heparin-like hexasaccharides, D-GlcNHSO3-6-SO4-alpha-(1-->4)-L-IdoA-2-SO4-alpha-(1-->4)-D-GlcNHSO3-6-SO4-alpha-(1-->4)-L-IdoA-2-SO4-alpha-(1-->4)-D-GlcNHSO3-6-SO4-alpha-(1-->4)-L-IdoA-2-SO4-alpha-1-->iPr (1) and -->4)-L-IdoA-2-SO4-alpha-(1-->4)-D-GlcNHAc-6-SO4-alpha-(1-->4)-L-IdoA-alpha-(1-->4)-D-GlcNHSO3-alpha-(1-->4)-L-IdoA-2-SO4-alpha-1-->iPr (2), has been performed using 13C-nuclear magnetic resonance (NMR) relaxation parameters, T1, T2, and heteronuclear nuclear Overhauser effect (NOEs). Compound 1 is constituted from sequences corresponding to the major polysaccharide heparin region, while compound 2 contains a sequence never found in natural heparin. They differ from each other only in sulphation patterns, and are capable of stimulating fibroblast growth factors (FGFs)-1 induced mitogenesis. Both oligosaccharides exhibit a remarkable anisotropic overall motion in solution as revealed by their anisotropic ratios (tau /tau||), 4.0 and 3.0 respectively. This is a characteristic behaviour of natural glycosaminoglycans (GAG) which has also been observed for the antithrombin (AT) binding pentasaccharide D-GlcNHSO3-6-SO4-alpha-(1-->4)-D-GlcA-beta-(1-->4)-D-GlcNHSO3-(3,6-SO4)-alpha-(1-->4)-L-IdoA-2-SO4-alpha-(1-->4)-D-GlcNHSO3-6-SO4-alpha-1-->Me (3) (Hricovíni, M., Guerrini, M., Torri, G., Piani, S., and Ungarelli, F. (1995) Conformational analysis of heparin epoxide in aqueous solution. An NMR relaxation study. Carbohydr. Res., 277, 11-23). The motional properties observed for 1 and 2 provide additional support to the suitability of these compounds as heparin models in agreement with previous structural (de Paz, J.L., Angulo, J., Lassaletta, J.M., Nieto, P.M., Redondo-Horcajo, M., Lozano, R.M., Jiménez-Gallego, G., and Martín-Lomas, M. (2001) The activation of fibroblast growth factors by heparin: synthesis, structure and biological activity of heparin-like oligosaccharides. Chembiochem, 2, 673-685; Ojeda, R., Angulo, J., Nieto, P.M., and Martin-Lomas. M. (2002) The activation of fibroblast growth factors by heparin: synthesis and structural study of rationally modified heparin-like oligosaccharides. Can. J. Chem,. 80, 917-936; Lucas, R., Angulo, J., Nieto, P.M., and Martin-Lomas, M. (2003) Synthesis and structural studies of two new heparin-like hexasaccharides. Org. Biomol. Chem., 1, 2253-2266) and biological data (Angulo, J., Ojeda, R., de Paz, J.L., Lucas, R., Nieto, P.M., Lozano, R.M., Redondo-Horcajo, M., Giménez-Gallego, G., and Martín-Lomas, M. (2004) The activation of fibroblast growth factors (FGFs) by glycosaminoglycans: influence of the sulphation pattern on the biological activity of FGF-1. Chembiochem, 5, 55-61). Fast internal motions observed for the less sulphated compound 2, as compared with 1, may be related to their different behavior in stimulating FGF1-induced mitogenic activity.

Analysis of vector magnetic anomalies over the Bayonnaise Knoll caldera obtained from a deep-sea magnetic exploration by AUV

NASA Astrophysics Data System (ADS)

Sayanagi, K.; Isezaki, N.; Matsuo, J.; Harada, M.; Kasaya, T.

2011-12-01

Geophysical surveys near the seafloor are very effective methods in order to investigate fine structures of the oceanic crust. Such surveys have increased in researches and developments of the seafloor, and will be more and more necessary in the future. For example, seabed resources like hydrothermal deposits have recently focused attention behind the international situation for natural resources like a competition of resources development. In order to estimate accurate abundance of those resources, the above detailed investigations should be needed because of low resolution of geophysical surveys on the sea and low efficiency of exploratory drilling. From such a viewpoint, we have been developing a measurement system for magnetic explorations using an AUV and a deep-tow system. The magnetic exploration system consists of two 3-axis flux-gate magnetometers, one/two Overhauser magnetometer(s), an optical fiber gyro, a main unit (control, communication, recording), and an onboard unit. These devices except for the onboard unit are installed in pressure cases (depth limit: 6000m). Thus this system can measure three components and total intensity of the geomagnetic field in the deep sea. In 2009, the first test of the magnetic exploration system was carried out in the Kumano Basin using AUV Urashima and towing vehicle Yokosuka Deep-Tow during the R/V Yokosuka YK09-09 cruise. In this test, we sank a small magnetic target to the seafloor, and examined how the system worked. As a result, we successfully detected magnetic anomaly of the target to confirm the expected performance of that in the sea. In 2010, the magnetic exploration system was further tested in the Bayonnaise Knoll area both using a titanium towing frame during the R/V Bosei-maru cruise and using AUV Urashima during the R/V Yokosuka YK10-17 cruise. The purpose of these tests was to evaluate the performance of the system in an actual hydrothermal deposit area for practical applications of that. The Bayonnaise Knoll is a submarine caldera with an outer rim of 2.5-3 km and a floor of 840-920 m, which is located in the Izu-Ogasawara arc. A large hydrothermal deposit, Hakurei deposit, lies in the southeast part of the caldera. In the R/V Bosei-maru cruise, we observed three components of magnetic anomalies at depths of 400-570 m along SE-NW and WE tracks across the caldera. In the R/V Yokosuka YK10-17 cruise, we observed three components and total intensity of magnetic anomalies at altitudes of 60-100 m around the Hakurei deposit and at depth of 500 m above the caldera. The analysis of these data is now energetically pushed forward. A 3D gridded data set of the vector magnetic anomaly in the latter cruise was made by solving the Laplace's equation in the areas where observation data were not available, which is the unique procedure for analysis of the vector anomalies. Several magnetization solutions have been so far obtained by successive approximation and inversion methods. We will here present the measurement of the geomagnetic field and analysis of magnetization structure in Bayonnaise Knoll caldera. Note that this study has been supported by the Ministry of Education, Culture, Sports, Science & Technology (MEXT).

Testing the three axis magnetometer and gradiometer MOURA and data comparison on San Pablo de los Montes Observatory.

NASA Astrophysics Data System (ADS)

Belen Fernandez, Ana; Sanz, Ruy; Covisa, Pablo; Tordesillas, Jose Manuel; Diaz-Michelena, Marina

2013-04-01

A magnetometer and gradiometer named MOURA has been developed with the objective to measure the magnetic field on Mars in the frame of Mars MetNet Precursor Mission (MMPM) [1]. MOURA is a compact, miniaturized, intelligent and low cost instrument, based on two sets of triaxial magnetometers separated one centimeter from each other to do gradiometry studies. It has a resolution of 2.2 nT, and a field range of + 65μT, which can be extended to +130 μT when sensors are saturated. [2] These sensor heads are Anisotropic MagnetoResistances (AMR) Commercial-Off-The-Shelf (COTS) by Honeywell, specifically HMC1043, which has been selected due to their relative low consumption, weight and size, factors very important for the mission with very limited mass and power budget (shared 150 g for three full payloads). Also, this technology has been previously successfully employed on board Unmanned Aerial Vehicles (UAV) to perform geomagnetic surveys in extreme conditions areas [3], and in several space missions for different applications. [4] After the development of the MOURA Engineering Qualification Model (EQM) in November 2011, an exhaustive set of tests have been performed to validate and fully characterize the instrument. Compensation equations have been derived for the temperature corrections in the operation range (between -135 °C and 30 °C) in controlled environments. These compensation equations have been applied to field data, which have shown to follow the daily Earth's magnetic field variations as registered by San Pablo Geomagnetic Observatory (IAGA code: SPT) (available at www.ign.es and www.intermagnet.org) with deviations lower than 40 nT. These deviations were attributed to several error factors as the different locations between MOURA and SPT and other possible different geomagnetic conditions. Due to the above, a measurement campaign on SPT installations are been done. The main objective is to compare MOURA measurements on a relevant environment, with data obtained by SPT magnetometers. This is considered the last step prior to Mars in situ measurements. SPT employs for geomagnetic observations a fluxgate magnetometer FGE-Danish Meteorological Institute and a fluxgate vector magnetometer Geomag M390, both equipped with Overhauser effect magnetometers GSM90. The conditions into the rooms that contain these instruments are controlled. The equipments are situated on several pillars fixed strategically at Earth surface avoiding vibrations and other Earth movement that could affect measurement due to changes on the sensor position, the region is magnetically clean and the temperature variation is very low. Magnetic measurements are performed by MOURA for several days located on one of these pillars. These measurements are compared with SPT reference instrumentation with the aim to obtain a direct and very accurate evaluation of MOURA facing reference instrumentation. http://metnet.fmi.fi/index.php Development of miniaturized instrumentation for Planetary Exploration and its application to the Mars MetNet Precursor Mission. H. Guerrero et al. EGU General Assembly 2010, held 2-7 May, 2010 in Vienna, Austria, p.13330 Funaki, M.; Hirasawa, N.; and the Ant-Plane Group. Outline of a small unmanned aerial vehicle (Ant-Plane) designed for Antartic research. Polar Science 2008, 2, 129-142. M. Diaz-Michelena Sensors 2009, 9(4), 2271-2288

Development of new exploration tools for seabed mineral resources - Result of R/V YOKOSUKA research cruise YK09-09 -

NASA Astrophysics Data System (ADS)

Harada, M.; Sayanagi, K.; Kasaya, T.; Sawa, T.; Goto, T.; Tada, N.; Ichihara, H.; Asada, M.; Nakajima, T.; Isezaki, N.

2009-12-01

Detailed information on subsurface structure under seafloor is necessary for the estimation of seabed resources such as the hydrothermal deposit and methane hydrate. Although advantages of geophysical exploration near seafloor are expected for the seabed resource survey, efficient method has not been well-established. The authors started a project to develop exploration tools for seabed resources under the financial support of MEXT-Japan. We carry out research and development mainly regarding measurement of the magnetic field with high-resolution and high-sampling rate electric exploration devices with accurately controlled active source signals. Developed tools will be mounted underwater platforms such as deep-tow system, ROV (remotely operated vehicle), and AUV (autonomous undersea vehicle). We carried out the research cruise (vessel: JAMSTEC R/V YOKOSUKA YK09-09, cruise period: 19-29 July 2009, area surveyed: Kumano-nada, off Kii Peninsula, Japan) to investigate the performance of developed equipments for magnetic exploration. We mounted an Overhauser and two flux-gate magnetometers on the deep-tow and the AUV URASHIMA. To inspect the efficiency of equipments, it is better to measure the magnetic anomaly which is caused by known magnetic source. Therefore, we made a magnetic target which is consisted of 50 neodymium magnets. Before the navigation, the magnetic target was put under water and its position was measured by the acoustic method. The depth of target is about 2,050 meters, and the measurement was performed in the circle of a radius of about 300 meters. The vehicles were navigated at heights of 25 meters for AUV, and about 15 meters for deep-tow. Each of underwater navigation was practiced for two times. Both performances were carried out successfully, which means that we detected the significant magnetic anomalies caused by the target. We will be able to estimate three-dimensional distribution of anomalous magnetic field, and the source property of magnetic target. However, we have to resolve a lot of problems; (1) elimination of noises caused by the vehicles themselves, and their attitude, and (2) precise estimation of the position of vehicles. We will introduce the results of the research cruise and data processing in the presentation. Acknowledgement: We are grateful to captain Mr. E. Ukekura, chief officer Mr. S. Kusaka, chief AUV/DT operator Mr. T. Sakurai, and operation team, who made our difficult trials in the navigation possible by their professional skill. We also thank to the YOKOSUKA marine crew for overall support, and the engineers who take part in the development of equipments. This study is financially supported by the Ministry of Education, Culture, Sports, Science and Technology, Japan.

a Combined Molecular Dynamics and NMR Spectroscopic Protocol for the Conformational Analysis of Oligosaccharides.

NASA Astrophysics Data System (ADS)

Varma, Vikram

A combined experimental and theoretical protocol for the conformational analysis of oligosaccharides is presented. Three disaccharides, methyl alpha - scD-mannopyranosyl-(1 to 3)-alpha- scD-mannopyranoside, methyl beta- scD-galactopyranosyl-(1 to 4)-beta- scD-glucopyranoside, and propyl beta- scD-2-acetamido -2-deoxy glucopyranosyl-(1 to 3)- alpha- scL-rhamnopyranoside, are used to evaluate a protocol for conformational analysis that makes use of molecular dynamics calculations with the CHARMM force field. Dynamics trajectories computed in vacuo and in water are used to calculate time-averaged NMR parameters such as spin-lattice relaxation times (T_1 ), Nuclear Overhauser Enhancements (NOE), and heteronuclear spin-spin coupling constants (^3J _{rm CH}). The calculated NMR parameters are then compared to experimental values and used to evaluate the computational procedure. The energetically accessible conformations are effectively sampled by the simulations. The method has been extended to the conformational analysis of higher-order oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus Group A, and the Shigella flexneri Y O-antigen. The Streptococcus Group A cell-wall polysaccharide is comprised of a backbone of rhamnopyranosyl units connected by alternating alpha- scL-(1 to 3) and alpha- scL -(1 to 2) linkages, to which are attached N-acetyl-beta- scD-glucosamine ( beta- scD-GlcpNAc) residues at the 3 positions of the rhamnose backbone.rm A&rm B^'qquad A^'& rm Bqquad Acr[{-alpha}{-}L{-}Rha {it p}{-}(1to2){-alpha }{-}L{-}Rha{it p} {-}(1to3){-alpha}{ -}L{-}Rha{it p}-(1to2) -alpha-L-Rha{it p}{-}(1 to3){-alpha}{-}L{- }Rha{it p}{-}cr&uparrow(1 to3)&uparrow(1to3)crbeta {-}D{-}&rm Glc{it p }NAcqquadbeta{-}D{-}& rm Glc{it p}NAccr&rm C ^'&rm C] A branched trisaccharide (A^' -(C)B), a tetrasaccharide (A^' -(C)B-A), a pentasaccharide (C^' -B^'-A ^'-(C)B), and two hexasaccharides (C^'-B^ '-A^' -(C)B-A) and (A-(C^')B ^'-A^' -(C)B), have been chosen for study. The Shigella flexneri Y O-antigen is a linear polysaccharide that is composed of rhamnose units linked alpha- scL-(1 to 3) and alpha- scL-(1 to 2), interspersed by N-acetyl-beta - scD-glucosamine (beta- scD -GlcpNAc) to form a periodic repeating unit ABCD. &rm A&rm B&rm C&rm Dcr [{-alpha}{-}L {-}Rha{it p}-(1to2){ -alpha}{-}L{-}Rha{it p}{-}(1to3){-alpha} {-}L{-}Rha{it p}{ -}(1to3){-}beta{-}D {-}Glc{it p}NAc{-}(1 to2){-}]_{it n}A heptasaccharide corresponding to the fragment (ABCDA^'B ^'C^' ) of the Shigella flexneri Y polysaccharide has been investigated. The conformational properties of all of the oligosaccharides have been studied using molecular dynamics simulations. Interproton distances derived from ROESY spectra are used to determine the starting conformations of the oligosaccharides used in the dynamics calculations, and dynamics simulations are computed with proton pairs constrained to the ROESY -derived distances, as well as with the constraints removed. These dynamics trajectories are used to calculate ROESY buildup curves with CROSREL, a program that treats cross relaxation by means of a full matrix relaxation approach. The calculated buildup curves compare favorably with the experimental buildup curves. The study demonstrates that molecular dynamics, in conjunction with NMR spectroscopy, can be a useful tool in the understanding of the conformational behavior of oligosaccharides in solution. The results provide a model for antigen topology that can be used to infer some of the critical features of antibody-antigen interactions.

Identification of shallow geothermal anomalies in the Timanfaya National Park (Lanzarote, Canary Islands) through combined geophysical prospecting techniques

NASA Astrophysics Data System (ADS)

Gómez-Ortiz, David; Blanco-Montenegro, Isabel; Martín-Crespo, Tomás; Arnoso, José; Solla, Mercedes; Montesinos, Fuensanta G.; Vélez, Emilio; Calvo-Rathert, Manuel; Sánchez, Nieves; Lorenzo, Henrique; Soler, Vicente

2017-04-01

The Timanfaya National Park is a volcanic area in the southwest of Lanzarote Island (Canary Archipelago, Spain) resulting from the 1730-1736 eruption period. Several active geothermal anomalies have been identified from 1970's. Their location is important to prevent hazards in this restricted touristic area of the park. Presently, only some regional geophysical studies based on gravity, magnetic and seismic data have been undertaken to model the crustal structure of Lanzarote Island. This work presents a new study about the geothermal anomalies in the Timanfaya National Park by the analysis and joint interpretation of electrical resistivity tomography (ERT), magnetic anomalies and electromagnetic induction data (EMI). All analyzed data have been obtained over areas which had not been surveyed before. The studied geothermal field is located at the Islote de Hilario visitor's centre. One 50m-long GPR profile was carried out in May 2012 along the location of a known geothermal anomaly developed over pyroclastic deposits. The two main characteristics are: a) no continuous subhorizontal reflections are displayed up to 12 m depth and, b) the intensity of the reflections varies laterally in good agreement with the location of the geothermal anomalies (the higher the ground temperature, the greater the intensity of the GPR signal). Thus, an outline of the subsurface area with higher temperatures can be observed, indicating that the heat source is deeper at the beginning of the profile and extends laterally and progressively shallower towards the end. Temporal variation of the shallow temperature distribution was also investigated by repeating the same GPR profile in April 2015. Although both profiles look quite similar, subtle variations of the GPR signal intensity suggest a certain temporal variation of the ground temperature. In November 2012 a land magnetic survey was carried out in Timanfaya. In the Islote de Hilario area, total field magnetic data were acquired with an Overhauser magnetometer following a 75m-long profile which coincides in the first 50 m with the GPR profile. Three additional profiles (two of them parallel and one orthogonal to the first one) completed the survey, allowing the interpolation of the data into a regular grid. The resulting reduced-to-the-pole anomaly map displays some magnetic lows which could be related with high temperatures at shallow depths causing the loss of magnetic properties within the subsurface volcanic rocks. Forward modelling has been carried out to characterize the magnetic sources and to analyze the correlations with GPR data. These models have been constrained with NRM and susceptibility data measured in the laboratory for samples from the Timanfaya lava flows. Preliminary results of EMI data show high resistivity areas in good agreement with the location of the shallow geothermal anomalies, the magnetic lows and the high GPR signal intensity. The comparison of the results obtained from the different techniques reveals that the joint interpretation of ERT, magnetic anomalies and EMI methods provides reliable models useful for the location of shallow geothermal anomalies. These non-destructive geophysical techniques are of crucial importance in areas of special protection such as National Parks.

Space Environment Effects on Materials : An Overview

NASA Technical Reports Server (NTRS)

Garrett, Henry B.

2006-01-01

A general overview on the space environment and its effects on materials is presented. The topics include: 1) Impact of Space Effects on Spacecraft Costs; 2) Space Environment Effects on Spacecraft by Source; 3) Primary Source of Space Effects: The Sun; 4) The Earth's Environment; 5) Trapped Radiation Belts; 6) Aurora Are Everywhere; 7) Spacecraft Interactions; 8) Atmospheric Effects; 9) Contaminant Effects on Materials; 10) Meteoroid/Debris Effects on Materials; 11) Spacecraft Surface Charging; 12) Surface Discharge Effects; 13) Internal Electrostatic Discharge--Satellite Killer; 14) Plasma Interactions DS-1 Ion Engines; 15) Radiation Effects on Spacecraft Systems and Materials; 16) Total Ionizing Dose Effects Total Ionizing Dose Effects; 17) Man-Made Sources of Space Effects Man-Made Sources of Space Effects; and 18) Space Environments Versus Interactions.

15 CFR 930.151 - Interstate coastal effect.

Code of Federal Regulations, 2010 CFR

2010-01-01

... management program. Effects are not just environmental effects, but include effects on coastal uses. Effects include both direct effects which result from the activity and occur at the same time and place as the... time or farther removed in distance, but are still reasonably foreseeable. Indirect effects are effects...

1987 Annual Conference on Nuclear and Space Radiation Effects, Snowmass Village, CO, July 28-31, 1987, Proceedings

NASA Technical Reports Server (NTRS)

1987-01-01

Various papers on nuclear and space radiation effects are presented. The general topics addressed include: basic mechanisms of radiation effects, single-event phenomena, temperature and field effects, modeling and characterization of radiation effects, IC radiation effects and hardening, and EMP/SGEMP/IEMP phenomena. Also considered are: dosimetry/energy-dependent effects, sensors in and for radiation environments, spacecraft charging and space radiation effects, radiation effects and devices, radiation effects on isolation technologies, and hardness assurance and testing techniques.

Proton Damage Effects on Carbon Nanotube Field-Effect Transistors

DTIC Science & Technology

2014-06-19

PROTON DAMAGE EFFECTS ON CARBON NANOTUBE FIELD-EFFECT TRANSISTORS THESIS Evan R. Kemp, Ctr...United States. AFIT-ENP-T-14-J-39 PROTON DAMAGE EFFECTS ON CARBON NANOTUBE FIELD-EFFECT TRANSISTORS THESIS Presented to...PROTON DAMAGE EFFECTS ON CARBON NANOTUBE FIELD-EFFECT TRANSISTORS Evan R. Kemp, BS Ctr, USAF Approved: // Signed

What matters when judging intentionality-moral content or normative status? Testing the rational scientist model of the side-effect.

PubMed

Papadopoulos, C; Hayes, B K

2018-06-01

Previous work has demonstrated a "side-effect effect," such that intentionality is more likely to be attributed to agents who bring about negatively valenced as opposed to positively valenced side effects. The rational-scientist model explains this by suggesting that norm-violating side effects are more informative for inferring intentionality than norm-conforming side effects. In the present study we reexamined this account, addressing limitations of previous empirical tests (e.g., Uttich & Lombrozo, Cognition 116: 87-100, 2010). Side-effect valence and norm status were manipulated factorially, enabling an examination of the impact of norm status on intentionality judgments in both positively and negatively valenced side effects. Additionally, the impact of side-effect norm status on the perceived valences of side effects and agents was examined. Effects of norm status were found for both positive and negative side effects. Violation of an ostensibly neutral norm led to negative perceptions of the side effect. However, a norm status effect on intentionality judgments persisted when these effects were controlled. These results support the view that the side-effect effect is the result of the rational use of social-cognitive evidence.

No blank slates: Pre-existing schemas about pharmaceuticals predict memory for side effects.

PubMed

Heller, Monika K; Chapman, Sarah C E; Horne, Rob

2017-04-01

Attribution of symptoms as medication side effects is informed by pre-existing beliefs about medicines and perceptions of personal sensitivity to their effects (pharmaceutical schemas). We tested whether (1) pharmaceutical schemas were associated with memory (recall/recognition) for side effect information (2) memory explained the attribution of a common unrelated symptom as a side effect. In this analogue study participants saw the patient leaflet of a fictitious asthma drug listing eight side effects. We measured recall and recognition memory for side effects and used a vignette to test whether participants attributed an unlisted common symptom (headache) as a side effect. Participants who perceived pharmaceuticals as more harmful in general recalled fewer side effects correctly (r Correct Recall  = -.273), were less able to differentiate between listed and unlisted side effects (r Recognition Sensitivity  = -.256) and were more likely to attribute the unlisted headache symptom as a side effect (r side effect attribution  = .381, ps < .01). The effect of harm beliefs on side effect attribution was partially mediated by correct recall of side effects. Pharmaceutical schemas are associated with memory for side effect information. Memory may explain part of the association between pharmaceutical schemas and the attribution of unrelated symptoms as side effects.

Influence of verbal instructions on effect-based action control.

PubMed

Eder, Andreas B; Dignath, David

2017-03-01

According to ideomotor theory, people use bidirectional associations between movements and their effects for action selection and initiation. Our experiments examined how verbal instructions of action effects influence response selection without prior experience of action effects in a separate acquisition phase. Instructions for different groups of participants specified whether they should ignore, attend, learn, or intentionally produce acoustic effects produced by button presses. Results showed that explicit instructions of action-effect relations trigger effect-congruent action tendencies in the first trials following the instruction; in contrast, no evidence for effect-based action control was observed in these trials when instructions were to ignore or to attend to the action effects. These findings show that action-effect knowledge acquired through verbal instruction and direct experience is similarly effective for effect-based action control as long as the relation between the movement and the effect is clearly spelled out in the instruction.

Does the use of efficacy or effectiveness evidence in cost-effectiveness analysis matter?

PubMed

Dilokthornsakul, Piyameth; Chaiyakunapruk, Nathorn; Campbell, Jonathan D

2017-01-02

To test the association of clinical evidence type, efficacy-based or effectiveness-based ("E"), versus whether or not asthma interventions' cost-effectiveness findings are favorable. We conducted a systematic review of PubMed, EMBASE, Tufts CEA registry, Cochrane CENTRAL, and the UK National Health Services Economic Evaluation Database from 2009 to 2014. All cost-effectiveness studies evaluating asthma medication(s) were included. Clinical evidence type, "E," was classified as efficacy-based if the evidence was from an explanatory randomized controlled trial(s) or meta-analysis, while evidence from pragmatic trial(s) or observational study(s) was classified as effectiveness-based. We defined three times the World Health Organization cost-effectiveness willingness-to-pay (WTP) threshold or less as a favorable cost-effectiveness finding. Logistic regression tested the likelihood of favorable versus unfavorable cost-effectiveness findings against the type of "E." 25 cost-effectiveness studies were included. Ten (40.0%) studies were effectiveness-based, yet 15 (60.0%) studies were efficacy-based. Of 17 studies using endpoints that could be compared to WTP threshold, 7 out of 8 (87.5%) effectiveness-based studies yielded favorable cost-effectiveness results, whereas 4 out of 9 (44.4%) efficacy-based studies yielded favorable cost-effectiveness results. The adjusted odds ratio was 15.12 (95% confidence interval; 0.59 to 388.75) for effectiveness-based versus efficacy-based achieving favorable cost-effectiveness findings. More asthma cost-effectiveness studies used efficacy-based evidence. Studies using effectiveness-based evidence trended toward being more likely to disseminate favorable cost-effective findings than those using efficacy. Health policy decision makers should pay attention to the type of clinical evidence used in cost-effectiveness studies for accurate interpretation and application.

The Expertise Reversal Effect Is a Variant of the More General Element Interactivity Effect

ERIC Educational Resources Information Center

Chen, Ouhao; Kalyuga, Slava; Sweller, John

2017-01-01

Within the framework of cognitive load theory, the element interactivity and the expertise reversal effects usually are not treated as closely related effects. We argue that the two effects may be intertwined with the expertise reversal effect constituting a particular example of the element interactivity effect. Specifically, the element…

Effect of Communication Style on Perceptions of Medication Side Effect Risk among Pharmacy Students.

PubMed

Sawant, Ruta V; Beatty, Collin R; Sansgiry, Sujit S

2016-10-25

Objective. To assess the effect of communication style, and frequency and severity of medication side-effects, on pharmacy students' perception of risk of experiencing side effects. Methods. One hundred responses from pharmacy students were obtained using an online survey. Participants were presented with a drug information box containing drug name, drug usage, and one side-effect associated with the drug. Information on side-effect for each drug was presented in one of eight experimental conditions, in a 2 (side-effect frequency: low, high), X2 (side-effect severity: mild, severe) X2 (communication style: verbal, verbal + natural frequency) factorial design. Risk perception of experiencing side effects was measured. Results. Communication style was found to have a significant impact on risk perception depending on the context of frequency and severity associated with the side effect. Conclusion. Communication style plays a significant role in formulating risk perceptions of medication side effects. Training in pharmaceutical counseling should include special emphasis on effective language use.

Longitudinal multilevel models of the big-fish-little-pond effect on academic self-concept: counterbalancing contrast and reflected-glory effects in Hong Kong schools.

PubMed

Marsh, H W; Kong, C K; Hau, K T

2000-02-01

Longitudinal multilevel path models (7,997 students, 44 high schools, 4 years) evaluated effects of school-average achievement and perceived school status on academic self-concept in Hong Kong, which has a collectivist culture with a highly achievement-segregated high school system. Consistent with a priori predictions based on the big-fish-little-pond effect (BFLPE), higher school-average achievements led to lower academic self-concepts (contrast effect), whereas higher perceived school status had a counterbalancing positive effect on self-concept (reflected-glory, assimilation effect). The negative BFLPE is the net effect of counterbalancing influences, stronger negative contrast effects, and weaker positive assimilation effects so that controlling perceived school status led to purer--and even more negative--contrast effects. Attending a school where school-average achievement is high simultaneously resulted in a more demanding basis of comparison for one's own accomplishments (the stronger negative contrast effect) and a source of pride (the weaker positive assimilation effect).

Biological Effects of Atomic Radiations; ACCIONES BIOLOGICAS DE LAS RADIACIONES ATOMICAS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patetta-Queirolo, M.A.

1959-02-01

A resume is presented of each class in a course on the biological effects of nuclear radiations. The topics discussed include the physical and chemical bases of radiation effects, primary and secondary processes, accumulated effects, biochemical and cellular effects, radiation effects on living organisms and tissues, radioecology, genetic effects, cytogenetic effects, genetics of radiation in mammals, response of mammals to irradiation, dosimetry, and protection against radiations. (J.S.R.)

The neglected nonlocal effects of deforestation

NASA Astrophysics Data System (ADS)

Winckler, Johannes; Reick, Christian; Pongratz, Julia

2017-04-01

Deforestation changes surface temperature locally via biogeophysical effects by changing the water, energy and momentum balance. Adding to these locally induced changes (local effects), deforestation at a given location can cause changes in temperature elsewhere (nonlocal effects). Most previous studies have not considered local and nonlocal effects separately, but investigated the total (local plus nonlocal) effects, for which global deforestation was found to cause a global mean cooling. Recent modeling and observational studies focused on the isolated local effects: The local effects are relevant for local living conditions, and they can be obtained from in-situ and satellite observations. Observational studies suggest that the local effects of potential deforestation cause a warming when averaged globally. This contrast between local warming and total cooling indicates that the nonlocal effects of deforestation are causing a cooling and thus counteract the local effects. It is still unclear how the nonlocal effects depend on the spatial scale of deforestation, and whether they still compensate the local warming in a more realistic spatial distribution of deforestation. To investigate this, we use a fully coupled climate model and separate local and nonlocal effects of deforestation in three steps: Starting from a forest world, we simulate deforestation in one out of four grid boxes using a regular spatial pattern and increase the number of deforestation grid boxes step-wise up to three out of four boxes in subsequent simulations. To compare these idealized spatial distributions of deforestation to a more realistic case, we separate local and nonlocal effects in a simulation where deforestation is applied in regions where it occurred historically. We find that the nonlocal effects scale nearly linearly with the number of deforested grid boxes, and the spatial distribution of the nonlocal effects is similar for the regular spatial distribution of deforestation and the more realistic pattern. Globally averaged, the deforestation-induced warming of the local effects is counteracted by the nonlocal effects, which are about three times as strong as the local effects (up to 0.1K local warming versus -0.3K nonlocal cooling). Thus, the nonlocal effects are more cooling than the local effects are warming, and this is valid not only for idealized simulations of large-scale deforestation, but also for a more realistic deforestation scenario. We conclude that the local effects of deforestation only yield an incomplete picture of the total climate effects by biogeophysical pathways. While the local effects capture the direct climatic response at the site of deforestation, the nonlocal effects have to be included if the biogeophysical effects of deforestation are considered for an implementation in climate policies.

A Multi-Scale Perspective of the Effects of Forest Fragmentation on Birds in Eastern Forests

Treesearch

Frank R. Thompson; Therese M. Donovan; Richard M. DeGraff; John Faaborg; Scott K. Robinson

2002-01-01

We propose a model that considers forest fragmentation within a spatial hierarchy that includes regional or biogeographic effects, landscape-level fragmentation effects, and local habitat effects. We hypothesize that effects operate "top down" in that larger scale effects provide constraints or context for smaller scale effects. Bird species' abundance...

Relationships between direct predation and risk effects.

PubMed

Creel, Scott; Christianson, David

2008-04-01

Risk effects arise when prey alter their behavior in response to predators, and these responses carry costs. Empirical studies have found that risk effects can be large. Nonetheless, studies of predation in vertebrate conservation and management usually consider only direct predation. Given the ubiquity and strength of behavioral responses to predators by vertebrate prey, it is not safe to assume that risk effects on dynamics can be ignored. Risk effects can be larger than direct effects. Risk effects can exist even when the direct rate of predation is zero. Risk effects and direct effects do not necessarily change in parallel. When risk effects reduce reproduction rather than survival, they are easily mistaken for limitation by food supply.

Dissociating action-effect activation and effect-based response selection.

PubMed

Schwarz, Katharina A; Pfister, Roland; Wirth, Robert; Kunde, Wilfried

2018-05-25

Anticipated action effects have been shown to govern action selection and initiation, as described in ideomotor theory, and they have also been demonstrated to determine crosstalk between different tasks in multitasking studies. Such effect-based crosstalk was observed not only in a forward manner (with a first task influencing performance in a following second task) but also in a backward manner (the second task influencing the preceding first task), suggesting that action effect codes can become activated prior to a capacity-limited processing stage often denoted as response selection. The process of effect-based response production, by contrast, has been proposed to be capacity-limited. These observations jointly suggest that effect code activation can occur independently of effect-based response production, though this theoretical implication has not been tested directly at present. We tested this hypothesis by employing a dual-task set-up in which we manipulated the ease of effect-based response production (via response-effect compatibility) in an experimental design that allows for observing forward and backward crosstalk. We observed robust crosstalk effects and response-effect compatibility effects alike, but no interaction between both effects. These results indicate that effect activation can occur in parallel for several tasks, independently of effect-based response production, which is confined to one task at a time. Copyright © 2018 Elsevier B.V. All rights reserved.

40 CFR 721.72 - Hazard communication program.

Code of Federal Regulations, 2011 CFR

2011-07-01

... irritation. (ii) Respiratory complications. (iii) Central nervous system effects. (iv) Internal organ effects... irritation (B) Respiratory complications (C) Central nervous system effects (D) Internal organ effects (E... irritation (B) Respiratory complications (C) Central nervous system effects (D) Internal organ effects (E...

40 CFR 721.72 - Hazard communication program.

Code of Federal Regulations, 2010 CFR

2010-07-01

... irritation. (ii) Respiratory complications. (iii) Central nervous system effects. (iv) Internal organ effects... irritation (B) Respiratory complications (C) Central nervous system effects (D) Internal organ effects (E... irritation (B) Respiratory complications (C) Central nervous system effects (D) Internal organ effects (E...

40 CFR 721.72 - Hazard communication program.

Code of Federal Regulations, 2012 CFR

2012-07-01

... irritation. (ii) Respiratory complications. (iii) Central nervous system effects. (iv) Internal organ effects... irritation (B) Respiratory complications (C) Central nervous system effects (D) Internal organ effects (E... irritation (B) Respiratory complications (C) Central nervous system effects (D) Internal organ effects (E...

40 CFR 721.72 - Hazard communication program.

Code of Federal Regulations, 2014 CFR

2014-07-01

... irritation. (ii) Respiratory complications. (iii) Central nervous system effects. (iv) Internal organ effects... irritation (B) Respiratory complications (C) Central nervous system effects (D) Internal organ effects (E... irritation (B) Respiratory complications (C) Central nervous system effects (D) Internal organ effects (E...

40 CFR 721.72 - Hazard communication program.

Code of Federal Regulations, 2013 CFR

2013-07-01

... irritation. (ii) Respiratory complications. (iii) Central nervous system effects. (iv) Internal organ effects... irritation (B) Respiratory complications (C) Central nervous system effects (D) Internal organ effects (E... irritation (B) Respiratory complications (C) Central nervous system effects (D) Internal organ effects (E...

Long-term and short-term action-effect links and their impact on effect monitoring.

PubMed

Wirth, Robert; Steinhauser, Robert; Janczyk, Markus; Steinhauser, Marco; Kunde, Wilfried

2018-04-23

People aim to produce effects in the environment, and according to ideomotor theory, actions are selected and executed via anticipations of their effects. Further, to ensure that an action has been successful and an effect has been realized, we must be able to monitor the consequences of our actions. However, action-effect links might vary between situations, some might apply for a majority of situations, while others might only apply to special occasions. With a combination of behavioral and electrophysiological markers, we show that monitoring of self-produced action effects interferes with other tasks, and that the length of effect monitoring is determined by both, long-term action-effect links that hold for most situations, and short-term action-effect links that emerge from a current setting. Effect monitoring is fast and frugal when these action-effect links allow for valid anticipation of action effects, but otherwise effect monitoring takes longer and delays a subsequent task. Specific influences of long-term and short-term links on the P1/N1 and P3a further allow to dissect the temporal dynamics of when these links interact for the purpose of effect monitoring. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

EXPERIMENTAL STUDIES ON THE PROTECTIVE EFFECT OF SEVERAL PHARMACOLOGICAL AGENTS AGAINST X-IRRADIATION (in Japanese)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shakudo, Y.

The protective effects of several pharmacological agents against lethal radiation effects were tested in mice. Noradrenaline, phenylephrine, naphazoline, tetrahydrozoline, and methoxamine markedly reduced radiation mortality when injected 5 min before exposure. Adrenaline and phenylethylamine had little protective effect, while ephedrine had no effect. Cocain was moderately effective, while caffein had little effect. (C.H.)

Effect of Visual Experience on Face Processing: A Developmental Study of Inversion and Non-Native Effects

ERIC Educational Resources Information Center

Sangrigoli, Sandy; de Schonen, Scania

2004-01-01

In adults, three phenomena are taken to demonstrate an experience effect on face recognition: an inversion effect, a non-native face effect (so-called "other-race" effect) and their interaction. It is crucial for our understanding of the developmental perception mechanisms of object processing to discover when these effects are present in…

A Cost-Effectiveness Analysis Model for Evaluating and Planning Secondary Vocational Programs

ERIC Educational Resources Information Center

Kim, Jin Eun

1977-01-01

This paper conceptualizes a cost-effectiveness analysis and describes a cost-effectiveness analysis model for secondary vocational programs. It generates three kinds of cost-effectiveness measures: program effectiveness, cost efficiency, and cost-effectiveness and/or performance ratio. (Author)

Good cope, bad cope: adaptive and maladaptive coping strategies following a critical negative work event.

PubMed

Brown, Steven P; Westbrook, Robert A; Challagalla, Goutam

2005-07-01

The authors examined the moderating effects of coping tactics on the relationship between negative emotion and work performance. Findings indicate an adverse effect of emotion on performance; however, this effect is moderated by coping tactics. Venting (expressing one's negative feelings to others) amplified the adverse effects of negative emotion. Self-control had mixed effects: On one hand, it buffered the adverse effects of negative emotion, yet on the other hand, it had a negative direct effect on outcomes. Task focus had a positive direct effect on performance but no buffering (moderating) effect. Implications of these findings for understanding the effects of negative emotion and coping in the workplace are discussed. Copyright 2005 APA, all rights reserved.

Statistical properties of four effect-size measures for mediation models.

PubMed

Miočević, Milica; O'Rourke, Holly P; MacKinnon, David P; Brown, Hendricks C

2018-02-01

This project examined the performance of classical and Bayesian estimators of four effect size measures for the indirect effect in a single-mediator model and a two-mediator model. Compared to the proportion and ratio mediation effect sizes, standardized mediation effect-size measures were relatively unbiased and efficient in the single-mediator model and the two-mediator model. Percentile and bias-corrected bootstrap interval estimates of ab/s Y , and ab(s X )/s Y in the single-mediator model outperformed interval estimates of the proportion and ratio effect sizes in terms of power, Type I error rate, coverage, imbalance, and interval width. For the two-mediator model, standardized effect-size measures were superior to the proportion and ratio effect-size measures. Furthermore, it was found that Bayesian point and interval summaries of posterior distributions of standardized effect-size measures reduced excessive relative bias for certain parameter combinations. The standardized effect-size measures are the best effect-size measures for quantifying mediated effects.

Employment effects of active labor market programs for sick-listed workers.

PubMed

Holm, Anders; Høgelund, Jan; Gørtz, Mette; Rasmussen, Kristin Storck; Houlberg, Helle Sofie Bøje

2017-03-01

We use register data of 88,948 sick-listed workers in Denmark over the period 2008-2011 to investigate the effect of active labor market programs on the duration until returning to non-subsidized employment and the duration of this employment. To identify causal treatment effects, we exploit over-time variation in the use of active labor market programs in 98 job centers and time-to- event. We find that ordinary education and subsidized job training have significant positive employment effects. Subsidized job training has a large, positive effect on the transition into employment but no effect on the subsequent employment duration. In contrast, ordinary education has a positive effect on employment duration but no effect on the transition into employment. The latter effect is the result of two opposing effects, a large positive effect of having completed education and a large negative lock-in effect, with low re-employment chances during program participation. Copyright © 2017. Published by Elsevier B.V.

Effect of Crataegus Usage in Cardiovascular Disease Prevention: An Evidence-Based Approach

PubMed Central

Wang, Jie; Xiong, Xingjiang; Feng, Bo

2013-01-01

Hawthorn (Crataegus oxyacantha) is a widely used Chinese herb for treatment of gastrointestinal ailments and heart problems and consumed as food. In North America, the role of treatment for heart problems dates back to 1800. Currently, evidence is accumulating from various in vivo and in vitro studies that hawthorn extracts exert a wide range of cardiovascular pharmacological properties, including antioxidant activity, positive inotropic effect, anti-inflammatory effect, anticardiac remodeling effect, antiplatelet aggregation effect, vasodilating effect, endothelial protective effect, reduction of smooth muscle cell migration and proliferation, protective effect against ischemia/reperfusion injury, antiarrhythmic effect, lipid-lowering effect and decrease of arterial blood pressure effect. On the other hand, reviews of placebo-controlled trials have reported both subjective and objective improvement in patients with mild forms of heart failure (NYHA I–III), hypertension, and hyperlipidemia. This paper discussed the underlying pharmacology mechanisms in potential cardioprotective effects and elucidated the clinical applications of Crataegus and its various extracts. PMID:24459528

A Meta Analytical Approach Regarding School Effectiveness: The True Size of School Effects and the Effect Size of Educational Leadership.

ERIC Educational Resources Information Center

Bosker, Roel J.; Witziers, Bob

School-effectiveness research has not yet been able to identify the factors of effective and noneffective schools, the real contribution of the significant factors, the true sizes of school effects, and the generalizability of school-effectiveness results. This paper presents findings of a meta analysis, the Dutch PSO programme, that was used to…

LED and Semiconductor Photo-effects on Living Things

NASA Astrophysics Data System (ADS)

Fujiyasu, Hiroshi; Ishigaki, Takemitsu; Fujiyasu, Kentarou; Ujihara, Shirou; Watanabe, Naoharu; Sunayama, Shunji; Ikoma, Shuuji

We have studied LED irradiation effects on plants and animals in the visible to UV region of light from GaN LEDs. The results are as follows. Blue light considers to be effective for pearl cultivation or for attraction of small fishes living in near the surface of sea such as Pompano or Sardine, white light radiation is effective for cultivation of botanical plankton for shells. Other experiments of UV light irradiation attracting effect on baby sea turtle and the germination UV effect of mushroom, green light weight enhance effect on baby pigs, light vernalization effect of vegitable and Ge far infrared therapic effect on human body are also given.

Small- and Large-Effect Quantitative Trait Locus Interactions Underlie Variation in Yeast Sporulation Efficiency

PubMed Central

Lorenz, Kim; Cohen, Barak A.

2012-01-01

Quantitative trait loci (QTL) with small effects on phenotypic variation can be difficult to detect and analyze. Because of this a large fraction of the genetic architecture of many complex traits is not well understood. Here we use sporulation efficiency in Saccharomyces cerevisiae as a model complex trait to identify and study small-effect QTL. In crosses where the large-effect quantitative trait nucleotides (QTN) have been genetically fixed we identify small-effect QTL that explain approximately half of the remaining variation not explained by the major effects. We find that small-effect QTL are often physically linked to large-effect QTL and that there are extensive genetic interactions between small- and large-effect QTL. A more complete understanding of quantitative traits will require a better understanding of the numbers, effect sizes, and genetic interactions of small-effect QTL. PMID:22942125

Importance of placebo effect in cough clinical trials.

PubMed

Eccles, Ron

2010-01-01

Cough is a unique symptom because, unlike sneeze and other symptoms, it can be under voluntary control and this complicates clinical trials on cough medicines. All over-the-counter cough medicines (OTC) are very effective treatments because of their placebo effect. The placebo effect is enhanced by expectancy related to advertising, brand, packaging, and formulation. This placebo effect creates a problem for the conduct of clinical trials on OTC cough medicines that attempt to demonstrate the efficacy of a pharmacological agent above that of any placebo effect. Up to 85% of the efficacy of some cough medicines can be attributed to a placebo effect. The placebo effect apparent in clinical trials consists of several components: natural recovery, regression of cough response toward mean, demulcent effect, effect of sweetness, voluntary control, and effects related to expectancy and meaning of the treatment. The placebo effect has been studied most in the pain model, and placebo analgesia is reported to depend on the activation of endogenous opioid systems in the brain; this model may be applicable to cough. A balanced placebo design may help to control for the placebo effect, but this trial design may not be acceptable due to deception of patients. The placebo effect in clinical trials may be controlled by use of a crossover design, where feasible, and the changes in the magnitude of the placebo effect in this study design are discussed.

All Effects of Psychophysical Variables on Color Attributes: A Classification System

PubMed Central

Pridmore, Ralph W.; Melgosa, Manuel

2015-01-01

This paper reports the research and structuring of a classification system for the effects of psychophysical variables on the color attributes. A basic role of color science is to psychophysically specify color appearance. An early stage is to specify the effects of the psychophysical variables (as singles, pairs, etc) on the color attributes (as singles, pairs, etc), for example to model color appearance. Current data on effects are often scarce or conflicting. Few effects are well understood, and the practice of naming effects after their discoverer(s) is inadequate and can be confusing. The number and types of possible effects have never been systematically analyzed and categorized. We propose a simple and rigorous system of classification including nomenclature. The total range of effects is computed from the possible combinations of three psychophysical variables (luminance, dominant wavelength, purity) and six color attributes (lightness, brightness, hue, chroma, colorfulness, saturation) in all modes of appearance. Omitting those effects that are normally impossible to perceive at any one time (such as four- or five-dimensional colors), the total number perceivable is 161 types of effects for all modes of appearance. The type of effect is named after the psychophysical stimulus (or stimuli) and the relevant color attribute(s), e.g., Luminance-on-hue effect (traditionally known as Bezold-Brucke effect). Each type of effect may include slightly different effects with infinite variations depending on experimental parameters. PMID:25859845

The Activation of Effect Codes in Response Preparation: New Evidence from an Indirect Priming Paradigm

PubMed Central

Ziessler, Michael; Nattkemper, Dieter; Vogt, Stefan

2012-01-01

Evidence for the anticipation of environmental effects as an integral part of response planning comes mainly from experiments in which the effects were physically presented. Thus, in these studies it cannot be excluded that effect codes were activated during response preparation only because the effects were displayed as external stimuli before response execution. In order to provide more clear-cut evidence for the anticipation of response effects in action planning, we performed a series of three experiments using a new paradigm, where displaying effect codes before the response was avoided. Participants first learned arbitrary effects of key-pressing responses. In the following test phase they were instructed to execute a response only if a Go stimulus was presented after a variable stimulus onset asynchrony (SOA). The Go stimulus was either compatible or incompatible with the effect, but independent of the response. In Experiment 1 we tested the paradigm with two responses and two effects. We found a significant compatibility effect: If the Go stimulus was compatible with the response effect, responses were initiated faster than in incompatible trials. In Experiment 2 response effects were only present in the acquisition phase, but not in the test phase. The compatibility effect disappeared, indicating that the results of Experiment 1 were indeed related to the anticipation of the forthcoming response effects. In Experiment 3 we extended this paradigm by using a larger number of stimuli and response alternatives. Again we found a robust compatibility effect, which can only be explained if the effect representations are active before response execution. The compatibility effects in Experiments 1 and 3 did not depend on the SOA. The fact that the Go stimulus affected response preparation at any time indicates that the role of effect anticipation is not limited to response selection. PMID:23293623

16 CFR 313.18 - Effective date; transition rule.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Effective date; transition rule. 313.18... PRIVACY OF CONSUMER FINANCIAL INFORMATION Relation to Other Laws; Effective Date § 313.18 Effective date; transition rule. (a) Effective date—(1) General rule. This part is effective November 13, 2000. In order to...

1989 IEEE Annual Conference on Nuclear and Space Radiation Effects, 26th, Marco Island, FL, July 25-29, 1989, Proceedings. Part 1

NASA Technical Reports Server (NTRS)

Ochoa, Agustin, Jr. (Editor)

1989-01-01

Various papers on nuclear science are presented. The general topics addressed include: basic mechanics of radiation effects, dosimetry and energy-dependent effects, hardness assurance and testing techniques, spacecraft charging and space radiation effects, EMP/SGEMP/IEMP phenomena, device radiation effects and hardening, radiation effects on isolation technologies, IC radiation effects and hardening, and single-event phenomena.

1988 IEEE Annual Conference on Nuclear and Space Radiation Effects, 25th, Portland, OR, July 12-15, 1988, Proceedings

NASA Technical Reports Server (NTRS)

Coakley, Peter G. (Editor)

1988-01-01

The effects of nuclear and space radiation on the performance of electronic devices are discussed in reviews and reports of recent investigations. Topics addressed include the basic mechanisms of radiation effects, dosimetry and energy-dependent effects, sensors in and for radiation environments, EMP/SGEMP/IEMP phenomena, radiation effects on isolation technologies, and spacecraft charging and space radiation effects. Consideration is given to device radiation effects and hardening, hardness assurance and testing techniques, IC radiation effects and hardening, and single-event phenomena.

Regulation with placebo effects.

PubMed

Malani, Anup

2008-12-01

A growing scientific literature supports the existence of placebo effects from a wide range of health interventions and for a range of medical conditions. This Article reviews this literature, examines the implications for law and policy, and suggests future areas for research on placebo effects. In particular, it makes the case for altering the drug approval process to account for, if not credit, placebo effects. It recommends that evidence of placebo effects be permitted as a defense in cases alleging violations of informed consent or false advertising. Finally, it finds that tort law already has doctrines such as joint and several liability to account for placebo effects. Future research on placebo effects should focus on whether awareness of placebo effects can disable these effects and whether subjects can control their own placebo effects.

Neither fixed nor random: weighted least squares meta-regression.

PubMed

Stanley, T D; Doucouliagos, Hristos

2017-03-01

Our study revisits and challenges two core conventional meta-regression estimators: the prevalent use of 'mixed-effects' or random-effects meta-regression analysis and the correction of standard errors that defines fixed-effects meta-regression analysis (FE-MRA). We show how and explain why an unrestricted weighted least squares MRA (WLS-MRA) estimator is superior to conventional random-effects (or mixed-effects) meta-regression when there is publication (or small-sample) bias that is as good as FE-MRA in all cases and better than fixed effects in most practical applications. Simulations and statistical theory show that WLS-MRA provides satisfactory estimates of meta-regression coefficients that are practically equivalent to mixed effects or random effects when there is no publication bias. When there is publication selection bias, WLS-MRA always has smaller bias than mixed effects or random effects. In practical applications, an unrestricted WLS meta-regression is likely to give practically equivalent or superior estimates to fixed-effects, random-effects, and mixed-effects meta-regression approaches. However, random-effects meta-regression remains viable and perhaps somewhat preferable if selection for statistical significance (publication bias) can be ruled out and when random, additive normal heterogeneity is known to directly affect the 'true' regression coefficient. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

A unified frame of predicting side effects of drugs by using linear neighborhood similarity.

PubMed

Zhang, Wen; Yue, Xiang; Liu, Feng; Chen, Yanlin; Tu, Shikui; Zhang, Xining

2017-12-14

Drug side effects are one of main concerns in the drug discovery, which gains wide attentions. Investigating drug side effects is of great importance, and the computational prediction can help to guide wet experiments. As far as we known, a great number of computational methods have been proposed for the side effect predictions. The assumption that similar drugs may induce same side effects is usually employed for modeling, and how to calculate the drug-drug similarity is critical in the side effect predictions. In this paper, we present a novel measure of drug-drug similarity named "linear neighborhood similarity", which is calculated in a drug feature space by exploring linear neighborhood relationship. Then, we transfer the similarity from the feature space into the side effect space, and predict drug side effects by propagating known side effect information through a similarity-based graph. Under a unified frame based on the linear neighborhood similarity, we propose method "LNSM" and its extension "LNSM-SMI" to predict side effects of new drugs, and propose the method "LNSM-MSE" to predict unobserved side effect of approved drugs. We evaluate the performances of LNSM and LNSM-SMI in predicting side effects of new drugs, and evaluate the performances of LNSM-MSE in predicting missing side effects of approved drugs. The results demonstrate that the linear neighborhood similarity can improve the performances of side effect prediction, and the linear neighborhood similarity-based methods can outperform existing side effect prediction methods. More importantly, the proposed methods can predict side effects of new drugs as well as unobserved side effects of approved drugs under a unified frame.

Drug side effect extraction from clinical narratives of psychiatry and psychology patients

PubMed Central

Kocher, Jean-Pierre A; Chute, Christopher G; Savova, Guergana K

2011-01-01

Objective To extract physician-asserted drug side effects from electronic medical record clinical narratives. Materials and methods Pattern matching rules were manually developed through examining keywords and expression patterns of side effects to discover an individual side effect and causative drug relationship. A combination of machine learning (C4.5) using side effect keyword features and pattern matching rules was used to extract sentences that contain side effect and causative drug pairs, enabling the system to discover most side effect occurrences. Our system was implemented as a module within the clinical Text Analysis and Knowledge Extraction System. Results The system was tested in the domain of psychiatry and psychology. The rule-based system extracting side effects and causative drugs produced an F score of 0.80 (0.55 excluding allergy section). The hybrid system identifying side effect sentences had an F score of 0.75 (0.56 excluding allergy section) but covered more side effect and causative drug pairs than individual side effect extraction. Discussion The rule-based system was able to identify most side effects expressed by clear indication words. More sophisticated semantic processing is required to handle complex side effect descriptions in the narrative. We demonstrated that our system can be trained to identify sentences with complex side effect descriptions that can be submitted to a human expert for further abstraction. Conclusion Our system was able to extract most physician-asserted drug side effects. It can be used in either an automated mode for side effect extraction or semi-automated mode to identify side effect sentences that can significantly simplify abstraction by a human expert. PMID:21946242

CD-1 and Balb/cJ mice do not show enduring antidepressant-like effects of ketamine in tests of acute antidepressant efficacy.

PubMed

Bechtholt-Gompf, Anita J; Smith, Karen L; John, Catherine S; Kang, Hannah H; Carlezon, William A; Cohen, Bruce M; Ongür, Dost

2011-06-01

In patients, ketamine is a fast-acting antidepressant that can induce long-lasting symptom relief. Similar rapid effects have been reported in rodents, but reports of lasting effects are limited. We sought to extend past findings by examining dose-response curves that overlap with the individual doses previously reported to induce lasting effects in rodents and determining whether effects generalize to the tail suspension test (TST) and Balb/cJ mice. Using common tests of antidepressant efficacy we first confirmed our ability to detect the effects of desipramine, a well-characterized antidepressant drug. Next, we sought to determine whether two non-competitive NMDA antagonists, ketamine and MK-801, had long-lasting antidepressant-like effects in CD-1 mice, a strain that has often been used to demonstrate the short-term antidepressant-like effects of ketamine. Finally, we examined the short- and long-term effects of ketamine in a mouse strain that is more sensitive to antidepressant-like effects, Balb/cJ mice. In CD-1 mice, desipramine treatment yielded significant short-term antidepressant-like effects in the TST and the forced swimming test (FST). However, no significant enduring effects of ketamine or MK-801 were observed 1 week later. Short-term effects of ketamine in the TST were observed in Balb/cJ mice, but lasting effects were absent 1 week later. Although the TST and FST have been widely used to detect antidepressant-like effects in mice, they do not appear to be sensitive to long-lasting antidepressant-like effects of ketamine in mice and, therefore, do not model the therapeutic effects of ketamine that have been reported in humans with major depression.

Understanding Treatment Effect Estimates When Treatment Effects Are Heterogeneous for More Than One Outcome.

PubMed

Brooks, John M; Chapman, Cole G; Schroeder, Mary C

2018-06-01

Patient-centred care requires evidence of treatment effects across many outcomes. Outcomes can be beneficial (e.g. increased survival or cure rates) or detrimental (e.g. adverse events, pain associated with treatment, treatment costs, time required for treatment). Treatment effects may also be heterogeneous across outcomes and across patients. Randomized controlled trials are usually insufficient to supply evidence across outcomes. Observational data analysis is an alternative, with the caveat that the treatments observed are choices. Real-world treatment choice often involves complex assessment of expected effects across the array of outcomes. Failure to account for this complexity when interpreting treatment effect estimates could lead to clinical and policy mistakes. Our objective was to assess the properties of treatment effect estimates based on choice when treatments have heterogeneous effects on both beneficial and detrimental outcomes across patients. Simulation methods were used to highlight the sensitivity of treatment effect estimates to the distributions of treatment effects across patients across outcomes. Scenarios with alternative correlations between benefit and detriment treatment effects across patients were used. Regression and instrumental variable estimators were applied to the simulated data for both outcomes. True treatment effect parameters are sensitive to the relationships of treatment effectiveness across outcomes in each study population. In each simulation scenario, treatment effect estimate interpretations for each outcome are aligned with results shown previously in single outcome models, but these estimates vary across simulated populations with the correlations of treatment effects across patients across outcomes. If estimator assumptions are valid, estimates across outcomes can be used to assess the optimality of treatment rates in a study population. However, because true treatment effect parameters are sensitive to correlations of treatment effects across outcomes, decision makers should be cautious about generalizing estimates to other populations.

Can Oxytocin Enhance the Placebo Effect?

ClinicalTrials.gov

2018-02-06

Oxytocin Effect on Memory Performance During Phase 1; Oxytocin Effect on Memory Performance During Phase 2; Oxytocin Effect on Memory Performance During Phase 3; Oxytocin Effect on Memory Performance During Phase 4

Triple-effect absorption chiller cycle: A step beyond double-effect cycles

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeVault, R.C.

1990-01-01

Many advanced'' absorption cycles have been proposed during the current century. Of the hundreds of absorption cycles which have been patented throughout the world, all commercially manufactured products for air conditioning buildings have been variations of just two basic absorption cycles: single-effect and condenser-coupled double-effect cycles. The relatively low cooling coefficients of performance (COPs) inherent in single-effect and double-effect cycles limits the economic applicability of absorption air conditioners (chillers) in the United States. A triple-effect absorption chiller cycle is discussed. This cycle uses two condensers and two absorbers to achieve the triple effect.'' Depending on the absorption fluids selected, thismore » triple-effect cycle is predicted to improve cooling COPs by 18% to 60% compared with the equivalent double-effect cycle. This performance improvement is obtained without increasing the total amount of heat-transfer surface area needed for the heat exchangers. A comparison between the calculated performances of a double-effect cycle and a triple-effect cycle (both using ammonia-water (NH{sub 3}/H{sub 2}O) as the absorption fluid pair) is presented. The triple-effect cycle is predicted to have an 18% higher cooling COP (1.41 compared with 1.2 for a double-effect), lower pressure (47.70 atm (701 psi) instead of 68.05 atm (1000 psi)), significantly reduced pumping power (less than one-half that of the double-effect cycle), and potentially lower construction cost (33% less total heat exchange needed). Practical implications for this triple-effect cycle are discussed. 16 refs., 5 figs., 1 tab.« less

Incidence and severity of self-reported chemotherapy side effects in routine care: A prospective cohort study

PubMed Central

Haas, Marion; Viney, Rosalie; Pearson, Sallie-Anne; Haywood, Philip; Brown, Chris; Ward, Robyn

2017-01-01

Aim Chemotherapy side effects are often reported in clinical trials; however, there is little evidence about their incidence in routine clinical care. The objective of this study was to describe the frequency and severity of patient-reported chemotherapy side effects in routine care across treatment centres in Australia. Methods We conducted a prospective cohort study of individuals with breast, lung or colorectal cancer undergoing chemotherapy. Side effects were identified by patient self-report. The frequency, prevalence and incidence rates of side effects were calculated by cancer type and grade, and cumulative incidence curves for each side effect computed. Frequencies of side effects were compared between demographic subgroups using chi-squared statistics. Results Side effect data were available for 449 eligible individuals, who had a median follow-up of 5.64 months. 86% of participants reported at least one side effect during the study period and 27% reported a grade IV side effect, most commonly fatigue or dyspnoea. Fatigue was the most common side effect overall (85%), followed by diarrhoea (74%) and constipation (74%). Prevalence and incidence rates were similar across side effects and cancer types. Age was the only demographic factor associated with the incidence of side effects, with older people less likely to report side effects. Conclusion This research has produced the first Australian estimates of self-reported incidence of chemotherapy side effects in routine clinical care. Chemotherapy side effects in routine care are common, continue throughout chemotherapy and can be serious. This work confirms the importance of observational data in providing clinical practice-relevant information to decision-makers. PMID:29016607

Incidence and severity of self-reported chemotherapy side effects in routine care: A prospective cohort study.

PubMed

Pearce, Alison; Haas, Marion; Viney, Rosalie; Pearson, Sallie-Anne; Haywood, Philip; Brown, Chris; Ward, Robyn

2017-01-01

Chemotherapy side effects are often reported in clinical trials; however, there is little evidence about their incidence in routine clinical care. The objective of this study was to describe the frequency and severity of patient-reported chemotherapy side effects in routine care across treatment centres in Australia. We conducted a prospective cohort study of individuals with breast, lung or colorectal cancer undergoing chemotherapy. Side effects were identified by patient self-report. The frequency, prevalence and incidence rates of side effects were calculated by cancer type and grade, and cumulative incidence curves for each side effect computed. Frequencies of side effects were compared between demographic subgroups using chi-squared statistics. Side effect data were available for 449 eligible individuals, who had a median follow-up of 5.64 months. 86% of participants reported at least one side effect during the study period and 27% reported a grade IV side effect, most commonly fatigue or dyspnoea. Fatigue was the most common side effect overall (85%), followed by diarrhoea (74%) and constipation (74%). Prevalence and incidence rates were similar across side effects and cancer types. Age was the only demographic factor associated with the incidence of side effects, with older people less likely to report side effects. This research has produced the first Australian estimates of self-reported incidence of chemotherapy side effects in routine clinical care. Chemotherapy side effects in routine care are common, continue throughout chemotherapy and can be serious. This work confirms the importance of observational data in providing clinical practice-relevant information to decision-makers.

Side Effect Perceptions and Their Impact on Treatment Decisions in Women.

PubMed

Waters, Erika A; Pachur, Thorsten; Colditz, Graham A

2017-04-01

Side effects prompt some patients to forego otherwise-beneficial therapies. This study explored which characteristics make side effects particularly aversive. We used a psychometric approach, originating from research on risk perception, to identify the factors (or components) underlying side effect perceptions. Women ( N = 149) aged 40 to 74 years were recruited from a patient registry to complete an online experiment. Participants were presented with hypothetical scenarios in which an effective and necessary medication conferred a small risk of a single side effect (e.g., nausea, dizziness). They rated a broad range of side effects on several characteristics (e.g., embarrassing, treatable). In addition, we collected 4 measures of aversiveness for each side effect: choosing to take the medication, willingness to pay to avoid the side effect (WTP), negative affective attitude associated with the side effect, and how each side effect ranks among others in terms of undesirability. A principal components analysis (PCA) was used to identify the components underlying side effect perceptions. Then, for each aversiveness measure separately, regression analyses were used to determine which components predicted differences in aversiveness among the side effects. The PCA revealed 4 components underlying side effect perceptions: affective challenge (e.g., frightening), social challenge (e.g., disfiguring), physical challenge (e.g., painful), and familiarity (e.g., common). Side effects perceived as affectively and physically challenging elicited the highest levels of aversiveness across all 4 measures. Understanding what side effect characteristics are most aversive may inform interventions to improve medical decisions and facilitate the translation of novel biomedical therapies into clinical practice.

Consumers mediate the effects of experimental ocean acidification and warming on primary producers.

PubMed

Alsterberg, Christian; Eklöf, Johan S; Gamfeldt, Lars; Havenhand, Jonathan N; Sundbäck, Kristina

2013-05-21

It is well known that ocean acidification can have profound impacts on marine organisms. However, we know little about the direct and indirect effects of ocean acidification and also how these effects interact with other features of environmental change such as warming and declining consumer pressure. In this study, we tested whether the presence of consumers (invertebrate mesograzers) influenced the interactive effects of ocean acidification and warming on benthic microalgae in a seagrass community mesocosm experiment. Net effects of acidification and warming on benthic microalgal biomass and production, as assessed by analysis of variance, were relatively weak regardless of grazer presence. However, partitioning these net effects into direct and indirect effects using structural equation modeling revealed several strong relationships. In the absence of grazers, benthic microalgae were negatively and indirectly affected by sediment-associated microalgal grazers and macroalgal shading, but directly and positively affected by acidification and warming. Combining indirect and direct effects yielded no or weak net effects. In the presence of grazers, almost all direct and indirect climate effects were nonsignificant. Our analyses highlight that (i) indirect effects of climate change may be at least as strong as direct effects, (ii) grazers are crucial in mediating these effects, and (iii) effects of ocean acidification may be apparent only through indirect effects and in combination with other variables (e.g., warming). These findings highlight the importance of experimental designs and statistical analyses that allow us to separate and quantify the direct and indirect effects of multiple climate variables on natural communities.

Side Effect Perceptions and their Impact on Treatment Decisions in Women

PubMed Central

Waters, Erika A.; Pachur, Thorsten; Colditz, Graham A.

2016-01-01

Background Side effects prompt some patients to forego otherwise-beneficial therapies. This study explored which characteristics make side effects particularly aversive. Methods We used a psychometric approach, originating from research on risk perception, to identify the factors (or components) underlying side effect perceptions. Women (N=149) aged 40–74 were recruited from a patient registry to complete an online experiment. Participants were presented with hypothetical scenarios in which an effective and necessary medication conferred a small risk of a single side effect (e.g., nausea, dizziness). They rated a broad range of side effects on several characteristics (e.g., embarrassing, treatable). In addition, we collected four measures of aversiveness for each side effect: choosing to take the medication, willingness to pay to avoid the side effect (WTP), negative affective attitude associated with the side effect, and how each side effect ranks among others in terms of undesirability. A principle-components analysis (PCA) was used to identify the components underlying side effect perceptions. Then, for each aversiveness measure separately, regression analyses were used to determine which components predicted differences in aversiveness among the side effects. Results The PCA revealed four components underlying side effect perceptions: affective challenge (e.g., frightening), social challenge (e.g., disfiguring), physical challenge (e.g., painful), and familiarity (e.g., common). Side effects perceived as affectively and physically challenging elicited the highest levels of aversiveness across all four measures. Conclusions Understanding what side effect characteristics are most aversive may inform interventions to improve medical decisions and facilitate the translation of novel biomedical therapies into clinical practice. PMID:27216581

Molecular and Clinical Effects of Green Tea and Fermented Papaya Preparation on Diabetes and Cardiovascular Diseases

ClinicalTrials.gov

2014-11-14

Assess the Effect of Green Tea on Diabetes; Assess the Effect of Fermented Papaya Pretration on Diabetes; Effects of Green Tea and FPP on C-reactive Proteins; Effects of Green Tea and FPP of Lipid Profiles in Diabetes; Effect of Green Tea and FPP on Atheroma Formation

Separating Gender Composition Effects from Peer Effects in Education

ERIC Educational Resources Information Center

Jahanshahi, Babak

2017-01-01

This paper aims to demonstrate the importance of controlling for endogenous peer effects in estimating the influence of gender peer effects on educational outcomes. Using Manski's linear-in-means model, this paper illustrates that the estimation of gender peer effects is potentially biased in the presence of endogenous peer effect in education.…

Time-Indexed Effect Size for P-12 Reading and Math Program Evaluation

ERIC Educational Resources Information Center

Lee, Jaekyung; Finn, Jeremy; Liu, Xiaoyan

2012-01-01

This study contextualizes an effect-size-like index of educational treatment effects or any group mean differences in academic achievement by referencing time. The new effect size metric can enrich effect size interpretations while serving as a supplement (but not substitute) for conventional standardized effect size measures. Specifically, the…

Calculating and reporting effect sizes to facilitate cumulative science: a practical primer for t-tests and ANOVAs

PubMed Central

Lakens, Daniël

2013-01-01

Effect sizes are the most important outcome of empirical studies. Most articles on effect sizes highlight their importance to communicate the practical significance of results. For scientists themselves, effect sizes are most useful because they facilitate cumulative science. Effect sizes can be used to determine the sample size for follow-up studies, or examining effects across studies. This article aims to provide a practical primer on how to calculate and report effect sizes for t-tests and ANOVA's such that effect sizes can be used in a-priori power analyses and meta-analyses. Whereas many articles about effect sizes focus on between-subjects designs and address within-subjects designs only briefly, I provide a detailed overview of the similarities and differences between within- and between-subjects designs. I suggest that some research questions in experimental psychology examine inherently intra-individual effects, which makes effect sizes that incorporate the correlation between measures the best summary of the results. Finally, a supplementary spreadsheet is provided to make it as easy as possible for researchers to incorporate effect size calculations into their workflow. PMID:24324449

Cognitive effects of two nutraceuticals Ginseng and Bacopa benchmarked against modafinil: a review and comparison of effect sizes

PubMed Central

Neale, Chris; Camfield, David; Reay, Jonathon; Stough, Con; Scholey, Andrew

2013-01-01

Over recent years there has been increasing research into both pharmaceutical and nutraceutical cognition enhancers. Here we aimed to calculate the effect sizes of positive cognitive effect of the pharmaceutical modafinil in order to benchmark the effect of two widely used nutraceuticals Ginseng and Bacopa (which have consistent acute and chronic cognitive effects, respectively). A search strategy was implemented to capture clinical studies into the neurocognitive effects of modafinil, Ginseng and Bacopa. Studies undertaken on healthy human subjects using a double‐blind, placebo‐controlled design were included. For each study where appropriate data were included, effect sizes (Cohen's d) were calculated for measures showing significant positive and negative effects of treatment over placebo. The highest effect sizes for cognitive outcomes were 0.77 for modafinil (visuospatial memory accuracy), 0.86 for Ginseng (simple reaction time) and 0.95 for Bacopa (delayed word recall). These data confirm that neurocognitive enhancement from well characterized nutraceuticals can produce cognition enhancing effects of similar magnitude to those from pharmaceutical interventions. Future research should compare these effects directly in clinical trials. PMID:23043278

Inverse target- and cue-priming effects of masked stimuli.

PubMed

Mattler, Uwe

2007-02-01

The processing of a visual target that follows a briefly presented prime stimulus can be facilitated if prime and target stimuli are similar. In contrast to these positive priming effects, inverse priming effects (or negative compatibility effects) have been found when a mask follows prime stimuli before the target stimulus is presented: Responses are facilitated after dissimilar primes. Previous studies on inverse priming effects examined target-priming effects, which arise when the prime and the target stimuli share features that are critical for the response decision. In contrast, 3 experiments of the present study demonstrate inverse priming effects in a nonmotor cue-priming paradigm. Inverse cue-priming effects exhibited time courses comparable to inverse target-priming effects. Results suggest that inverse priming effects do not arise from specific processes of the response system but follow from operations that are more general.

Exploring Modality Compatibility in the Response-Effect Compatibility Paradigm.

PubMed

Földes, Noémi; Philipp, Andrea M; Badets, Arnaud; Koch, Iring

2017-01-01

According to ideomotor theory , action planning is based on anticipatory perceptual representations of action-effects. This aspect of action control has been investigated in studies using the response-effect compatibility (REC) paradigm, in which responses have been shown to be facilitated if ensuing perceptual effects share codes with the response based on dimensional overlap (i.e., REC). Additionally, according to the notion of ideomotor compatibility, certain response-effect (R-E) mappings will be stronger than others because some response features resemble the anticipated sensory response effects more strongly than others (e.g., since vocal responses usually produce auditory effects, an auditory stimulus should be anticipated in a stronger manner following vocal responses rather than following manual responses). Yet, systematic research on this matter is lacking. In the present study, two REC experiments aimed to explore the influence of R-E modality mappings. In Experiment 1, vocal number word responses produced visual effects on the screen (digits vs. number words; i.e., visual-symbolic vs. visual-verbal effect codes). The REC effect was only marginally larger for visual-verbal than for visual-symbolic effects. Using verbal effect codes in Experiment 2, we found that the REC effect was larger with auditory-verbal R-E mapping than with visual-verbal R-E mapping. Overall, the findings support the hypothesis of a role of R-E modality mappings in REC effects, suggesting both further evidence for ideomotor accounts as well as code-specific and modality-specific contributions to effect anticipation.

Alcoholics Anonymous Effectiveness: Faith Meets Science

PubMed Central

Kaskutas, Lee Ann

2009-01-01

Research on the effectiveness of Alcoholics Anonymous (AA) is controversial and is subject to widely divergent interpretations. The goal of this paper is to provide a focused review of the literature on AA effectiveness that will allow readers to judge the evidence for AA effectiveness themselves. The review organizes the research on AA effectiveness according to six criterion required for establishing causation: (1) magnitude of effect; (2) dose response effect; (3) consistent effect; (4) temporally accurate effects; (5) specific effects; (6) plausibility. The evidence for criteria 1, 2, 3, 4 and 6 is very strong: Rates of abstinence are about twice as high among those who attend AA (criteria 1, magnitude); higher levels of attendance are related to higher rates of abstinence (criteria 2, dose-response); these relationships are found for different samples and follow-up periods (criteria 3, consistency); prior AA attendance is predictive of subsequent abstinence (criteria 4, temporal); and mechanisms of action predicted by theories of behavior change are present in AA (criteria 6, plausibility). However, rigorous experimental evidence establishing the specificity of an effect for AA or Twelve Step Facilitation/TSF (criteria 5) is mixed, with 2 trials finding a positive effect for AA, 1 trial finding a negative effect for AA, and 1 trial finding a null effect. Studies addressing specificity using statistical approaches have had two contradictory findings, and two that reported significant effects for AA after adjusting for potential confounders such as motivation to change. PMID:19340677

A multilevel model of organizational health culture and the effectiveness of health promotion.

PubMed

Lin, Yea-Wen; Lin, Yueh-Ysen

2014-01-01

Organizational health culture is a health-oriented core characteristic of the organization that is shared by all members. It is effective in regulating health-related behavior for employees and could therefore influence the effectiveness of health promotion efforts among organizations and employees. This study applied a multilevel analysis to verify the effects of organizational health culture on the organizational and individual effectiveness of health promotion. At the organizational level, we investigated the effect of organizational health culture on the organizational effectiveness of health promotion. At the individual level, we adopted a cross-level analysis to determine if organizational health culture affects employee effectiveness through the mediating effect of employee health behavior. The study setting consisted of the workplaces of various enterprises. We selected 54 enterprises in Taiwan and surveyed 20 full-time employees from each organization, for a total sample of 1011 employees. We developed the Organizational Health Culture Scale to measure employee perceptions and aggregated the individual data to formulate organization-level data. Organizational effectiveness of health promotion included four dimensions: planning effectiveness, production, outcome, and quality, which were measured by scale or objective indicators. The Health Promotion Lifestyle Scale was adopted for the measurement of health behavior. Employee effectiveness was measured subjectively in three dimensions: self-evaluated performance, altruism, and happiness. Following the calculation of descriptive statistics, hierarchical linear modeling (HLM) was used to test the multilevel hypotheses. Organizational health culture had a significant effect on the planning effectiveness (β = .356, p < .05) and production (β = .359, p < .05) of health promotion. In addition, results of cross-level moderating effect analysis by HLM demonstrated that the effects of organizational health culture on three dimensions of employee effectiveness were completely mediated by health behavior. The construct connections established in this multilevel model will help in the construction of health promotion theories. The findings remind business executives that organizational health culture and employee health behavior help improve employee effectiveness.

Potential effectiveness of anti-smoking advertisement types in ten low and middle income countries: do demographics, smoking characteristics and cultural differences matter?

PubMed

Durkin, Sarah; Bayly, Megan; Cotter, Trish; Mullin, Sandra; Wakefield, Melanie

2013-12-01

Unlike high income countries, there is limited research to guide selection of anti-tobacco mass media campaigns in low and middle income countries, although some work suggests that messages emphasizing serious health harms perform better than other message types. This study aimed to determine whether certain types of anti-smoking advertisements are more likely to be accepted and perceived as effective across smokers in 10 low to middle income countries. 2399 18-34 year old smokers were recruited in Bangladesh, China, Egypt, India, Indonesia, Mexico, Philippines, Russia, Turkey and Vietnam to view and rate 10 anti-tobacco ads. Five ads were shown in all countries and five ads were chosen by country representatives, providing a total of 37 anti-smoking ads across all countries (10 graphic health effects ads, 6 simulated health effects, 8 emotional stories of health effects, 7 other health effects and 6 non-health effects). Smokers rated ads on a series of 5-point scales containing aggregated measures of Message Acceptance and Perceived Effectiveness. All ads and materials were translated into the local language of the testing regions. In multivariate analysis, graphic health effects ads were most likely to be accepted and perceived as effective, followed by simulated health effects ads, health effects stories, other health effects ads, and then non-health effects ads. Interaction analyses indicated that graphic health effects ads were less likely to differ in acceptance or perceived effectiveness across countries, gender, age, education, parental status and amount smoked, and were less likely to be affected by cultural differences between characters and contexts in ads and those within each country. Ads that did not emphasize the health effects of smoking were most prone to inconsistent impact across countries and population subgroups. Graphic ads about the negative health effects of smoking may be most suitable for wide population broadcast in low and middle income countries. Copyright © 2013 Elsevier Ltd. All rights reserved.

Geographical Variations in the Interaction of Relative Age Effects in Youth and Adult Elite Soccer.

PubMed

Steingröver, Christina; Wattie, Nick; Baker, Joseph; Helsen, Werner F; Schorer, Jörg

2017-01-01

Selection biases based on the use of cut-off dates and the timing of athletes' birthdates have been termed relative age effects. These effects have been shown to differentially affect individuals involved in sport. For example, young male soccer players born early in their age group are overrepresented in elite teams while studies in adult soccer indicated potential carry-over effects from talent development systems. This two-study approach focuses on the processes within multi-year age groups in youth and adult elite soccer and on the role of players' age position within the age band with regard to players' birth year and birth month. Study 1 tests for an interaction of two different types of relative age effects among data from participants in the last five Under-17 FIFA World Cups (2007-2015). Analyses revealed a significant global within-year effect and varying birthdate distributions were found between confederations. Even stronger effects were found for constituent year effects. For the total sample, a multi-way frequency analysis (MFA) revealed an interaction with a pattern of a stronger within-year effect for the younger year group. This study highlights the need to consider interactions between different types of age effects. The main aim of Study 2 was to test for carry-over effects from previously found constituent year effects among players participating in the 2014 soccer World Cup and, therefore, to test for long-term effects of age grouping structures used during earlier stages of talent development. A secondary purpose of this study was to replicate findings on the existence of within-year effects and to test whether effects vary between continental confederations. No significant interaction between constituent year and within-year effects was shown by the MFA among the World Cup sample and previous findings on varying within-year effects were replicated. Results indicate that long-term effects of age grouping structures in earlier high-level talent development structures exist.

Weak trophic links between a crab-spider and the effective pollinators of a rewardless orchid

NASA Astrophysics Data System (ADS)

Quintero, Carolina; Corley, Juan C.; Aizen, Marcelo A.

2015-01-01

Sit and wait predators hunting on flowers are considered to be exploiters of plant-pollinator mutualisms. Several studies have shown that plant-pollinator interactions can be highly susceptible to the impact of a third trophic level, via consumptive (direct) and non-consumptive (indirect) effects that alter pollinator behavior and, ultimately, plant fitness. However, most flowering plants attract a wide array of flower visitors, from which only a subset will be effective pollinators. Hence, a negative effect of an ambush predator on plant fitness should be expected only when: (i) the effective pollinators are part of the predators' diet and/or (ii) the non-consumptive effects of predator presence (e.g. dead prey) alter the behavior of effective pollinators and pollen movement among individual plants. We analyzed the direct and indirect effects of a crab-spider (Misumenops pallidus), on the pollination and reproductive success of Chloraea alpina, a Patagonian rewardless orchid. Our results indicate that most of the flower visitors do not behave as effective pollinators and most effective pollinators were not observed as prey for the crab-spider. In terms of non-consumptive effects, inflorescences with and without spiders and/or dead-prey did not vary the frequency of flower visitors, nor pollinia removal or deposition. Hence, it is not surprising that M. pallidus has a neutral effect on pollinia removal and deposition as well as on fruit and seed set. Similar to other rewardless orchids, the low reproductive success of C. alpina (∼6% fruit set) was associated with the limited number of visits by effective pollinators. Negative top-down effects of a flower-visitor predator on plant pollination may not be anticipated without studying the direct and indirect effects of this predator on the effective pollinators. In pollination systems where effective pollinators visited flowers erratically, such as in deceptive orchids, we expect weak or no effect of predators on plant fitness.

Geographical Variations in the Interaction of Relative Age Effects in Youth and Adult Elite Soccer

PubMed Central

Steingröver, Christina; Wattie, Nick; Baker, Joseph; Helsen, Werner F.; Schorer, Jörg

2017-01-01

Selection biases based on the use of cut-off dates and the timing of athletes’ birthdates have been termed relative age effects. These effects have been shown to differentially affect individuals involved in sport. For example, young male soccer players born early in their age group are overrepresented in elite teams while studies in adult soccer indicated potential carry-over effects from talent development systems. This two-study approach focuses on the processes within multi-year age groups in youth and adult elite soccer and on the role of players’ age position within the age band with regard to players’ birth year and birth month. Study 1 tests for an interaction of two different types of relative age effects among data from participants in the last five Under-17 FIFA World Cups (2007–2015). Analyses revealed a significant global within-year effect and varying birthdate distributions were found between confederations. Even stronger effects were found for constituent year effects. For the total sample, a multi-way frequency analysis (MFA) revealed an interaction with a pattern of a stronger within-year effect for the younger year group. This study highlights the need to consider interactions between different types of age effects. The main aim of Study 2 was to test for carry-over effects from previously found constituent year effects among players participating in the 2014 soccer World Cup and, therefore, to test for long-term effects of age grouping structures used during earlier stages of talent development. A secondary purpose of this study was to replicate findings on the existence of within-year effects and to test whether effects vary between continental confederations. No significant interaction between constituent year and within-year effects was shown by the MFA among the World Cup sample and previous findings on varying within-year effects were replicated. Results indicate that long-term effects of age grouping structures in earlier high-level talent development structures exist. PMID:28326044

The pros and cons of masked priming.

PubMed

Forster, K I

1998-03-01

Masked priming paradigms offer the promise of tapping automatic, strategy-free lexical processing, as evidenced by the lack of expectancy disconfirmation effects, and proportionality effects in semantic priming experiments. But several recent findings suggest the effects may be prelexical. These findings concern nonword priming effects in lexical decision and naming, the effects of mixed-case presentation on nonword priming, and the dependence of priming on the nature of the distractors in lexical decision, suggesting possible strategy effects. The theory underlying each of these effects is discussed, and alternative explanations are developed that do not preclude a lexical basis for masked priming effects.

Side effects associated with anti-HIV drugs.

PubMed

Highleyman, L

1998-04-01

Many side effects are associated with the use of anti-HIV drugs, impacting the development of drug resistance and the quality of life for HIV-patients. Concern about side effects is a primary factor in deterring people from beginning HIV therapy. Frequency and severity of side effects vary greatly, but they are frequently more common and severe in people who are taking a new drug or who have advanced HIV disease. Information on side effects comes largely from clinical trials; however, many side effects are not discovered until the drug has been approved and used by larger numbers of people. Side effects vary from serious toxicities that require stopping treatment to uncomfortable or annoying side effects that interfere with daily life. A table categorizes the four major side effects (nausea, fever, skin rash, and fatigue) and divides them into grades that describe their intensity. A chart lists the side effects associated with specific anti-HIV drugs. Suggestions for managing side effects are included.

Nocebo Effects and Scratching Behaviour in Itch.

PubMed

Bartels, Danielle J P; van Laarhoven, Antoinette I M; van de Kerkhof, Peter C M; Evers, Andrea W M

2018-06-01

Nocebo effects, i.e. reduced treatment effects due to patients' negative expectations, play a role in itch. Recent studies have shown that nocebo effects can be induced experimentally in itch and even be reversed into the placebo effect. It is not known whether these effects generalize to itch-associated scratching behaviour. The aim of this study was to determine whether induction and reversion of nocebo effects in itch evoked by electrical and histamine stimuli generalized to scratching. Ninety-seven healthy participants were recruited to the study. The manipulation was successful, as during the nocebo learning phase, increased scratching responses were found for higher intensity compared with lower intensity itch stimuli. During the testing phase of induction or reversion of the nocebo effect, however, no significant nocebo effects or reversed nocebo effects, were found in scratching. Thus, no straightforward generalization of nocebo effects from itch to scratching was found in this laboratory setting. Further investigation into possible generalization is needed in different settings and in patients with chronic itch.

A Three-way Decomposition of a Total Effect into Direct, Indirect, and Interactive Effects

PubMed Central

VanderWeele, Tyler J.

2013-01-01

Recent theory in causal inference has provided concepts for mediation analysis and effect decomposition that allow one to decompose a total effect into a direct and an indirect effect. Here, it is shown that what is often taken as an indirect effect can in fact be further decomposed into a “pure” indirect effect and a mediated interactive effect, thus yielding a three-way decomposition of a total effect (direct, indirect, and interactive). This three-way decomposition applies to difference scales and also to additive ratio scales and additive hazard scales. Assumptions needed for the identification of each of these three effects are discussed and simple formulae are given for each when regression models allowing for interaction are used. The three-way decomposition is illustrated by examples from genetic and perinatal epidemiology, and discussion is given to what is gained over the traditional two-way decomposition into simply a direct and an indirect effect. PMID:23354283

[Effects decomposition in mediation analysis: a numerical example].

PubMed

Zugna, Daniela; Richiardi, Lorenzo

2018-01-01

Mediation analysis aims to decompose the total effect of the exposure on the outcome into a direct effect (unmediated) and an indirect effect (mediated by a mediator). When the interest also lies on understanding whether the exposure effect differs in different sub-groups of study population or under different scenarios, the mediation analysis needs to be integrated with interaction analysis. In this setting it is necessary to decompose the total effect not only into two components, the direct and indirect effects, but other two components linked to interaction. The interaction between the exposure and the mediator in their effect on the outcome could indeed act through the effect of the exposure on the mediator or through the mediator when the mediator is not totally explained by the exposure. We describe options for decomposition, proposed in literature, of the total effect and we illustrate them through a hypothetical example of the effect of age at diagnosis of cancer on survival, mediated and unmediated by the therapeutical approach, and a numerical example.

[Effects of nurses' perception of servant leadership on leader effectiveness, satisfaction and additional effort: focused on the mediating effects of leader trust and value congruence].

PubMed

Han, Sang Sook; Kim, Nam Eun

2012-02-01

This study was done to examine the effects of nurses' perception of servant leadership on leader effectiveness, satisfaction and promoting additional effort. The focus was the mediating effects of leader trust and value congruence. Data were collected from 361 RN-BSN students and nurses participating in nationally attended in-service training programs. Data were analyzed using descriptive statistics and structural analysis with SPSS 17.0 windows program and Amos 7.0. Direct effects of nurses' perception of servant leadership were negative, but mediating effects of trust and value congruency were positively correlated with leader effectiveness, satisfaction and additional effort, that is servant leadership should be effective through mediating factors. The study results indicate that if the middle managers of nurses can build leader trust and value congruency between nurses through servant leadership, leader effectiveness, satisfaction and additional effort on the part of the nurses could result in a positive change in the long term.

Estimating linear effects in ANOVA designs: the easy way.

PubMed

Pinhas, Michal; Tzelgov, Joseph; Ganor-Stern, Dana

2012-09-01

Research in cognitive science has documented numerous phenomena that are approximated by linear relationships. In the domain of numerical cognition, the use of linear regression for estimating linear effects (e.g., distance and SNARC effects) became common following Fias, Brysbaert, Geypens, and d'Ydewalle's (1996) study on the SNARC effect. While their work has become the model for analyzing linear effects in the field, it requires statistical analysis of individual participants and does not provide measures of the proportions of variability accounted for (cf. Lorch & Myers, 1990). In the present methodological note, using both the distance and SNARC effects as examples, we demonstrate how linear effects can be estimated in a simple way within the framework of repeated measures analysis of variance. This method allows for estimating effect sizes in terms of both slope and proportions of variability accounted for. Finally, we show that our method can easily be extended to estimate linear interaction effects, not just linear effects calculated as main effects.

X-Ray Irradiation Effects in Top Contact, Pentacene Based Field Effect Transistors for Space Related Applications

DTIC Science & Technology

2006-01-01

Journal Article POSTPRINT 3. DATES COVERED (From - To) 2006 4. TITLE AND SUBTITLE X-ray irradiation effects in top contact, pentacene based field 5a...Preliminary studies of the effect of x-ray irradiation, typically used to simulate radiation effects in space, on top contract, pentacene based field effect...irradiation, radiation, radiation effects, pentacene 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 19a. NAME OF

Interactions among resource partitioning, sampling effect, and facilitation on the biodiversity effect: a modeling approach.

PubMed

Flombaum, Pedro; Sala, Osvaldo E; Rastetter, Edward B

2014-02-01

Resource partitioning, facilitation, and sampling effect are the three mechanisms behind the biodiversity effect, which is depicted usually as the effect of plant-species richness on aboveground net primary production. These mechanisms operate simultaneously but their relative importance and interactions are difficult to unravel experimentally. Thus, niche differentiation and facilitation have been lumped together and separated from the sampling effect. Here, we propose three hypotheses about interactions among the three mechanisms and test them using a simulation model. The model simulated water movement through soil and vegetation, and net primary production mimicking the Patagonian steppe. Using the model, we created grass and shrub monocultures and mixtures, controlled root overlap and grass water-use efficiency (WUE) to simulate gradients of biodiversity, resource partitioning and facilitation. The presence of shrubs facilitated grass growth by increasing its WUE and in turn increased the sampling effect, whereas root overlap (resource partitioning) had, on average, no effect on sampling effect. Interestingly, resource partitioning and facilitation interacted so the effect of facilitation on sampling effect decreased as resource partitioning increased. Sampling effect was enhanced by the difference between the two functional groups in their efficiency in using resources. Morphological and physiological differences make one group outperform the other; once these differences were established further differences did not enhance the sampling effect. In addition, grass WUE and root overlap positively influence the biodiversity effect but showed no interactions.

Wind-Tunnel Investigation of a Full-Scale Canard-Configured General Aviation Airplane

NASA Technical Reports Server (NTRS)

Yip, L. P.

1985-01-01

An investigation was conducted in the Langley 30- by 60-Foot Tunnel to determine the aerodynamic characteristics of a powered, full-scale model of a general aviation airplane employing a canard. Although primary emphasis of the investigation was placed on evaluating the aerodynamic performance and the stability and control characteristics of the basic configuration, tests were also conducted to study the following effects of varying the basic configuration: effect of Reynolds number; effect of canard; effect of outboard wing leading-edge droop; effect of center-of-gravity location; effect of elevator trim; effect of landing gear; effect of lateral-directional control; effect of power; effect of fixed transition; effect of water spray; effects of canard incidence, canard airfoil section, and canard position; and effects of winglets and upper winglet size. Additional aspects of the study were to determine the boundary-layer transition characteristics of airfoil surfaces and the effect of fixing the boundary layer to be turbulent by means of a transition strip near the leading edge. The tests were conducted at Reynolds numbers from 0.60 x 10 to the 6th power to 2.25x10 to the 6th power, based on the wing mean aerodynamic chord, at angles of attack from -4.5 deg to 41.5 deg, and at angles of sideslip from -15 deg to 15 deg.

Planning, Execution, and Assessment of Effects-Based Operations (EBO)

DTIC Science & Technology

2006-05-01

time of execution that would maximize the likelihood of achieving a desired effect. GMU has developed a methodology, named ECAD -EA (Effective...Algorithm EBO Effects Based Operations ECAD -EA Effective Course of Action-Evolutionary Algorithm GMU George Mason University GUI Graphical...Probability Profile Generation ........................................................72 A.2.11 Running ECAD -EA (Effective Courses of Action Determination

RF verification tasks underway at the Harris Corporation for multiple aperture reflector system

NASA Technical Reports Server (NTRS)

Gutwein, T. A.

1982-01-01

Mesh effects on gain and patterns and adjacent aperture coupling effects for "pie" and circular apertures are discussed. Wire effects for Harris model with Langley scale model results included for assessing D/lamda effects, and wire effects with adjacent aperture coupling were determined. Reflector surface distortion effects (pillows and manufacturing roughness) were studied.

School Effectiveness at Primary Level of Education in Relation to Classroom Teaching

ERIC Educational Resources Information Center

Panigrahi, Manas Ranjan

2014-01-01

The study aims to investigate the relationship of School Effectiveness with regard to classroom teaching at primary level of education. The objectives of the study were to identify the more-effective and less-effective schools; to find out the differences between more-effective and less-effective schools in relation to physical facilities, Head…

Effects and Side Effects of Flemish School Inspection

ERIC Educational Resources Information Center

Penninckx, Maarten; Vanhoof, Jan; De Maeyer, Sven; Van Petegem, Peter

2016-01-01

Despite the increased importance of school inspection in recent years, the current knowledge base does not provide a clear view on the effects and side effects of being inspected. More evidence is needed in more diverse educational contexts. This article responds to this need with a quantitative study on the effects and side effects of school…

47 CFR 1.427 - Effective date of rules.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 1 2011-10-01 2011-10-01 false Effective date of rules. 1.427 Section 1.427... Proceedings § 1.427 Effective date of rules. (a) Any rule issued by the Commission will be made effective not... the date on which the rule becomes effective, the effective date shall be 30 days after the date on...

Stress, Coping and Coffee Consumption

DTIC Science & Technology

1991-08-30

Henry and Stephens (1980) have found evidence for this role for caffeine as an intensifier for stress effects on plasma renin, corticosterone , and...have learned a lot. Vll TABLE OF CONTENTS Introduction Stress, coping and perceived control Stress Coping Perceived control Effects of caffeine...Central nervous system effects of caffeine Mood effects of caffeine Health effects of caffeine cardiovascular effects caffeine and

Nonclassical Properties of Q-Deformed Superposition Light Field State

NASA Technical Reports Server (NTRS)

Ren, Min; Shenggui, Wang; Ma, Aiqun; Jiang, Zhuohong

1996-01-01

In this paper, the squeezing effect, the bunching effect and the anti-bunching effect of the superposition light field state which involving q-deformation vacuum state and q-Glauber coherent state are studied, the controllable q-parameter of the squeezing effect, the bunching effect and the anti-bunching effect of q-deformed superposition light field state are obtained.

36 CFR 1258.16 - Effective date.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Effective date. 1258.16... AVAILABILITY AND USE FEES § 1258.16 Effective date. The fees in this part are effective on October 1, 2007. If your order was received by NARA before this effective date, we will charge the fees in effect at the...

36 CFR 1258.16 - Effective date.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 36 Parks, Forests, and Public Property 3 2011-07-01 2011-07-01 false Effective date. 1258.16... AVAILABILITY AND USE FEES § 1258.16 Effective date. The fees in this part are effective on October 1, 2007. If your order was received by NARA before this effective date, we will charge the fees in effect at the...

17 CFR 230.486 - Effective date of post-effective amendments and registration statements filed by certain closed...

Code of Federal Regulations, 2013 CFR

2013-04-01

... 17 Commodity and Securities Exchanges 2 2013-04-01 2013-04-01 false Effective date of post....486 Effective date of post-effective amendments and registration statements filed by certain closed... section, a post-effective amendment to a registration statement, or a registration statement filed for the...

17 CFR 230.486 - Effective date of post-effective amendments and registration statements filed by certain closed...

Code of Federal Regulations, 2012 CFR

2012-04-01

... 17 Commodity and Securities Exchanges 2 2012-04-01 2012-04-01 false Effective date of post....486 Effective date of post-effective amendments and registration statements filed by certain closed... section, a post-effective amendment to a registration statement, or a registration statement filed for the...

17 CFR 230.486 - Effective date of post-effective amendments and registration statements filed by certain closed...

Code of Federal Regulations, 2014 CFR

2014-04-01

... 17 Commodity and Securities Exchanges 3 2014-04-01 2014-04-01 false Effective date of post....486 Effective date of post-effective amendments and registration statements filed by certain closed... section, a post-effective amendment to a registration statement, or a registration statement filed for the...

17 CFR 230.486 - Effective date of post-effective amendments and registration statements filed by certain closed...

Code of Federal Regulations, 2011 CFR

2011-04-01

... 17 Commodity and Securities Exchanges 2 2011-04-01 2011-04-01 false Effective date of post....486 Effective date of post-effective amendments and registration statements filed by certain closed... section, a post-effective amendment to a registration statement, or a registration statement filed for the...

17 CFR 230.485 - Effective date of post-effective amendments filed by certain registered investment companies.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 17 Commodity and Securities Exchanges 2 2011-04-01 2011-04-01 false Effective date of post... Investment Companies; Business Development Companies § 230.485 Effective date of post-effective amendments... provided in this section, a post-effective amendment to a registration statement filed by a registered open...

17 CFR 230.485 - Effective date of post-effective amendments filed by certain registered investment companies.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 17 Commodity and Securities Exchanges 2 2012-04-01 2012-04-01 false Effective date of post... Investment Companies; Business Development Companies § 230.485 Effective date of post-effective amendments... provided in this section, a post-effective amendment to a registration statement filed by a registered open...

[Comprehensive analysis on "toxicity and effect" of Chinese pharmaceutical preparations].

PubMed

Hu, Hui-Ling; Fu, Chao-Mei; Zhao, Xuan; Zhang, Jin-Ming; Gao, Fei; He, Yao; Fu, Shu; Li, Ling

2016-09-01

The manufacturing process of Chinese medicines is the significant link to achieve "effect-enhancing and toxicity-reducing", including an interaction between "toxicity and effect". This paper would elucidate the effects of Chinese herbal compound decoction, preparation, dosage forms, route of administration and quality of pharmaceutical excipients on "toxicity-effect" theory from the formulation approaches. The article pointed out that the comprehensive analysis on "toxicity-effect" theory should be strengthened from the aspects of overall manufacturing, fundamental research and modern Chinese preparation, to explore the mechanism of "effect-enhancing and toxicity-reducing" in the manufacturing process, clarify the core status of Chinese preparation in "toxicity-effect" theory, and ensure the security and effectiveness in traditional Chinese medicine clinical application. Copyright© by the Chinese Pharmaceutical Association.

Optically Tunable Magnetoresistance Effect: From Mechanism to Novel Device Application.

PubMed

Liu, Pan; Lin, Xiaoyang; Xu, Yong; Zhang, Boyu; Si, Zhizhong; Cao, Kaihua; Wei, Jiaqi; Zhao, Weisheng

2017-12-28

The magnetoresistance effect in sandwiched structure describes the appreciable magnetoresistance effect of a device with a stacking of two ferromagnetic layers separated by a non-magnetic layer (i.e., a sandwiched structure). The development of this effect has led to the revolution of memory applications during the past decades. In this review, we revisited the magnetoresistance effect and the interlayer exchange coupling (IEC) effect in magnetic sandwiched structures with a spacer layer of non-magnetic metal, semiconductor or organic thin film. We then discussed the optical modulation of this effect via different methods. Finally, we discuss various applications of these effects and present a perspective to realize ultralow-power, high-speed data writing and inter-chip connection based on this tunable magnetoresistance effect.

The electromagnetic wave energy effect(s) in microwave-assisted organic syntheses (MAOS).

PubMed

Horikoshi, Satoshi; Watanabe, Tomoki; Narita, Atsushi; Suzuki, Yumiko; Serpone, Nick

2018-03-26

Organic reactions driven by microwaves have been subjected for several years to some enigmatic phenomenon referred to as the microwave effect, an effect often mentioned in microwave chemistry but seldom understood. We identify this microwave effect as an electromagnetic wave effect that influences many chemical reactions. In this article, we demonstrate its existence using three different types of microwave generators with dissimilar oscillation characteristics. We show that this effect is operative in photocatalyzed TiO 2 reactions; it negatively influences electro-conductive catalyzed reactions, and yet has but a negligible effect on organic syntheses. The relationship between this electromagnetic wave effect and chemical reactions is elucidated from such energetic considerations as the photon energy and the reactions' activation energies.

A Novel Ontology Approach to Support Design for Reliability considering Environmental Effects

PubMed Central

Sun, Bo; Li, Yu; Ye, Tianyuan

2015-01-01

Environmental effects are not considered sufficiently in product design. Reliability problems caused by environmental effects are very prominent. This paper proposes a method to apply ontology approach in product design. During product reliability design and analysis, environmental effects knowledge reusing is achieved. First, the relationship of environmental effects and product reliability is analyzed. Then environmental effects ontology to describe environmental effects domain knowledge is designed. Related concepts of environmental effects are formally defined by using the ontology approach. This model can be applied to arrange environmental effects knowledge in different environments. Finally, rubber seals used in the subhumid acid rain environment are taken as an example to illustrate ontological model application on reliability design and analysis. PMID:25821857

A novel ontology approach to support design for reliability considering environmental effects.

PubMed

Sun, Bo; Li, Yu; Ye, Tianyuan; Ren, Yi

2015-01-01

Environmental effects are not considered sufficiently in product design. Reliability problems caused by environmental effects are very prominent. This paper proposes a method to apply ontology approach in product design. During product reliability design and analysis, environmental effects knowledge reusing is achieved. First, the relationship of environmental effects and product reliability is analyzed. Then environmental effects ontology to describe environmental effects domain knowledge is designed. Related concepts of environmental effects are formally defined by using the ontology approach. This model can be applied to arrange environmental effects knowledge in different environments. Finally, rubber seals used in the subhumid acid rain environment are taken as an example to illustrate ontological model application on reliability design and analysis.

Differential response of surface temperature and atmospheric temperature to the biogeophysical effects of deforestation

NASA Astrophysics Data System (ADS)

Winckler, J.; Reick, C. H.; Lejeune, Q.; Pongratz, J.

2017-12-01

Deforestation influences temperature locally by changing the water, energy and momentum balance. While most observation-based studies and some modeling studies focused on the effects on surface temperature, other studies focused on the effects on near-surface air temperature. However, these two variables may respond differently to deforestation because changes in albedo and surface roughness may alter the land-atmosphere coupling and thus the vertical temperature distribution. Thus it is unclear whether it is possible to compare studies that assess the impacts of deforestation on these two different variables. Here, we analyze the biogeophysical effects of global-scale deforestation in the climate model MPI-ESM separately for surface temperature, 2m-air temperature and temperature the lowest atmospheric model layer. We investigate why the response of these variables differs by isolating the effects of only changing surface albedo and only changing surface roughness and by separating effects that are induced at the location of deforestation (local effects) from effects that are induced by advection and changes in circulation (nonlocal effects). Concerning surface temperature, we find that the local effects of deforestation lead to a global mean warming which is overcompensated by the nonlocal effects (up to 0.1K local warming versus -0.3K nonlocal cooling). The surface warming in the local effects is largely driven by the change in surface roughness while the cooling in the nonlocal effects is largely driven by the change in surface albedo. The nonlocal effects are largely consistent across surface temperature, 2m-air temperature, and the temperature of the lowest atmospheric layer. However, the local effects strongly differ across the three considered variables. The local effects are strong for surface temperature, but substantially weaker in the 2m-air temperature and largely absent in the lowest atmospheric layer. We conclude that studies focusing on the deforestation effects on surface temperature should not be compared to studies focusing on the effects on air temperature. While the local effects on surface temperature are useful for model evaluation, they might be less relevant for local adaptation and mitigation than previously thought because they might largely be absent in the atmosphere.

A meta-analysis on the effectiveness of computer-assisted instruction in science education

NASA Astrophysics Data System (ADS)

Bayraktar, Sule

2000-10-01

The purposes of this study were to determine whether Computer-Assisted Instruction (CAI) had an overall positive effect on student achievement in secondary and college level science education when compared with traditional forms of instruction and to determine whether specific study or program characteristics were related to CAI effectiveness. This study employed a meta analytic research approach. First, the research studies comparing student achievement between CAI and traditional instruction in science were located by using electronic search databases. The search resulted in 42 studies producing 108 effect sizes. Second, the study features and effect sizes for each study were coded. Finally, the effect sizes provided from each study were combined to provide an overall effect size, and relationships between effect sizes and study features were then examined. The overall effect size was found to be 0.273 standard deviations, suggesting that CAI has a small positive effect on student achievement in science education at the college and secondary levels when compared with traditional forms of instruction. An effect size of 0.273 standard deviations indicates that an average student exposed to CAI exceeded the performance of 62% of the students who were taught by using traditional instructional methods. In other words, the typical student moved from the 50th percentile to the 62 nd percentile in science when CAI was used. All variables excluding school level and publication status were found to be related to effect sizes. According to the results of the analysis, CAI was most effective in physics education and had little effect on chemistry and biology achievement. Simulation and tutorial programs had significant effects on student achievement in science education but drill and practice was not found effective. The results also indicated that individual utilization of CAI was preferable. Another finding from the study is that experimenter-developed software was more effective than commercial, and that CAI was more effective than traditional instruction when the duration of treatment was shorter than 4 weeks. Furthermore, the results also indicated that the effectiveness of CAI in science subject areas decreased over the decades.

Decreasing the Burden of Side Effects Through Positive Message Framing: an Experimental Proof-of-Concept Study.

PubMed

Wilhelm, Marcel; Rief, Winfried; Doering, Bettina K

2018-05-21

Informing patients about treatment side effects increases the occurrence and intensity of side effects. Since the obligatory informed consent procedure in drug treatments requires transparency and nocebo research suggests that the informed consent of a drug leads to an increased occurrence of the mentioned side effects, the aim of this proof of concept study was to determine the effect of two different framings of informed consent on the occurrence, intensity, and perceived threat of side effects. Healthy male participants (n = 80) were randomized to one of two framing groups. The positive framing group was informed that the common side effect dizziness was a sign that the drug had started to work, while the neutral framing group was told that dizziness is an unpleasant but well-known side effect. Side effects were measured after the administration of metoprolol, an antihypertensive agent. Post hoc moderator analyses investigated the effect of pre-existing negative beliefs about the general harm of medication on the framing manipulation. Metoprolol-specific drug-attributed side effects were rated significantly less threatening in the positive framing group. The between-group effect size (Cohen's d) was small (d = 0.38, p = 0.049). Exploratory post hoc moderator analyses suggest that participants who believed that medication is a source of harmful effects benefited from positive framing, compared to neutral framing of drug-attributed side effects. Positive framing was partially effective in decreasing specific side effect measures, particularly among participants with a tendency to believe that medicine is harmful. Informed consent procedures should therefore be personalized, focusing on patients with negative treatment beliefs.

Task difficulty moderates the revelation effect.

PubMed

Aßfalg, André; Currie, Devon; Bernstein, Daniel M

2017-05-01

Tasks that precede a recognition probe induce a more liberal response criterion than do probes without tasks-the "revelation effect." For example, participants are more likely to claim that a stimulus is familiar directly after solving an anagram, relative to a condition without an anagram. Revelation effect hypotheses disagree whether hard preceding tasks should produce a larger revelation effect than easy preceding tasks. Although some studies have shown that hard tasks increase the revelation effect as compared to easy tasks, these studies suffered from a confound of task difficulty and task presence. Conversely, other studies have shown that the revelation effect is independent of task difficulty. In the present study, we used new task difficulty manipulations to test whether hard tasks produce larger revelation effects than easy tasks. Participants (N = 464) completed hard or easy preceding tasks, including anagrams (Exps. 1 and 2) and the typing of specific arrow key sequences (Exps. 3-6). With sample sizes typical of revelation effect experiments, the effect sizes of task difficulty on the revelation effect varied considerably across experiments. Despite this variability, a consistent data pattern emerged: Hard tasks produced larger revelation effects than easy tasks. Although the present study falsifies certain revelation effect hypotheses, the general vagueness of revelation effect hypotheses remains.

Anticipation of delayed action-effects: learning when an effect occurs, without knowing what this effect will be.

PubMed

Dignath, David; Janczyk, Markus

2017-09-01

According to the ideomotor principle, behavior is controlled via a retrieval of the sensory consequences that will follow from the respective movement ("action-effects"). These consequences include not only what will happen, but also when something will happen. In fact, recollecting the temporal duration between response and effect takes time and prolongs the initiation of the response. We investigated the associative structure of action-effect learning with delayed effects and asked whether participants acquire integrated action-time-effect episodes that comprise a compound of all three elements or whether they acquire separate traces that connect actions to the time until an effect occurs and actions to the effects that follow them. In three experiments, results showed that participants retrieve temporal intervals that follow from their actions even when the identity of the effect could not be learned. Furthermore, retrieval of temporal intervals in isolation was not inferior to retrieval of temporal intervals that were consistently followed by predictable action-effects. More specifically, when tested under extinction, retrieval of action-time and action-identity associations seems to compete against each other, similar to overshadowing effects reported for stimulus-response conditioning. Together, these results suggest that people anticipate when the consequences of their action will occur, independently from what the consequences will be.

The Portevin–Le Chatelier effect: a review of experimental findings

PubMed Central

Yilmaz, Ahmet

2011-01-01

The Portevin–Le Chatelier (PLC) effect manifests itself as an unstable plastic flow during tensile tests of some dilute alloys under certain regimes of strain rate and temperature. The plastic strain becomes localized in the form of bands which move along a specimen gauge in various ways as the PLC effect occurs. Because the localization of strain causes degradation of the inherent structural properties and surface quality of materials, understanding the effect is crucial for the effective use of alloys. The characteristic behaviors of localized strain bands and techniques commonly used to study the PLC effect are summarized in this review. A brief overview of experimental findings, the effect of material properties and test parameters on the PLC effect, and some discussion on the mechanisms of the effect are included. Tests for predicting the early failure of structural materials due to embrittlement induced by the PLC effect are also discussed. PMID:27877450

Age differences in perceptions of memory strategy effectiveness for recent and remote memory.

PubMed

Lineweaver, Tara T; Horhota, Michelle; Crumley, Jessica; Geanon, Catherine T; Juett, Jacqueline J

2018-03-01

We examined whether young and older adults hold different beliefs about the effectiveness of memory strategies for specific types of memory tasks and whether memory strategies are perceived to be differentially effective for young, middle-aged, and older targets. Participants rated the effectiveness of five memory strategies for 10 memory tasks at three target ages (20, 50, and 80 years old). Older adults did not strongly differentiate strategy effectiveness, viewing most strategies as similarly effective across memory tasks. Young adults held strategy-specific beliefs, endorsing external aids and physical health as more effective than a positive attitude or internal strategies, without substantial differentiation based on task. We also found differences in anticipated strategy effectiveness for targets of different ages. Older adults described cognitive and physical health strategies as more effective for older than middle-aged targets, whereas young adults expected these strategies to be equally effective for middle-aged and older target adults.

The Effect of Cognitive Control on Different Types of Auditory Distraction.

PubMed

Bell, Raoul; Röer, Jan P; Marsh, John E; Storch, Dunja; Buchner, Axel

2017-09-01

Deviant as well as changing auditory distractors interfere with short-term memory. According to the duplex model of auditory distraction, the deviation effect is caused by a shift of attention while the changing-state effect is due to obligatory order processing. This theory predicts that foreknowledge should reduce the deviation effect, but should have no effect on the changing-state effect. We compared the effect of foreknowledge on the two phenomena directly within the same experiment. In a pilot study, specific foreknowledge was impotent in reducing either the changing-state effect or the deviation effect, but it reduced disruption by sentential speech, suggesting that the effects of foreknowledge on auditory distraction may increase with the complexity of the stimulus material. Given the unexpected nature of this finding, we tested whether the same finding would be obtained in (a) a direct preregistered replication in Germany and (b) an additional replication with translated stimulus materials in Sweden.

Variations in judgments of intentional action and moral evaluation across eight cultures.

PubMed

Robbins, Erin; Shepard, Jason; Rochat, Philippe

2017-07-01

Individuals tend to judge bad side effects as more intentional than good side effects (the Knobe or side-effect effect). Here, we assessed how widespread these findings are by testing eleven adult cohorts of eight highly contrasted cultures on their attributions of intentional action as well as ratings of blame and praise. We found limited generalizability of the original side-effect effect, and even a reversal of the effect in two rural, traditional cultures (Samoa and Vanuatu) where participants were more likely to judge the good side effect as intentional. Three follow-up experiments indicate that this reversal of the side-effect effect is not due to semantics and may be linked to the perception of the status of the protagonist. These results highlight the importance of factoring cultural context in our understanding of moral cognition. Copyright © 2017. Published by Elsevier B.V.

Mere exposure and the endowment effect on consumer decision making.

PubMed

Tom, Gail; Nelson, Carolyn; Srzentic, Tamara; King, Ryan

2007-03-01

Previous researchers (e.g., J. A. Bargh, 1992, 2002) demonstrated the importance of nonconscious processes on consumer choice behavior. Using an advertisement, the authors determined the effect of two nonconscious processes--the mere exposure effect, which increases object preference by increasing consumer exposure to an object, and the endowment effect, which increases object valuation by providing consumer possession of an object--on consumer behavior. Although the mere exposure effect and endowment effect did not produce an interaction, they produced independent effects. The endowment effect increased object valuation but not object preference. The mere exposure effect increased object preference but not object valuation. Thus, at the unconscious level, an increase in object preference does not lead to an increase in object valuation, nor does an increase in object valuation lead to an increase in object preference. The authors discuss the importance of developing measures of unconscious process in advertising effectiveness.

STOL aircraft transient ground effects. Part 1: Fundamental analytical study

NASA Technical Reports Server (NTRS)

Goldhammer, M. I.; Crowder, J. P.; Smyth, D. N.

1975-01-01

The first phases of a fundamental analytical study of STOL ground effects were presented. Ground effects were studied in two dimensions to establish the importance of nonlinear effects, to examine transient aspects of ascent and descent near the ground, and to study the modelling of the jet impingement on the ground. Powered lift system effects were treated using the jet-flap analogy. The status of a three-dimensional jet-wing ground effect method was presented. It was shown, for two-dimensional unblown airfoils, that the transient effects are small and are primarily due to airfoil/freestream/ground orientation rather than to unsteady effects. The three-dimensional study showed phenomena similar to the two-dimensional results. For unblown wings, the wing/freestream/ground orientation effects were shown to be of the same order of magnitude as for unblown airfoils. This may be used to study the nonplanar, nonlinear, jet-wing ground effect.

Small and inconsistent effects of whole body vibration on athletic performance: a systematic review and meta-analysis.

PubMed

Hortobágyi, Tibor; Lesinski, Melanie; Fernandez-Del-Olmo, Miguel; Granacher, Urs

2015-08-01

We quantified the acute and chronic effects of whole body vibration on athletic performance or its proxy measures in competitive and/or elite athletes. Systematic literature review and meta-analysis. Whole body vibration combined with exercise had an overall 0.3 % acute effect on maximal voluntary leg force (-6.4 %, effect size = -0.43, 1 study), leg power (4.7 %, weighted mean effect size = 0.30, 6 studies), flexibility (4.6 %, effect size = -0.12 to 0.22, 2 studies), and athletic performance (-1.9 %, weighted mean effect size = 0.26, 6 studies) in 191 (103 male, 88 female) athletes representing eight sports (overall effect size = 0.28). Whole body vibration combined with exercise had an overall 10.2 % chronic effect on maximal voluntary leg force (14.6 %, weighted mean effect size = 0.44, 5 studies), leg power (10.7 %, weighted mean effect size = 0.42, 9 studies), flexibility (16.5 %, effect size = 0.57 to 0.61, 2 studies), and athletic performance (-1.2 %, weighted mean effect size = 0.45, 5 studies) in 437 (169 male, 268 female) athletes (overall effect size = 0.44). Whole body vibration has small and inconsistent acute and chronic effects on athletic performance in competitive and/or elite athletes. These findings lead to the hypothesis that neuromuscular adaptive processes following whole body vibration are not specific enough to enhance athletic performance. Thus, other types of exercise programs (e.g., resistance training) are recommended if the goal is to improve athletic performance.

Deconvolution from Wavefront Sensing Using Optimal Wavefront Estimators

DTIC Science & Technology

1996-12-01

Error Results ....... ............................ 86 B.1 Introduction ................................ 86 B.1.1 Effect of Light Level, my...86 B.1.2 Effect of Atmospheric Coherence Diameter, r0 . . 86 B.1.3 Effect of Tilt Removal ................... 86 B.2 Summary... Effect of Light Level, my .................... 89 C.1.2 Effect of Atmospheric Coherence Diameter, r0 . . 89 C.1.3 Effect of Tilt Removal

1990 IEEE Annual Conference on Nuclear and Space Radiation Effects, 27th, Reno, NV, July 16-20, 1990, Proceedings

NASA Technical Reports Server (NTRS)

Fleetwood, Daniel M. (Editor)

1990-01-01

Various papers on nuclear and space radiation effects are presented. The general topics addressed include: basic mechanisms of radiation effects, dosimetry and energy-dependent effects, hardness assurance and testing techniques, single-event upset and latchup, isolation technologies, device and integrated circuit effects and hardening, spacecraft charging and electromagnetic effects.

A General Model for Testing Mediation and Moderation Effects

PubMed Central

MacKinnon, David P.

2010-01-01

This paper describes methods for testing mediation and moderation effects in a dataset, both together and separately. Investigations of this kind are especially valuable in prevention research to obtain information on the process by which a program achieves its effects and whether the program is effective for subgroups of individuals. A general model that simultaneously estimates mediation and moderation effects is presented, and the utility of combining the effects into a single model is described. Possible effects of interest in the model are explained, as are statistical methods to assess these effects. The methods are further illustrated in a hypothetical prevention program example. PMID:19003535

Explanations for side effect aversion in preventive medical treatment decisions

PubMed Central

Waters, Erika A.; Weinstein, Neil D.; Colditz, Graham A.; Emmons, Karen

2008-01-01

Objective Many laypeople demonstrate excessive sensitivity to negative side effects of medical treatments, which may lead them to refuse beneficial therapies. This Internet-based experiment investigated three possible explanations for such “side effect aversion.” One was derived from mental accounting, one examined the mere presence of a side effect, and one focused on computational difficulties. Design Participants (N = 5,379) were presented with a hypothetical cancer preventive treatment situation that was or was not accompanied by one or two small side effects. The side effects were either beneficial or harmful. In all conditions the net absolute risk reduction associated with the treatment was 15%. Main Outcome Measures Participants indicated their willingness to accept treatment and their perceptions of the treatment’s effects on their overall cancer risk. Results Data were consistent only with the “mere presence” explanation of side effect aversion, the idea that side effects act as a strong negative cue that directly affects treatment appraisal. The number of negative side effects did not influence treatment willingness. Conclusion Side effect aversion is a challenge to informed decision making. Specific mechanisms that produce side effect aversion should be identified. PMID:19290712

Experimental investigation on the coupled effect of effective stress and gas slippage on the permeability of shale.

PubMed

Yang, Diansen; Wang, Wei; Chen, Weizhong; Wang, Shugang; Wang, Xiaoqiong

2017-03-17

Permeability is one of the most important parameters to evaluate gas production in shale reservoirs. Because shale permeability is extremely low, gas is often used in the laboratory to measure permeability. However, the measured apparent gas permeability is higher than the intrinsic permeability due to the gas slippage effect, which could be even more dominant for materials with nanopores. Increasing gas pressure during tests reduces gas slippage effect, but it also decreases the effective stress which in turn influences the permeability. The coupled effect of gas slippage and effective stress on shale permeability remains unclear. Here we perform laboratory experiments on Longmaxi shale specimens to explore the coupled effect. We use the pressure transient method to measure permeability under different stress and pressure conditions. Our results reveal that the apparent measured permeability is controlled by these two competing effects. With increasing gas pressure, there exists a pressure threshold at which the dominant effect on permeability switches from gas slippage to effective stress. Based on the Klinkenberg model, we propose a new conceptual model that incorporates both competing effects. Combining microstructure analysis, we further discuss the roles of stress, gas pressure and water contents on gas permeability of shale.

Involvement of the Warburg effect in non-tumor diseases processes.

PubMed

Chen, Zhe; Liu, Meiqing; Li, Lanfang; Chen, Linxi

2018-04-01

Warburg effect, as an energy shift from mitochondrial oxidative phosphorylation to aerobic glycolysis, is extensively found in various cancers. Interestingly, increasing researchers show that Warburg effect plays a crucial role in non-tumor diseases. For instance, inhibition of Warburg effect can alleviate pulmonary vascular remodeling in the process of pulmonary hypertension (PH). Interference of Warburg effect improves mitochondrial function and cardiac function in the process of cardiac hypertrophy and heart failure. Additionally, the Warburg effect induces vascular smooth muscle cell proliferation and contributes to atherosclerosis. Warburg effect may also involve in axonal damage and neuronal death, which are related with multiple sclerosis. Furthermore, Warburg effect significantly promotes cell proliferation and cyst expansion in polycystic kidney disease (PKD). Besides, Warburg effect relieves amyloid β-mediated cell death in Alzheimer's disease. And Warburg effect also improves the mycobacterium tuberculosis infection. Finally, we also introduce some glycolytic agonists. This review focuses on the newest researches about the role of Warburg effect in non-tumor diseases, including PH, tuberculosis, idiopathic pulmonary fibrosis (IPF), failing heart, cardiac hypertrophy, atherosclerosis, Alzheimer's diseases, multiple sclerosis, and PKD. Obviously, Warburg effect may be a potential therapeutic target for those non-tumor diseases. © 2017 Wiley Periodicals, Inc.

Cognitive effects of two nutraceuticals Ginseng and Bacopa benchmarked against modafinil: a review and comparison of effect sizes.

PubMed

Neale, Chris; Camfield, David; Reay, Jonathon; Stough, Con; Scholey, Andrew

2013-03-01

Over recent years there has been increasing research into both pharmaceutical and nutraceutical cognition enhancers. Here we aimed to calculate the effect sizes of positive cognitive effect of the pharmaceutical modafinil in order to benchmark the effect of two widely used nutraceuticals Ginseng and Bacopa (which have consistent acute and chronic cognitive effects, respectively). A search strategy was implemented to capture clinical studies into the neurocognitive effects of modafinil, Ginseng and Bacopa. Studies undertaken on healthy human subjects using a double-blind, placebo-controlled design were included. For each study where appropriate data were included, effect sizes (Cohen's d) were calculated for measures showing significant positive and negative effects of treatment over placebo. The highest effect sizes for cognitive outcomes were 0.77 for modafinil (visuospatial memory accuracy), 0.86 for Ginseng (simple reaction time) and 0.95 for Bacopa (delayed word recall). These data confirm that neurocognitive enhancement from well characterized nutraceuticals can produce cognition enhancing effects of similar magnitude to those from pharmaceutical interventions. Future research should compare these effects directly in clinical trials. © 2012 The Authors. British Journal of Clinical Pharmacology © 2012 The British Pharmacological Society.

Temporal Doppler Effect and Future Orientation: Adaptive Function and Moderating Conditions.

PubMed

Gan, Yiqun; Miao, Miao; Zheng, Lei; Liu, Haihua

2017-06-01

The objectives of this study were to examine whether the temporal Doppler effect exists in different time intervals and whether certain individual and environmental factors act as moderators of the effect. Using hierarchical linear modeling, we examined the existence of the temporal Doppler effect and the moderating effect of future orientation among 139 university students (Study 1), and then the moderating conditions of the temporal Doppler effect using two independent samples of 143 and 147 university students (Studies 2 and 3). Results indicated that the temporal Doppler effect existed in all of our studies, and that future orientation moderated the temporal Doppler effect. Further, time interval perception mediated the relationship between future orientation and the motivation to cope at long time intervals. Finally, positive affect was found to enhance the temporal Doppler effect, whereas control deprivation did not influence the effect. The temporal Doppler effect is moderated by the personality trait of future orientation and by the situational variable of experimentally manipulated positive affect. We have identified personality and environmental processes that could enhance the temporal Doppler effect, which could be valuable in cases where attention to a future task is necessary. © 2016 Wiley Periodicals, Inc.

Memory for Medication Side Effects in Younger and Older Adults: The Role of Subjective and Objective Importance

PubMed Central

Friedman, Michael C.; McGillivray, Shannon; Murayama, Kou; Castel, Alan D.

2014-01-01

Older adults often experience memory impairments, but can sometimes use selective processing and schematic support to remember important information. The current experiments investigate to what degree younger and healthy older adults remember medication side effects that were subjectively or objectively important to remember. Participants studied a list of common side effects, and rated how negative these effects were if they were to experience them, and were then given a free recall test. In Experiment 1, the severity of the side effects ranged from mild (e.g., itching) to severe (e.g., stroke), and in Experiment 2, certain side effects were indicated as critical to remember (i.e., “contact your doctor if you experience this”). There were no age differences in terms of free recall of the side effects, and older adults remembered more severe side effects relative to mild effects. However, older adults were less likely to recognize critical side effects on a later recognition test, relative to younger adults. The findings suggest that older adults can selectively remember medication side effects, but have difficulty identifying familiar but potentially critical side effects, and this has implications for monitoring medication use in older age. PMID:25331278

Edge and area effects on the occurrence of migrant forest songbirds

USGS Publications Warehouse

Parker, T.H.; Stansberry, B.M.; Becker, C.D.; Gipson, P.S.

2005-01-01

Concerns about forest fragmentation and its conservation implications have motivated numerous studies that investigate the influence of forest patch area and forest edge on songbird distribution patterns. The generalized effects of forest patch size and forest edge on animal distributions is still debatable because forest patch size and forest edge are often confounded and because of an incomplete synthesis of available data. To fill a portion of this gap, we incorporated all available published data (33 papers) in meta-analyses of forest edge and area effects on site occupancy patterns for 26 Neotropical migrant forest-nesting songbirds in eastern North America. All reported area effects are confounded or potentially confounded by edge effects, and we refer to these as "confounded" studies. The converse, however, is not true and most reported edge effects are independent of patch area. When considering only nonconfounded studies of edge effects, only 1 of 17 species showed significant edge avoidance and 3 had significant affinity for edges. In confounded studies, 12 of 22 species showed significant avoidance of small patches and edges, and 1 had an affinity for small patches and edges. Furthermore, average effect sizes averaged across studies or species tended to be higher for confounded studies than for edge studies. We discuss three possible reasons for differences in results between these two groups of studies. First, studies of edge effects tended to be carried out in landscapes with greater forest cover than studies of confounded effects; among confounded effects studies, as forest cover increased, we observed a nonsignificant trend towards decreasing strength of small patch or edge avoidance effects. Thus, the weaker effects in edge studies may be due to the fact that these studies were conducted in forest-dominated landscapes. Second, we may have detected strong effects only in confounded studies because area effects are much stronger than edge effects on bird occurrence, and area effects drive the results in confounded studies. Third, edge and area effects may interact in such a way that edge effects become more important as forest patch size decreases; thus, both edge and area effects are responsible for results in confounded studies. These three explanations cannot be adequately separated with existing data. Regardless, it is clear that fragmentation of forests into small patches is detrimental to many migrant songbird species. ??2005 Society for Conservation Biology.

Screening, prevention and treatment of cervical cancer -- a global and regional generalized cost-effectiveness analysis.

PubMed

Ginsberg, Gary Michael; Edejer, Tessa Tan-Torres; Lauer, Jeremy A; Sepulveda, Cecilia

2009-10-09

The paper calculates regional generalized cost-effectiveness estimates of screening, prevention, treatment and combined interventions for cervical cancer. Using standardised WHO-CHOICE methodology, a cervical cancer model was employed to provide estimates of screening, vaccination and treatment effectiveness. Intervention effectiveness was determined via a population state-transition model (PopMod) that simulates the evolution of a sub-regional population accounting for births, deaths and disease epidemiology. Economic costs of procedures and treatment were estimated, including programme overhead and training costs. In regions characterized by high income, low mortality and high existing treatment coverage, the addition of any screening programme to the current high treatment levels is very cost-effective. However, based on projections of the future price per dose (representing the economic costs of the vaccination excluding monopolistic rents and vaccine development cost) vaccination is the most cost-effective intervention. In regions characterized by low income, low mortality and existing treatment coverage around 50%, expanding treatment with or without combining it with screening appears to be cost-effective or very cost-effective. Abandoning treatment in favour of screening in a no-treatment scenario would not be cost-effective. Vaccination is usually the most cost-effective intervention. Penta or tri-annual PAP smears appear to be cost-effective, though when combined with HPV-DNA testing they are not cost-effective. In regions characterized by low income, high mortality and low treatment levels, expanding treatment with or without adding screening would be very cost-effective. A one off vaccination plus expanding treatment was usually very cost-effective. One-off PAP or VIA screening at age 40 are more cost-effective than other interventions though less effective overall. From a cost-effectiveness perspective, consideration should be given to implementing vaccination (depending on cost per dose and longevity of efficacy) and screening programmes on a worldwide basis to reduce the burden of disease from cervical cancer. Treatment should also be increased where coverage is low.

A random effects meta-analysis model with Box-Cox transformation.

PubMed

Yamaguchi, Yusuke; Maruo, Kazushi; Partlett, Christopher; Riley, Richard D

2017-07-19

In a random effects meta-analysis model, true treatment effects for each study are routinely assumed to follow a normal distribution. However, normality is a restrictive assumption and the misspecification of the random effects distribution may result in a misleading estimate of overall mean for the treatment effect, an inappropriate quantification of heterogeneity across studies and a wrongly symmetric prediction interval. We focus on problems caused by an inappropriate normality assumption of the random effects distribution, and propose a novel random effects meta-analysis model where a Box-Cox transformation is applied to the observed treatment effect estimates. The proposed model aims to normalise an overall distribution of observed treatment effect estimates, which is sum of the within-study sampling distributions and the random effects distribution. When sampling distributions are approximately normal, non-normality in the overall distribution will be mainly due to the random effects distribution, especially when the between-study variation is large relative to the within-study variation. The Box-Cox transformation addresses this flexibly according to the observed departure from normality. We use a Bayesian approach for estimating parameters in the proposed model, and suggest summarising the meta-analysis results by an overall median, an interquartile range and a prediction interval. The model can be applied for any kind of variables once the treatment effect estimate is defined from the variable. A simulation study suggested that when the overall distribution of treatment effect estimates are skewed, the overall mean and conventional I 2 from the normal random effects model could be inappropriate summaries, and the proposed model helped reduce this issue. We illustrated the proposed model using two examples, which revealed some important differences on summary results, heterogeneity measures and prediction intervals from the normal random effects model. The random effects meta-analysis with the Box-Cox transformation may be an important tool for examining robustness of traditional meta-analysis results against skewness on the observed treatment effect estimates. Further critical evaluation of the method is needed.

Adverse effects of aromatherapy: a systematic review of case reports and case series.

PubMed

Posadzki, Paul; Alotaibi, Amani; Ernst, Edzard

2012-01-01

This systematic review was aimed at critically evaluating the evidence regarding the adverse effects associated with aromatherapy. Five electronic databases were searched to identify all relevant case reports and case series. Forty two primary reports met our inclusion criteria. In total, 71 patients experienced adverse effects of aromatherapy. Adverse effects ranged from mild to severe and included one fatality. The most common adverse effect was dermatitis. Lavender, peppermint, tea tree oil and ylang-ylang were the most common essential oils responsible for adverse effects. Aromatherapy has the potential to cause adverse effects some of which are serious. Their frequency remains unknown. Lack of sufficiently convincing evidence regarding the effectiveness of aromatherapy combined with its potential to cause adverse effects questions the usefulness of this modality in any condition.

The focusing effect in backward Raman amplification in plasma

NASA Astrophysics Data System (ADS)

Li, Zhaoli; Peng, Hao; Zuo, Yanlei; Su, Jingxin; Yang, Suhui

2018-04-01

In this paper, the focusing effect on backward Raman amplification in plasma is investigated. A fluid model, used to simulate the backward Raman amplification and including the relativistic, ponderomotive, and thermal self-focusing and the mutual-focusing effect simultaneously, is proposed and investigated. The focusing effect is shown to severely distort the profile of the seed when the seed intensity was as high as 10 17 W/cm2. Reducing the plasma density can relax the focusing effect, but at the cost of decreasing the amplification efficiency. Changing the profile of the seed has a limited effect on mitigating the focusing effect. A Gaussian profile of the pump and a defocusing shape of the plasma density seem to be an effective way to mitigate the focusing effect without decreasing the amplification efficiency.

INTRACELLULAR SIGNALING BY BILE ACIDS

PubMed Central

Anwer, Mohammed Sawkat

2014-01-01

Bile acids, synthesized from cholesterol, are known to produce beneficial as well as toxic effects in the liver. The beneficial effects include choleresis, immunomodulation, cell survival, while the toxic effects include cholestasis, apoptosis and cellular toxicity. It is believed that bile acids produce many of these effects by activating intracellular signaling pathways. However, it has been a challenge to relate intracellular signaling to specific and at times opposing effects of bile acids. It is becoming evident that bile acids produce different effects by activating different isoforms of phosphoinositide 3-kinase (PI3K), Protein kinase Cs (PKCs), and mitogen activated protein kinases (MAPK). Thus, the apoptotic effect of bile acids may be mediated via PI3K-110γ, while cytoprotection induce by cAMP-GEF pathway involves activation of PI3K-p110α/β isoforms. Atypical PKCζ may mediate beneficial effects and nPKCε may mediate toxic effects, while cPKCα and nPKCδ may be involved in both beneficial and toxic effects of bile acids. The opposing effects of nPKCδ activation may depend on nPKCδ phosphorylation site(s). Activation of ERK1/2 and JNK1/2 pathway appears to mediate beneficial and toxic effects, respectively, of bile acids. Activation of p38α MAPK and p38β MAPK may mediate choleretic and cholestatic effects, respectively, of bile acids. Future studies clarifying the isoform specific effects on bile formation should allow us to define potential therapeutic targets in the treatment of cholestatic disorders. PMID:25378891

[Air pollution and cardiovascular toxicity: known risks].

PubMed

Kostrzewa, A; Filleul, L; Eilstein, D; Harrabi, I; Tessier, J F

2004-03-01

Review of studies about epidemiological and physiopathological knowledge of ambient air particles short-term cardio-vascular effects. CURRENTS AND STRONG POINTS: Many studies, in contrasted countries for pollution's sources, meteorological conditions or socio-demographical characteristics, have shown health effects due to ambient air particles. After having studied mainly the respiratory effects of particulate air pollution, epidemiologists are now interested in the cardio-vascular effects of ambient air particles. In fact, serious effects seem to exist in fragile people which can get to emergency department visits, hospitalisation and even death. In addition, studies have shown less serious effects, but likely to be frequent (cardiac symptoms, and stoppages for cardio-vascular causes, notably). The exact mechanism by which particles have cardio-vascular adverse health effects is unknown, but experimental and epidemiological studies have led to several hypotheses: local pulmonary effects seem to be followed by systemic effects, which would be responsible for effects on the electrical activity of the heart through cardiac autonomic dysfunction and effects on the blood supply to the heart. The objective of this work is to summarise epidemiological and physiopathological knowledge about the cardio-vascular effects of ambient air particles. To evaluate the real importance of cardio-vascular effects due to particulate air pollution and to identify their exact mechanism, a more precise knowledge of detailed causes of deaths and hospitalisations and a better knowledge of less serious effects, but likely to be frequent, is necessary. Equally, a detailed identification of fragile people is essential for developing preventive actions.

[Allelopathy of Andrographis paniculata vegetative].

PubMed

Li, Ming; Zhou, Xiao-Yan; Lu, Zhan-Hong

2010-12-01

Andrographis paniculata at vegetative stage were analyzed for the allelopathic effect on cabbage (Brassica chinensis), Radis (Raphanus sativus), and Desmodium styracifolium, and provided the theory reference for their application of compounding planting pattern in practice. Water extracts of Andrographis paniculata root, stem and leaf were used to dispose Brassica chinensis, Raphanus sativus and Desmodium styracifolium seeds, young seedlings. There were allelopathic effect of water extracts of Andrographis paniculata on seed germination of Brassica chinensis, Raphanus sativus and Desmodium styracifolium, but there were difference on allelopathic effect. The suppression effects of roots on seed germination rates of Brassica chinensis showed more significantly, the stems and leaves of Andrographis paniculata on the allelopathic effects on Brassica chinensis seed germination rate index was also significantly higher than the other two receptors plants. Under the treating condition of root, stem and leaf aqueous extracts of Andrographis paniculata, the root growth of receptors seeding mostly showed inhibition effect. Under low concentrations treated. The effects on the seedlings height of Raphanus sativus and Desmodium styracifolium showed the results in which low concentration promoted and high concentration inhibited, and with increasing concentration increased the promotion or inhibition effects. But in the measured concentration range, the effects on the seedlings height of Brassica chinensis were showed promote effect. Within the testing concentration range, water extracts of Andrographis paniculata on allelopathic effects of cabbage (Brassica chinensis), Radis (Raphanus sativus) and Desmodium styracifolium showed allelopathic effect, and roughly showed inhibiti effect. However, showed different effect in which high concentration inhibitied and low concentration promoted to different receptor.

Identifying Effective Components of Child Maltreatment Interventions: A Meta-analysis.

PubMed

van der Put, Claudia E; Assink, Mark; Gubbels, Jeanne; Boekhout van Solinge, Noëlle F

2018-06-01

There is a lack of knowledge about specific components that make interventions effective in preventing or reducing child maltreatment. The aim of the present meta-analysis was to increase this knowledge by summarizing findings on effects of interventions for child maltreatment and by examining potential moderators of this effect, such as intervention components and study characteristics. Identifying effective components is essential for developing or improving child maltreatment interventions. A literature search yielded 121 independent studies (N = 39,044) examining the effects of interventions for preventing or reducing child maltreatment. From these studies, 352 effect sizes were extracted. The overall effect size was significant and small in magnitude for both preventive interventions (d = 0.26, p < .001) and curative interventions (d = 0.36, p < .001). Cognitive behavioral therapy, home visitation, parent training, family-based/multisystemic, substance abuse, and combined interventions were effective in preventing and/or reducing child maltreatment. For preventive interventions, larger effect sizes were found for short-term interventions (0-6 months), interventions focusing on increasing self-confidence of parents, and interventions delivered by professionals only. Further, effect sizes of preventive interventions increased as follow-up duration increased, which may indicate a sleeper effect of preventive interventions. For curative interventions, larger effect sizes were found for interventions focusing on improving parenting skills and interventions providing social and/or emotional support. Interventions can be effective in preventing or reducing child maltreatment. Theoretical and practical implications are discussed.

76 FR 45485 - Proposed Flood Elevation Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-29

... Ohio River), Sugar Creek (backwater effects from Ohio River), Sugarcamp Creek (backwater effects from... (backwater effects from Ohio River), Sugar Creek (backwater effects from Ohio River), Sugarcamp Creek... Hickory Creek confluence. Sugar Creek (backwater effects from From the Cumberland None +343 Unincorporated...

A Bayesian Model of the Memory Colour Effect.

PubMed

Witzel, Christoph; Olkkonen, Maria; Gegenfurtner, Karl R

2018-01-01

According to the memory colour effect, the colour of a colour-diagnostic object is not perceived independently of the object itself. Instead, it has been shown through an achromatic adjustment method that colour-diagnostic objects still appear slightly in their typical colour, even when they are colourimetrically grey. Bayesian models provide a promising approach to capture the effect of prior knowledge on colour perception and to link these effects to more general effects of cue integration. Here, we model memory colour effects using prior knowledge about typical colours as priors for the grey adjustments in a Bayesian model. This simple model does not involve any fitting of free parameters. The Bayesian model roughly captured the magnitude of the measured memory colour effect for photographs of objects. To some extent, the model predicted observed differences in memory colour effects across objects. The model could not account for the differences in memory colour effects across different levels of realism in the object images. The Bayesian model provides a particularly simple account of memory colour effects, capturing some of the multiple sources of variation of these effects.

A Bayesian Model of the Memory Colour Effect

PubMed Central

Olkkonen, Maria; Gegenfurtner, Karl R.

2018-01-01

According to the memory colour effect, the colour of a colour-diagnostic object is not perceived independently of the object itself. Instead, it has been shown through an achromatic adjustment method that colour-diagnostic objects still appear slightly in their typical colour, even when they are colourimetrically grey. Bayesian models provide a promising approach to capture the effect of prior knowledge on colour perception and to link these effects to more general effects of cue integration. Here, we model memory colour effects using prior knowledge about typical colours as priors for the grey adjustments in a Bayesian model. This simple model does not involve any fitting of free parameters. The Bayesian model roughly captured the magnitude of the measured memory colour effect for photographs of objects. To some extent, the model predicted observed differences in memory colour effects across objects. The model could not account for the differences in memory colour effects across different levels of realism in the object images. The Bayesian model provides a particularly simple account of memory colour effects, capturing some of the multiple sources of variation of these effects. PMID:29760874

Cost-effectiveness and the socialization of health care.

PubMed

Musgrove, P

1995-01-01

The more health care is socialized, the more cost-effectiveness is an appropriate criterion for expenditure. Utility-maximizing individuals, facing divisibility of health care purchases and declining marginal health gains, and complete information about probable health improvements, should buy health care according to its cost-effectiveness. Absent these features, individual health spending will not be cost-effective; and in any case, differences in personal utilities and risk aversion will not lead to the same ranking of health care interventions for everyone. Private insurance frees consumers from concern for cost, which undermines cost-effectiveness, but lets them emphasize effectiveness, which favors value for money. This is most important for costly and cost-effective interventions, especially for poor people. Cost-effectiveness is more appropriate and easier to achieve under second-party insurance. More complete socialization of health care, via public finance, can yield greater efficiency by making insurance compulsory. Cost-effectiveness is also more attractive when taxpayers subsidize others' care: needs (effectiveness) take precedence over wants (utility). The gain in effectiveness may be greater, and the welfare loss from Pareto non-optimality smaller, in poor countries than in rich ones.

A cautionary note on the power of the test for the indirect effect in mediation analysis.

PubMed

Loeys, Tom; Moerkerke, Beatrijs; Vansteelandt, Stijn

2014-01-01

Recent simulation studies have pointed to the higher power of the test for the mediated effect vs. the test for the total effect, even in the presence of a direct effect. This has motivated applied researchers to investigate mediation in settings where there is no evidence of a total effect. In this paper we provide analytical insight into the circumstances under which higher power of the test for the mediated effect vs. the test for the total effect can be expected in the absence of a direct effect. We argue that the acclaimed power gain is somewhat deceptive and comes with a big price. On the basis of the results, we recommend that when the primary interest lies in mediation only, a significant test for the total effect should not be used as a prerequisite for the test for the indirect effect. However, because the test for the indirect effect is vulnerable to bias when common causes of mediator and outcome are not measured or not accounted for, it should be evaluated in a sensitivity analysis.

A cautionary note on the power of the test for the indirect effect in mediation analysis

PubMed Central

Loeys, Tom; Moerkerke, Beatrijs; Vansteelandt, Stijn

2015-01-01

Recent simulation studies have pointed to the higher power of the test for the mediated effect vs. the test for the total effect, even in the presence of a direct effect. This has motivated applied researchers to investigate mediation in settings where there is no evidence of a total effect. In this paper we provide analytical insight into the circumstances under which higher power of the test for the mediated effect vs. the test for the total effect can be expected in the absence of a direct effect. We argue that the acclaimed power gain is somewhat deceptive and comes with a big price. On the basis of the results, we recommend that when the primary interest lies in mediation only, a significant test for the total effect should not be used as a prerequisite for the test for the indirect effect. However, because the test for the indirect effect is vulnerable to bias when common causes of mediator and outcome are not measured or not accounted for, it should be evaluated in a sensitivity analysis. PMID:25628585

Functional mixed effects spectral analysis

PubMed Central

KRAFTY, ROBERT T.; HALL, MARTICA; GUO, WENSHENG

2011-01-01

SUMMARY In many experiments, time series data can be collected from multiple units and multiple time series segments can be collected from the same unit. This article introduces a mixed effects Cramér spectral representation which can be used to model the effects of design covariates on the second-order power spectrum while accounting for potential correlations among the time series segments collected from the same unit. The transfer function is composed of a deterministic component to account for the population-average effects and a random component to account for the unit-specific deviations. The resulting log-spectrum has a functional mixed effects representation where both the fixed effects and random effects are functions in the frequency domain. It is shown that, when the replicate-specific spectra are smooth, the log-periodograms converge to a functional mixed effects model. A data-driven iterative estimation procedure is offered for the periodic smoothing spline estimation of the fixed effects, penalized estimation of the functional covariance of the random effects, and unit-specific random effects prediction via the best linear unbiased predictor. PMID:26855437

Experimental Effects and Individual Differences in Linear Mixed Models: Estimating the Relationship between Spatial, Object, and Attraction Effects in Visual Attention

PubMed Central

Kliegl, Reinhold; Wei, Ping; Dambacher, Michael; Yan, Ming; Zhou, Xiaolin

2011-01-01

Linear mixed models (LMMs) provide a still underused methodological perspective on combining experimental and individual-differences research. Here we illustrate this approach with two-rectangle cueing in visual attention (Egly et al., 1994). We replicated previous experimental cue-validity effects relating to a spatial shift of attention within an object (spatial effect), to attention switch between objects (object effect), and to the attraction of attention toward the display centroid (attraction effect), also taking into account the design-inherent imbalance of valid and other trials. We simultaneously estimated variance/covariance components of subject-related random effects for these spatial, object, and attraction effects in addition to their mean reaction times (RTs). The spatial effect showed a strong positive correlation with mean RT and a strong negative correlation with the attraction effect. The analysis of individual differences suggests that slow subjects engage attention more strongly at the cued location than fast subjects. We compare this joint LMM analysis of experimental effects and associated subject-related variances and correlations with two frequently used alternative statistical procedures. PMID:21833292

Standardized Effect Sizes for Moderated Conditional Fixed Effects with Continuous Moderator Variables

PubMed Central

Bodner, Todd E.

2017-01-01

Wilkinson and Task Force on Statistical Inference (1999) recommended that researchers include information on the practical magnitude of effects (e.g., using standardized effect sizes) to distinguish between the statistical and practical significance of research results. To date, however, researchers have not widely incorporated this recommendation into the interpretation and communication of the conditional effects and differences in conditional effects underlying statistical interactions involving a continuous moderator variable where at least one of the involved variables has an arbitrary metric. This article presents a descriptive approach to investigate two-way statistical interactions involving continuous moderator variables where the conditional effects underlying these interactions are expressed in standardized effect size metrics (i.e., standardized mean differences and semi-partial correlations). This approach permits researchers to evaluate and communicate the practical magnitude of particular conditional effects and differences in conditional effects using conventional and proposed guidelines, respectively, for the standardized effect size and therefore provides the researcher important supplementary information lacking under current approaches. The utility of this approach is demonstrated with two real data examples and important assumptions underlying the standardization process are highlighted. PMID:28484404

Neutron-proton effective mass splitting in terms of symmetry energy and its density slope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chakraborty, S.; Sahoo, B.; Sahoo, S., E-mail: sukadevsahoo@yahoo.com

2015-01-15

Using a simple density-dependent finite-range effective interaction having Yukawa form, the density dependence of isoscalar and isovector effective masses is studied. The isovector effective mass is found to be different for different pairs of like and unlike nucleons. Using HVH theorem, the neutron-proton effective mass splitting is represented in terms of symmetry energy and its density slope. It is again observed that the neutron-proton effective mass splitting has got a positive value when isoscalar effective mass is greater than the isovector effective mass and has a negative value for the opposite case. Furthermore, the neutron-proton effective mass splitting is foundmore » to have a linear dependence on asymmetry β. The second-order symmetry potential has a vital role in the determination of density slope of symmetry energy but it does not have any contribution on neutron-proton effective mass splitting. The finite-range effective interaction is compared with the SLy2, SKM, f{sub −}, f{sub 0}, and f{sub +} forms of interactions.« less

Therapeutic effect of cefozopran (SCE-2787), a new parenteral cephalosporin, against experimental infections in mice.

PubMed Central

Iizawa, Y; Okonogi, K; Hayashi, R; Iwahi, T; Yamazaki, T; Imada, A

1993-01-01

The therapeutic effect of cefozopran (SCE-2787), a new semisynthetic parenteral cephalosporin, against experimental infections in mice was examined. Cefozopran was more effective than cefpiramide and was as effective as ceftazidime and cefpirome against acute respiratory tract infections caused by Klebsiella pneumoniae DT-S. In the model of chronic respiratory tract infection caused by K. pneumoniae 27, cefozopran was as effective as ceftazidime. The therapeutic effect of cefozopran against urinary tract infections caused by Pseudomonas aeruginosa P9 was superior to that of cefpirome and was equal to those of ceftazidime and cefclidin. In addition, cefozopran was more effective than ceftazidime and was as effective as flomoxef in a thigh muscle infection caused by methicillin-sensitive Staphylococcus aureus 308A-1. Against thigh muscle infections caused by methicillin-resistant S. aureus N133, cefozopran was the most effective agent. The potent therapeutic effect of cefozopran in those experimental infections in mice suggests that it would be effective against respiratory tract, urinary tract, and soft tissue infections caused by a variety of gram-positive and gram-negative bacteria in humans. PMID:8431004

Durability of structural lumber products at high temperatures. Part I, 66C at 75% RH and 82C at 30% RH

Treesearch

David W. Green; James W. Evans; Bruce A. Craig

2003-01-01

The effect of temperature on properties can be separated into reversible and permanent effects. The National Design Specification (NDS) provides factors (Ct) for reducing properties for reversible effects but provides little guidance on permanent effects. The primary objective of this paper is to evaluate the effect of prolonged heating (permanent effect) on the...

5 CFR 890.806 - When can former spouses change enrollment or reenroll and what are the effective dates?

Code of Federal Regulations, 2010 CFR

2010-01-01

... met. (b) Effective date—generally. (1) Except as otherwise provided, an enrollment takes effect on the... otherwise take effect. (2) A change of enrollment takes effect on the first day of the first pay period that... only at any time. (2) A change of enrollment to self only takes effect on the first day of the first...

Decomposition Analysis of Wastewater Pollutant Discharges in Industrial Sectors of China (2001-2009) Using the LMDI I Metho

PubMed Central

Lei, Hongjun; Xia, Xunfeng; Li, Changjia; Xi, Beidou

2012-01-01

China’s industry accounts for 46.8% of the national Gross Domestic Product (GDP) and plays an important strategic role in its economic growth. On the other hand, industrial wastewater is also the major source of water pollution. In order to examine the relationship between the underlying driving forces and various environmental indicators, values of two critical industrial wastewater pollutant discharge parameters (Chemical Oxygen Demand (COD) and ammonia nitrogen (NH4-N)), between 2001 and 2009, were decomposed into three factors: i.e., production effects (caused by change in the scale of economic activity), structure effects (caused by change in economic structure) and intensity effects (caused by change in technological level of each sector), using additive version of the Logarithmic Mean Divisia Index (LMDI I) decomposition method. Results showed that: (1) the average annual effect of COD discharges in China was −2.99%, whereas the production effect, the structure effect, and the intensity effect were 14.64%, −1.39%, and −16.24%, respectively. Similarly, the average effect of NH4-N discharges was −4.03%, while the production effect, the structure effect, and the intensity effect were 16.18%, −2.88%, and −17.33%, respectively; (2) the production effect was the major factor responsible for the increase in COD and NH4-N discharges, accounting for 45% and 44% of the total contribution, respectively; (3) the intensity effect, which accounted for 50% and 48% of the total contribution, respectively, exerted a dominant decremental effect on COD and NH4-N discharges; intensity effect was further decomposed into cleaner production effect and pollution abatement effect with the cleaner production effect accounting for 60% and 55% of the reduction of COD and NH4-N, respectively; (4) the major contributors to incremental COD and NH4-N discharges were divided among industrial sub-sectors and the top contributors were identified. Potential restructuring and regulation measures were proposed for pollutant reduction. PMID:22829800

An approximation of herd effect due to vaccinating children against seasonal influenza - a potential solution to the incorporation of indirect effects into static models.

PubMed

Van Vlaenderen, Ilse; Van Bellinghen, Laure-Anne; Meier, Genevieve; Nautrup, Barbara Poulsen

2013-01-22

Indirect herd effect from vaccination of children offers potential for improving the effectiveness of influenza prevention in the remaining unvaccinated population. Static models used in cost-effectiveness analyses cannot dynamically capture herd effects. The objective of this study was to develop a methodology to allow herd effect associated with vaccinating children against seasonal influenza to be incorporated into static models evaluating the cost-effectiveness of influenza vaccination. Two previously published linear equations for approximation of herd effects in general were compared with the results of a structured literature review undertaken using PubMed searches to identify data on herd effects specific to influenza vaccination. A linear function was fitted to point estimates from the literature using the sum of squared residuals. The literature review identified 21 publications on 20 studies for inclusion. Six studies provided data on a mathematical relationship between effective vaccine coverage in subgroups and reduction of influenza infection in a larger unvaccinated population. These supported a linear relationship when effective vaccine coverage in a subgroup population was between 20% and 80%. Three studies evaluating herd effect at a community level, specifically induced by vaccinating children, provided point estimates for fitting linear equations. The fitted linear equation for herd protection in the target population for vaccination (children) was slightly less conservative than a previously published equation for herd effects in general. The fitted linear equation for herd protection in the non-target population was considerably less conservative than the previously published equation. This method of approximating herd effect requires simple adjustments to the annual baseline risk of influenza in static models: (1) for the age group targeted by the childhood vaccination strategy (i.e. children); and (2) for other age groups not targeted (e.g. adults and/or elderly). Two approximations provide a linear relationship between effective coverage and reduction in the risk of infection. The first is a conservative approximation, recommended as a base-case for cost-effectiveness evaluations. The second, fitted to data extracted from a structured literature review, provides a less conservative estimate of herd effect, recommended for sensitivity analyses.

Effects of Varenicline on Ethanol-Induced Conditioned Place Preference, Locomotor Stimulation, and Sensitization

PubMed Central

Gubner, Noah R.; McKinnon, Carrie S.; Phillips, Tamara J.

2014-01-01

Background Varenicline, a partial nicotinic acetylcholine receptor (nAChR) agonist, is a promising new drug for the treatment of alcohol (ethanol) dependence. Varenicline has been approved by the Food and Drug Administration as a smoking cessation therapeutic and has also been found to reduce ethanol consumption in humans and animal models of alcohol use. The current studies examined the hypotheses that varenicline attenuates the stimulant and sensitizing effects of ethanol, and reduces the motivational effects of ethanol-associated cues. The goal was to determine if these effects of varenicline contribute to its pharmacotherapeutic effects for alcohol dependence. In addition, effects of varenicline on acute stimulation and/or on the acquisition of sensitization would suggest a role for nAChR involvement in these effects of ethanol. Methods Dose-dependent effects of varenicline on the expression of ethanol-induced conditioned place preference (CPP), locomotor activation, and behavioral sensitization were examined. These measures model motivational effects of ethanol-associated cues, euphoric or stimulatory effects of ethanol, and ethanol-induced neuroadaptation. All studies used DBA/2J mice, an inbred strain with high sensitivity to these ethanol-related effects. Results Varenicline did not significantly attenuate the expression of ethanol-induced CPP. Varenicline reduced locomotor activity and had the most pronounced effect in the presence of ethanol, with the largest effect on acute ethanol-induced locomotor stimulation and a trend for varenicline to attenuate the expression of ethanol-induced sensitization. Conclusions Because varenicline did not attenuate the expression of ethanol-induced CPP, it may not be effective at reducing the motivational effects of ethanol-associated cues. This outcome suggests that reductions in the motivational effects of ethanol-associated cues may not be involved in how varenicline reduces ethanol consumption. However, varenicline did have effects on locomotor behavior and significantly attenuated acute ethanol-induced locomotor stimulation. In humans who drink while taking varenicline, it might similarly reduce stimulant responses and have an impact on continued drinking. General sedative effects in such individuals should be carefully considered. PMID:25581658

Cost-effectiveness analysis of intracameral cefuroxime use for prophylaxis of endophthalmitis after cataract surgery.

PubMed

Sharifi, Emile; Porco, Travis C; Naseri, Ayman

2009-10-01

To evaluate the cost-effectiveness of intracameral cefuroxime for postoperative endophthalmitis prophylaxis, and to determine the efficacy threshold necessary for alternative antibiotics to attain cost-effective equivalence with intracameral cefuroxime. Cost-effectiveness analysis. We study a hypothetical cohort of 100,000 patients undergoing cataract surgery as a part of the cost analysis. A cost-effectiveness model was constructed to analyze different antibiotic prophylactic regimens for postoperative endophthalmitis with intracameral cefuroxime as our base case. Efficacy was defined as the absolute reduction in rate of infection from background rate of infection, which was sourced from the literature. Antibiotic cost data were derived from the Red Book 2007 edition, and salary data were taken from the United States Bureau of Labor Statistics. Multivariate sensitivity analysis assessed the performance of antibiotic options under different scenarios. Cost per case of endophthalmitis prevented; theoretical maximal cost-effectiveness; efficacy threshold necessary to achieve cost-effective equivalence with intracameral cefuroxime; ratio indicating how many times more effective or less expensive alternative antibiotics would have to be to achieve cost-effective equivalence with intracameral cefuroxime. The cost-effectiveness ratio for intracameral cefuroxime is $1403 per case of postoperative endophthalmitis prevented. By comparison, the least expensive topical fluoroquinolone in our study, ciprofloxacin, would have to be >8 times more effective than intracameral cefuroxime to achieve cost-effective equivalence. The most expensive topical fluoroquinolones studied, gatifloxacin and moxifloxacin, would have to be > or =19 times more effective than intracameral cefuroxime to achieve cost-effective equivalence. A sensitivity analysis reveals that even in the worst case scenario for intracameral cefuroxime efficacy and with a 50% reduction in the cost of 4th-generation fluoroquinolones, gatifloxacin and moxifloxacin would have to be > or =9 times more effective than intracameral cefuroxime to achieve cost-effective equivalence. Administration of intracameral cefuroxime is relatively cost-effective in preventing endophthalmitis after cataract surgery. Owing to their high costs, many commonly used topical antibiotics are not cost-effective compared with intracameral cefuroxime, even under optimistic assumptions about their efficacy.

An overview of health effects on noise

NASA Astrophysics Data System (ADS)

Osada, Y.

1988-12-01

Although noise can damage the inner ear and cause other pathological changes, its most common negative effects are non-somatic, such as a perception of noisiness and disturbance of daily activities. According to the definition of health by WHO, this should be considered as a health hazard. These health effects of noise can be classified into the following three categories: (I) hearing loss, perception of noisiness and masking are produced along the auditory pathway and are thus direct and specific effects of noise; (II) interference with performance, rest and sleep, a feeling of discomfort and some physiological effects are produced as indirect and non-specific effects via reticular formation of the midbrain; (III) annoyance is not merely a feeling of unpleasantness but the feeling of being bothered or troubled, and includes the development of a particular attitude toward the noise source. Individual or group behavioral responses will be evoked when annoyance develops. Annoyance and behavioral response are integrated and composite effects. The health effects of noise are modified by many factors related to both the noise and the individual. Noise level, frequency spectrum, duration and impulsiveness modify the effects. Sex, age, health status and mental character also have an influence on the effects. Direct effects of noise are most dependent on the physical nature of the noise and least dependent on human factors. Indirect effects are more dependent, and integrated effects most dependent, on human factors.

Relation between therapeutic response and side effects induced by methylphenidate as observed by parents and teachers of children with ADHD.

PubMed

Lee, James; Grizenko, Natalie; Bhat, Venkataramana; Sengupta, Sarojini; Polotskaia, Anna; Joober, Ridha

2011-04-21

The desired (therapeutic) and undesired (side) effects of methylphenidate might have underlying correlations. The aim of this study was to explore the strength and the possible sources of these correlations. One hundred and fifty-seven children with ADHD (6-12 years) were administered placebo and methylphenidate (0.5 mg/kg in a divided b.i.d. dose), each for a one-week period, in a double-blind, crossover trial. Therapeutic response was assessed using the Conners' Global Index for parents (CGI-Parents) and teachers (CGI-Teachers), while side effects were assessed using the Barkley Side Effects Rating Scale (SERS). The side effect profile as assessed by the SERS was similar to that of previous studies with insomnia, decreased appetite, and headaches showing significant treatment effects (p < 0.005). These "somatic/physical" side effects did not correlate with CGI-Parents or CGI-Teachers. However, the side effects of "irritability", "proneness to crying", and "anxiousness" showed significant relationships with CGI-Parents. These "mood/anxiety" side effects showed no significant correlations with the CGI-Teachers. The greater "mood/anxiety" side effects on methylphenidate and placebo, the less the parents observe improvement of their children while treated with methylphenidate. This suggests that the correlations between "mood/anxiety" side effects and poor response to treatment may be driven by observer effects rather than biological commonalities between therapeutic and side effects of methylphenidate.

Treatment Effect on Recidivism for Juveniles Who Have Sexually Offended: a Multilevel Meta-Analysis.

PubMed

Ter Beek, Ellis; Spruit, Anouk; Kuiper, Chris H Z; van der Rijken, Rachel E A; Hendriks, Jan; Stams, Geert Jan J M

2018-04-01

The current study investigated the effect on recidivism of treatment aimed at juveniles who have sexually offended. It also assessed the potential moderating effect of type of recidivism, and several treatment, participant and study characteristics. In total, 14 published and unpublished primary studies, making use of a comparison group and reporting on official recidivism rates, were included in a multilevel meta-analysis. This resulted in the use of 77 effect sizes, and 1726 participants. A three-level meta-analytic model was used to calculate the combined effect sizes (Cohens d) and to perform moderator analyses. Study quality was assessed with the EPHPP Quality Assessment Tool for Quantitative Studies. A moderate effect size was found (d = 0.37), indicating that the treatment groups achieved an estimated relative reduction in recidivism of 20.5% as compared to comparison groups. However, after controlling for publication bias, a significant treatment effect was no longer found. Type of recidivism did not moderate the effect of treatment, indicating that treatment groups were equally effective for all types of recidivism. Also, no moderating effects of participant or treatment characteristics were found. Regarding study characteristics, a shorter follow up time showed a trend for larger effect sizes, and the effect size calculation based on proportions yielded larger effect sizes than calculation via mean frequency of offending. Implications for future research and clinical practice are discussed.

Spatio-temporal dynamics of action-effect associations in oculomotor control.

PubMed

Riechelmann, Eva; Pieczykolan, Aleksandra; Horstmann, Gernot; Herwig, Arvid; Huestegge, Lynn

2017-10-01

While there is ample evidence that actions are guided by anticipating their effects (ideomotor control) in the manual domain, much less is known about the underlying characteristics and dynamics of effect-based oculomotor control. Here, we address three open issues. 1) Is action-effect anticipation in oculomotor control reflected in corresponding spatial saccade characteristics in inanimate environments? 2) Does the previously reported dependency of action latency on the temporal effect delay (action-effect interval) also occur in the oculomotor domain? 3) Which temporal effect delay is optimally suited to develop strong action-effect associations over time in the oculomotor domain? Participants executed left or right free-choice saccades to peripheral traffic lights, causing an (immediate or delayed) action-contingent light switch in the upper vs. lower part of the traffic light. Results indicated that saccades were spatially shifted toward the location of the upcoming change, indicating anticipation of the effect (location). Saccade latency was affected by effect delay, suggesting that corresponding time information is integrated into event representations. Finally, delayed (vs. immediate) effects were more effective in strengthening action-effect associations over the course of the experiment, likely due to greater saliency of perceptual changes occurring during target fixation as opposed to changes during saccades (saccadic suppression). Overall, basic principles underlying ideomotor control appear to generalize to the oculomotor domain. Copyright © 2017 Elsevier B.V. All rights reserved.

Lack of cocaine-like discriminative-stimulus effects of σ-receptor agonists in rats.

PubMed

Hiranita, Takato; Soto, Paul L; Tanda, Gianluigi; Katz, Jonathan L

2011-09-01

Previous studies demonstrated the effectiveness of selective σ-receptor (σR) agonists [1,3-di-o-tolylguanidine (DTG), PRE-084] as reinforcers in rats trained to self-administer cocaine. Similar to cocaine, these drugs increased nucleus accumbens shell dopamine levels, and effects of DTG, but not PRE-084, on dopamine seemed to be mediated by σRs. In addition, σR antagonists blocked self-administration of σR agonists, but were inactive against reinforcing and neurochemical effects of cocaine. Thus, pharmacologically distinct mechanisms likely underlie the reinforcing and neurochemical effects of σR agonists and cocaine. This study further examined the cocaine-like effects of σR agonists in rats trained to discriminate injections of cocaine from saline to assess the similarity of their subjective effects. Standard dopamine-uptake inhibitors (WIN 35,428, methylphenidate), but neither σR agonist (PRE-084, DTG), produced full cocaine-like discriminative-stimulus effects. The lack of effects of σR agonists was obtained regardless of route of administration (intraperitoneal, subcutaneous, or intravenous) or pretreatment time (5 or 30 min before sessions). The present results demonstrate differences in the discriminative-stimulus effects of cocaine and selective σR agonists, indicating that an overlap of subjective effects is not necessary for σR agonist self-administration. The previously found differences in neurochemical effects of cocaine and σR agonists may contribute to their different subjective effects.

Lack of Cocaine-Like Discriminative-Stimulus Effects of σ Receptor Agonists in Rats

PubMed Central

Hiranita, Takato; Soto, Paul L.; Tanda, Gianluigi; Katz, Jonathan L.

2013-01-01

Previous studies demonstrated effectiveness of selective sigma-receptor (σR) agonists (DTG, PRE-084) as reinforcers in rats trained to self-administer cocaine. Like cocaine, these drugs increased nucleus accumbens shell dopamine levels, and effects of DTG, but not PRE-084, on dopamine appeared to be mediated by σRs. Additionally, σR antagonists blocked self-administration of σR agonists, but were inactive against reinforcing and neurochemical effects of cocaine. Thus pharmacologically distinct mechanisms likely underlie the reinforcing and neurochemical effects of σR agonists and cocaine. The present study further examined the cocaine-like effects of σR agonists in rats trained to discriminate injections of cocaine from saline to assess the similarity of their subjective effects. Standard dopamine-uptake inhibitors (WIN 35,428, methylphenidate), but neither σR agonist (PRE-084, DTG) produced full cocaine-like discriminative-stimulus effects. The lack of effects of σR agonists was obtained regardless of route of administration (i.p., s.c. or i.v.) or pretreatment time (5- or 30-min before sessions). The present results demonstrate differences in the discriminative-stimulus effects of cocaine and selective σR agonists, indicating that an overlap of subjective effects is not necessary for σR agonist self-administration. The previously found differences in neurochemical effects of cocaine and σR agonists may contribute to their different subjective effects. PMID:21808192

[Comparison of the effects of BI-6, a new asymmetric bipyridine oxime, with HI-6 oxime and obidoxime in combination with atropine on soman and fosdrine toxicity in mice].

PubMed

Kassa, J

1999-01-01

The therapeutic efficacy of the new asymmetric bispyridinium oxime BI-6 against acute toxicity of the highly toxic organophosphate soman and the organophosphorus insecticide fosdrin by means of affecting the LD50 values of these noxiores substances was compared with the effect of the hitherto most perspective oxime HI-6 and the classic obidoxime always in combination with the identical dose of atropine. At the equimolar level the effect of oxime BI-6 against fosdrin completely equals the effects of both oximes HI-6 and obidoxime. The effect of oxime BI-6 against soman is even more marked than the effect of HI-6 but this difference is not statistically significant. On the other hand, at the equi-effective level, the effect of oxime BI-6 against soman is statistically significantly lower than the effect of HI-6, and against fosdrin it is even lower than the effect of both remaining oximes. The effects of the new oxime BI-6 equal, or slightly exceed the therapeutic effect of HI-6 but at the equimolar level only. At the equi-effective level which respects the toxicity of the oxime and is therefore more important for practical use, it is a therapeutically weaker reactivator of acetylcholinesterase than HI-6.

Basic optics of effect materials.

PubMed

Jones, Steven A

2010-01-01

Effect materials derive their color and effect primarily from thin-film interference. Effect materials have evolved over the decades from simple guanine crystals to the complex multilayer optical structures of today. The development of new complex effect materials requires an understanding of the optics of effect materials. Such an understanding would also benefit the cosmetic formulator as these new effect materials are introduced. The root of this understanding begins with basic optics. This paper covers the nature of light, interference of waves, thin-film interference, color from interference, and color travel.

RBE for late somatic effects in mice irradiated with 60 MeV protons relative to X-rays.

NASA Technical Reports Server (NTRS)

Darden, E. B., Jr.; Clapp, N. K.; Bender, R. S.; Jernigan, M. C.; Upton, A. C.

1971-01-01

Investigation of the relative biological effectiveness of energetic protons for the induction of somatic effects in a mammal (mice) following whole body irradiation. The proton energy used approximates the mean energy for proton spectra accompanying solar events. The effects on longevity and the incidence of major neoplastic diseases are summarized. The results obtained suggest that medium energy proton irradiation is no more effective, and on the whole, probably less effective, than conventional X radiation for the induction of late radiation effects in the mouse.

The prospects of selection for social genetic effects to improve welfare and productivity in livestock

PubMed Central

Ellen, Esther D.; Rodenburg, T. Bas; Albers, Gerard A. A.; Bolhuis, J. Elizabeth; Camerlink, Irene; Duijvesteijn, Naomi; Knol, Egbert F.; Muir, William M.; Peeters, Katrijn; Reimert, Inonge; Sell-Kubiak, Ewa; van Arendonk, Johan A. M.; Visscher, Jeroen; Bijma, Piter

2014-01-01

Social interactions between individuals living in a group can have both positive and negative effects on welfare, productivity, and health of these individuals. Negative effects of social interactions in livestock are easier to observe than positive effects. For example, laying hens may develop feather pecking, which can cause mortality due to cannibalism, and pigs may develop tail biting or excessive aggression. Several studies have shown that social interactions affect the genetic variation in a trait. Genetic improvement of socially-affected traits, however, has proven to be difficult until relatively recently. The use of classical selection methods, like individual selection, may result in selection responses opposite to expected, because these methods neglect the effect of an individual on its group mates (social genetic effects). It has become clear that improvement of socially-affected traits requires selection methods that take into account not only the direct effect of an individual on its own phenotype but also the social genetic effects, also known as indirect genetic effects, of an individual on the phenotypes of its group mates. Here, we review the theoretical and empirical work on social genetic effects, with a focus on livestock. First, we present the theory of social genetic effects. Subsequently, we evaluate the evidence for social genetic effects in livestock and other species, by reviewing estimates of genetic parameters for direct and social genetic effects. Then we describe the results of different selection experiments. Finally, we discuss issues concerning the implementation of social genetic effects in livestock breeding programs. This review demonstrates that selection for socially-affected traits, using methods that target both the direct and social genetic effects, is a promising, but sometimes difficult to use in practice, tool to simultaneously improve production and welfare in livestock. PMID:25426136

Separate and combined impact of acute naltrexone and alprazolam on subjective and physiological effects of oral d-amphetamine in stimulant users

PubMed Central

Marks, Katherine R.; Lile, Joshua A.; Stoops, William W.

2014-01-01

Rationale Opioid antagonists (e.g., naltrexone) and positive modulators of γ-aminobutyric-acidA (GABAA) receptors (e.g., alprazolam) modestly attenuate the abuse-related effects of stimulants like amphetamine. The use of higher doses to achieve greater efficacy is precluded by side effects. Combining naltrexone and alprazolam might safely maximize efficacy while avoiding the untoward effects of the constituent compounds. Objectives The present pilot study tested the hypothesis that acute pretreatment with the combination of naltrexone and alprazolam would not produce clinically problematic physiological effects or negative subjective effects and would reduce the positive subjective effects of d-amphetamine to a greater extent than the constituent drugs alone. Methods Eight nontreatment-seeking, stimulant-using individuals completed an outpatient experiment in which oral d-amphetamine (0, 15, and 30 mg) was administered following acute pretreatment with naltrexone (0 and 50 mg) and alprazolam (0 and 0.5 mg). Subjective effects, psychomotor task performance, and physiological measures were collected. Results Oral d-amphetamine produced prototypical physiological and stimulant-like positive subjective effects (e.g., VAS ratings of Active/Alert/Energetic, Good Effect, and High). Pretreatment with naltrexone, alprazolam, and their combination did not produce clinically problematic acute physiological effects or negative subjective effects. Naltrexone and alprazolam each significantly attenuated some of the subjective effects of d-amphetamine. The combination attenuated a greater number of subjective effects than the constituent drugs alone. Conclusions The present results support the continued evaluation of an opioid receptor antagonist combined with a GABAA-positive modulator using more clinically relevant experimental conditions like examining the effect of chronic dosing with these drugs on methamphetamine self-administration. PMID:24464531

Separate and combined impact of acute naltrexone and alprazolam on subjective and physiological effects of oral d-amphetamine in stimulant users.

PubMed

Marks, Katherine R; Lile, Joshua A; Stoops, William W; Rush, Craig R

2014-07-01

Opioid antagonists (e.g., naltrexone) and positive modulators of γ-aminobutyric-acidA (GABAA) receptors (e.g., alprazolam) modestly attenuate the abuse-related effects of stimulants like amphetamine. The use of higher doses to achieve greater efficacy is precluded by side effects. Combining naltrexone and alprazolam might safely maximize efficacy while avoiding the untoward effects of the constituent compounds. The present pilot study tested the hypothesis that acute pretreatment with the combination of naltrexone and alprazolam would not produce clinically problematic physiological effects or negative subjective effects and would reduce the positive subjective effects of d-amphetamine to a greater extent than the constituent drugs alone. Eight nontreatment-seeking, stimulant-using individuals completed an outpatient experiment in which oral d-amphetamine (0, 15, and 30 mg) was administered following acute pretreatment with naltrexone (0 and 50 mg) and alprazolam (0 and 0.5 mg). Subjective effects, psychomotor task performance, and physiological measures were collected. Oral d-amphetamine produced prototypical physiological and stimulant-like positive subjective effects (e.g., VAS ratings of Active/Alert/Energetic, Good Effect, and High). Pretreatment with naltrexone, alprazolam, and their combination did not produce clinically problematic acute physiological effects or negative subjective effects. Naltrexone and alprazolam each significantly attenuated some of the subjective effects of d-amphetamine. The combination attenuated a greater number of subjective effects than the constituent drugs alone. The present results support the continued evaluation of an opioid receptor antagonist combined with a GABAA-positive modulator using more clinically relevant experimental conditions like examining the effect of chronic dosing with these drugs on methamphetamine self-administration.

Special health care needs explains the effect of extremely low birth weight on math but not language achievement.

PubMed

Litt, Jonathan S; Minich, Nori; Taylor, H Gerry; Hack, Maureen

2017-12-01

Extremely low birth weight (ELBW; <1kg) adolescents are at risk for special health care needs (SHCN) and poor math achievement compared to normal birth weight (NBW) peers. SHCN are associated with poor academic achievement among NBW children. We hypothesize that SHCN explain the effect of ELBW on math achievement. We compared age 14 Woodcock-Johnson Calculation standard scores between 181 ELBW infants and 115 NBW controls. Persistent SHCN included: 1) prescription medication or equipment use, 2) subspecialty or therapeutic service use, or 3) hospitalization. We used nonlinear marginal effects models to decompose the total effect of ELBW on math into the following 4 components: the effect of ELBW controlling for SHCN, the effect of SHCN controlling for ELBW, effect modification by SHCN, and mediated interaction where SHCN is both causal mediator and effect modifier. Models were adjusted for sociodemographic factors. ELBW adolescents had lower mean math scores than NBW peers (81.3 vs. 96.4). SHCN were more common among ELBW adolescents (54.1% vs. 27%). The total effect of ELBW on math scores was -15.7 points (95% CI -21.0, -10.5). The effect of birth weight alone was -7.6 points (95% CI -13.7, -1.4); the effect of SHCN alone was negligible. SHCN interaction and mediated interaction effects each accounted for 25% of the total effect. Birth weight alone explains only half of the effect of ELBW on math achievement. We found evidence of effect modification and mediation by SHCN. Understanding these explanatory pathways may lead to targeted interventions for improved outcomes. Copyright © 2017. Published by Elsevier B.V.

Evaluation of the Combined Effect of Recombinant High-Density Lipoprotein Carrier and the Encapsulated Lovastatin in RAW264.7 Macrophage Cells Based on the Median-Effect Principle.

PubMed

Jiang, Cuiping; Zhao, Yi; Yang, Yun; He, Jianhua; Zhang, Wenli; Liu, Jianping

2018-03-05

Recombinant high-density lipoprotein (rHDL) displays a similar anti-atherosclerotic effect with native HDL and could also be served as a carrier of cardiovascular drug for atherosclerotic plaque targeting. In our previous studies, rHDL has shown a more potent anti-atherosclerotic efficacy as compared to the other conventional nanoparticles with a payload of lovastatin (LS). Therefore, we hypothesized that a synergistic anti-atherosclerotic effect of the rHDL carrier and the encapsulated LS might exist. In this study, the dose-effect relationships and the combined effect of the rHDL and LS were quantitatively evaluated in RAW 264.7 macrophage cells using the median-effect analysis, in which the rHDL carrier was regarded as a drug combined. Median-effect analysis suggested that rHDL and LS exerted a desirable synergistic inhibition on the oxLDL internalization at a ratio of 6:1 ( D m,LS : D m,rHDL ) in RAW 264.7 macrophage cells. About 50% of the reduction on the intracellular lipid contents was found when RAW264.7 cells were treated with LS-loaded rHDLs at their respective median-effect dose ( D m ) concentrations and a synergistic effect on the mediating cholesterol efflux was also observed, which verified the accuracy of the results obtained from the median-effect analysis. The mechanism underlying the synergistic effect of the rHDL carrier and the drug might be attributed to their potent inhibitory effects on SR-A expression. In conclusion, the median-effect analysis was proven to be a feasible method to quantitatively evaluate the synergistic effect of the biofunctional carrier and the drug encapsulated.

Changes in Risk Perception of the Health Effects of Radiation and Mental Health Status: The Fukushima Health Management Survey.

PubMed

Suzuki, Yuriko; Takebayashi, Yoshitake; Yasumura, Seiji; Murakami, Michio; Harigane, Mayumi; Yabe, Hirooki; Ohira, Tetsuya; Ohtsuru, Akira; Nakajima, Satomi; Maeda, Masaharu

2018-06-10

After the Fukushima nuclear power plant accident, numerous evacuees reported poor mental health status and high-risk perceptions of the health effects of radiation. However, the temporal associations between these variables have not yet been examined. Using data from the Fukushima Health Survey, we examined changes in risk perception of the health effects of radiation over time and assessed the effects of mental health on such changes using logistic regression analysis. Risk perception for delayed effect pertains a brief on health effect in later life (delayed effect), whereas that of genetic effect pertains a brief on health effect of future children and grandchildren (genetic effect). We found that many participants showed consistently high or low-risk perceptions over all three study years (2011⁻2013) (for delayed effect: 59% and 41% of participants were in the low and high-risk perception groups, respectively; for genetic effect: 47% and 53%, respectively). Stronger traumatic reactions (≥50 on the PTSD Checklist⁻Specific) significantly affected the odds of being in the high-risk perception group for the delayed and genetic effects, with the associations being strongest soon after the disaster: The adjusted ORs (95%CIs) were 2.05 (1.82⁻2.31), 1.86 (1.61⁻2.15), and 1.88 (1.62⁻2.17) for the delayed effect in 2011, 2012, and 2013, respectively, and 2.18 (1.92⁻2.48), 2.05 (1.75⁻2.40), and 1.82 (1.55⁻2.15) for the genetic effect. As initial mental health status had the strongest impact on later risk perceptions of radiation, it should be considered in early response and communication efforts.

The prospects of selection for social genetic effects to improve welfare and productivity in livestock.

PubMed

Ellen, Esther D; Rodenburg, T Bas; Albers, Gerard A A; Bolhuis, J Elizabeth; Camerlink, Irene; Duijvesteijn, Naomi; Knol, Egbert F; Muir, William M; Peeters, Katrijn; Reimert, Inonge; Sell-Kubiak, Ewa; van Arendonk, Johan A M; Visscher, Jeroen; Bijma, Piter

2014-01-01

Social interactions between individuals living in a group can have both positive and negative effects on welfare, productivity, and health of these individuals. Negative effects of social interactions in livestock are easier to observe than positive effects. For example, laying hens may develop feather pecking, which can cause mortality due to cannibalism, and pigs may develop tail biting or excessive aggression. Several studies have shown that social interactions affect the genetic variation in a trait. Genetic improvement of socially-affected traits, however, has proven to be difficult until relatively recently. The use of classical selection methods, like individual selection, may result in selection responses opposite to expected, because these methods neglect the effect of an individual on its group mates (social genetic effects). It has become clear that improvement of socially-affected traits requires selection methods that take into account not only the direct effect of an individual on its own phenotype but also the social genetic effects, also known as indirect genetic effects, of an individual on the phenotypes of its group mates. Here, we review the theoretical and empirical work on social genetic effects, with a focus on livestock. First, we present the theory of social genetic effects. Subsequently, we evaluate the evidence for social genetic effects in livestock and other species, by reviewing estimates of genetic parameters for direct and social genetic effects. Then we describe the results of different selection experiments. Finally, we discuss issues concerning the implementation of social genetic effects in livestock breeding programs. This review demonstrates that selection for socially-affected traits, using methods that target both the direct and social genetic effects, is a promising, but sometimes difficult to use in practice, tool to simultaneously improve production and welfare in livestock.

The direct and indirect effects of corruption on motor vehicle crash deaths.

PubMed

Hua, Law Teik; Noland, Robert B; Evans, Andrew W

2010-11-01

Recent empirical research has found that there is an inverted U-shaped or Kuznets relationship between income and motor vehicle crash (MVC) deaths, such that MVC deaths increase as national income increases and decrease after reaching a critical level. Corruption has been identified as one of the underlying factors that could affect this relationship, primarily by undermining institutional development and effective enforcement schemes. The total effect of corruption can be decomposed into two components, a direct and an indirect effect. The direct effect measures the immediate impact of corruption on MVC deaths by undermining effective enforcement and regulations, while the indirect effect captures the impact of corruption on hindering increases in per capita income and the consequent impact of reduced income on MVC deaths. By influencing economic growth, corruption can lead to an increase or decrease in MVC deaths depending on the income level. Using data from 60 countries between 1982 and 2003, these effects are estimated using linear panel and fixed effects negative binomial models. The estimation results suggest that corruption has different direct effects for less developed and highly developed countries. It has a negative (decreasing) effect on MVC deaths for less developed countries and a positive (increasing) effect on MVC deaths for highly developed countries. For highly developed countries, the total effect is positive at lower per capita income levels, but decreases with per capita income and becomes negative at per capita income levels of about US$ 38,248. For less developed countries, the total effect is negative within the sample range and decreases with increased per capita income. In summary, the results of this study suggest that reduction of corruption is likely a necessary condition to effectively tackle road safety problems. 2010 Elsevier Ltd. All rights reserved.

Placebo effects in competitive sport: qualitative data.

PubMed

Beedie, Christopher J

2007-01-01

The paper examines the placebo effect in sports performance. The possibility that the placebo effect is a more common phenomenon than the quantity of published research would suggest is briefly addressed. It is suggested that the placebo control design often used in sports performance research masks any placebo effects and thus presents a false picture of the mechanisms underlying performance-enhancing interventions in the real world. An electronic survey was sent to 48 competitive, international and professional athletes. Questions related to the placebo effect in competitive sport. Thirty responses were received. Data indicate that the majority (97%) of respondents believe that the placebo effect can exert an influence on sports performance, and that a significant number (73%) have experienced what they defined as a placebo effect. Inductive content analysis reveals that these experiences fall into several categories such as explicit placebo effects, inadvertent false beliefs, ritual and reverse placebo effects. Furthermore, 10 respondents (33%) offer explanations as to the nature of the placebo effect. Again, inductive content analysis reveals that these explanations fall into several categories including deliberate changes in competitive strategy, belief/expectancy, faith in a third party, and marketing. Overall, responses support previous experimental research and anecdotal reports that have found a relationship between belief and sports performance. It is suggested that further research be structured to not simply control for the placebo effect, but to elucidate it. Key pointsA survey of 30 athletes revealed that 73% have experienced a placebo effect in sport.Athletes suggest several potential explanations for these effects.Findings support the idea that placebo effects might be common in sport.Researchers and practitioners should be aware of the possible impact of these effects on research findings and competitive performance.

Health Related Quality of Life in Patients with Side-Effects after Antimuscarinic Treatment for Overactive Bladder.

PubMed

Kim, Aram; Lee, Kyu-Sung; Jung, Rangrhee; Na, Selee; Kim, Joon-Chul; Kim, Hyeong Gon; Choo, Myung-Soo

2017-09-01

Drug therapy is the mainstay of treatment for overactive bladder (OAB), but antimuscarinic agents possess side-effects. These side-effects decrease the patients' quality of life. We therefore assessed the impact of side-effects on health-related quality of life (HR-QoL) through an analysis of EQ-5D questionnaire. This study was designed to investigate the patients' satisfaction by quality weight of health status as affected by the side-effects of OAB medications. Patients who had OAB symptoms lasting longer than 3 months and have experienced side-effects after any antimuscarinic treatments filled in the EQ-5D questionnaire. The enrolled patients had two EQ-5D questionnaires for two different health statuses, i.e., presence or absence of side-effects. Quality weight was calculated using the ED-5D health status score with Korean tariff. One hundred patients were enrolled and completed the HR-QoL questionnaire. The most prevalent side-effect was dry mouth (61%) and 28% patients had dry mouth and constipation concurrently. Most of the patients with side-effects tried to endure and overcome these side-effects (79%), but 10% desired a change in medication, and 6% stopped medication altogether. The quality weight of EQ-5D without side-effects was 0.863, while the quality weight with side-effects was 0.666 (P < 0.001). The VAS score was 79 in patient without side-effects and 57 in those with side-effects, supporting the results of quality weight assessment. Overactive bladder patients may enjoy a better quality of life if side-effects associated with antimuscarinic therapy are fewer. © 2016 John Wiley & Sons Australia, Ltd.

Effects of heat waves on mortality: effect modification and confounding by air pollutants.

PubMed

Analitis, Antonis; Michelozzi, Paola; D'Ippoliti, Daniela; De'Donato, Francesca; Menne, Bettina; Matthies, Franziska; Atkinson, Richard W; Iñiguez, Carmen; Basagaña, Xavier; Schneider, Alexandra; Lefranc, Agnès; Paldy, Anna; Bisanti, Luigi; Katsouyanni, Klea

2014-01-01

Heat waves and air pollution are both associated with increased mortality. Their joint effects are less well understood. We explored the role of air pollution in modifying the effects of heat waves on mortality, within the EuroHEAT project. Daily mortality, meteorologic, and air pollution data from nine European cities for the years 1990-2004 were assembled. We defined heat waves by taking both intensity and duration into account. The city-specific effects of heat wave episodes were estimated using generalized estimating equation models, adjusting for potential confounders with and without inclusion of air pollutants (particles, ozone, nitrogen dioxide, sulphur dioxide, carbon monoxide). To investigate effect modification, we introduced an interaction term between heat waves and each single pollutant in the models. Random effects meta-analysis was used to summarize the city-specific results. The increase in the number of daily deaths during heat wave episodes was 54% higher on high ozone days compared with low, among people age 75-84 years. The heat wave effect on high PM10 days was increased by 36% and 106% in the 75-84 year and 85+ year age groups, respectively. A similar pattern was observed for effects on cardiovascular mortality. Effect modification was less evident for respiratory mortality, although the heat wave effect itself was greater for this cause of death. The heat wave effect was smaller (15-30%) after adjustment for ozone or PM10. The heat wave effect on mortality was larger during high ozone or high PM10 days. When assessing the effect of heat waves on mortality, lack of adjustment for ozone and especially PM10 overestimates effect parameters. This bias has implications for public health policy.

The cost-effectiveness of quality improvement projects: a conceptual framework, checklist and online tool for considering the costs and consequences of implementation-based quality improvement.

PubMed

Thompson, Carl; Pulleyblank, Ryan; Parrott, Steve; Essex, Holly

2016-02-01

In resource constrained systems, decision makers should be concerned with the efficiency of implementing improvement techniques and technologies. Accordingly, they should consider both the costs and effectiveness of implementation as well as the cost-effectiveness of the innovation to be implemented. An approach to doing this effectively is encapsulated in the 'policy cost-effectiveness' approach. This paper outlines some of the theoretical and practical challenges to assessing policy cost-effectiveness (the cost-effectiveness of implementation projects). A checklist and associated (freely available) online application are also presented to help services develop more cost-effective implementation strategies. © 2015 John Wiley & Sons, Ltd.

Non-targeted and delayed effects of exposure to ionizing radiation: I. Radiation-induced genomic instability and bystander effects in vitro

NASA Technical Reports Server (NTRS)

Morgan, William F.

2003-01-01

A long-standing dogma in the radiation sciences is that energy from radiation must be deposited in the cell nucleus to elicit a biological effect. A number of non-targeted, delayed effects of ionizing radiation have been described that challenge this dogma and pose new challenges to evaluating potential hazards associated with radiation exposure. These effects include induced genomic instability and non-targeted bystander effects. The in vitro evidence for non-targeted effects in radiation biology will be reviewed, but the question as to how one extrapolates from these in vitro observations to the risk of radiation-induced adverse health effects such as cancer remains open.

Advertising media and cigarette demand.

PubMed

Goel, Rajeev K

2011-01-01

Using state-level panel data for the USA spanning three decades, this research estimates the demand for cigarettes. The main contribution lies in studying the effects of cigarette advertising disaggregated across five qualitatively different groups. Results show cigarette demand to be near unit elastic, the income effects to be generally insignificant and border price effects and habit effects to be significant. Regarding advertising effects, aggregate cigarette advertising has a negative effect on smoking. Important differences across advertising media emerge when cigarette advertising is disaggregated. The effects of public entertainment and Internet cigarette advertising are stronger than those of other media. Anti-smoking messages accompanying print cigarette advertising seem relatively more effective. Implications for smoking control policy are discussed.

Non-targeted and delayed effects of exposure to ionizing radiation: II. Radiation-induced genomic instability and bystander effects in vivo, clastogenic factors and transgenerational effects

NASA Technical Reports Server (NTRS)

Morgan, William F.

2003-01-01

The goal of this review is to summarize the evidence for non-targeted and delayed effects of exposure to ionizing radiation in vivo. Currently, human health risks associated with radiation exposures are based primarily on the assumption that the detrimental effects of radiation occur in irradiated cells. Over the years a number of non-targeted effects of radiation exposure in vivo have been described that challenge this concept. These include radiation-induced genomic instability, bystander effects, clastogenic factors produced in plasma from irradiated individuals that can cause chromosomal damage when cultured with nonirradiated cells, and transgenerational effects of parental irradiation that can manifest in the progeny. These effects pose new challenges to evaluating the risk(s) associated with radiation exposure and understanding radiation-induced carcinogenesis.

ESTIMATING PERSON-CENTERED TREATMENT (PeT) EFFECTS USING INSTRUMENTAL VARIABLES: AN APPLICATION TO EVALUATING PROSTATE CANCER TREATMENTS

PubMed Central

BASU, ANIRBAN

2014-01-01

SUMMARY This paper builds on the methods of local instrumental variables developed by Heckman and Vytlacil (1999, 2001, 2005) to estimate person-centered treatment (PeT) effects that are conditioned on the person’s observed characteristics and averaged over the potential conditional distribution of unobserved characteristics that lead them to their observed treatment choices. PeT effects are more individualized than conditional treatment effects from a randomized setting with the same observed characteristics. PeT effects can be easily aggregated to construct any of the mean treatment effect parameters and, more importantly, are well suited to comprehend individual-level treatment effect heterogeneity. The paper presents the theory behind PeT effects, and applies it to study the variation in individual-level comparative effects of prostate cancer treatments on overall survival and costs. PMID:25620844

[The role of VEGF, HSP-70 and protein S-100B in the potentiation effect of the neuroprotective effect of hypercapnic hypoxia].

PubMed

Bespalov, A G; Tregub, P P; Kulikov, V P; Pijanzin, A I; Belousov, A A

2014-01-01

Studied the role of VEGF, HSP-70 and S-100B in potentiating hypercapnia neuroprotective effect of hypoxia. Demonstrated that neuroprotective effects when exposed hypercapnic hypoxia-mediated protein synthesis increased S-100B, mainly due to the action of carbon dioxide, and not oxygen deficiency. Neuroprotective effects of HSP-70 due to hypoxia, but the combined effect of hypoxia and hypercapnia gives a significant increase in the synthesis of HSP-70 in comparison with the isolated effect of hypoxia. Vascularization activated equally as hypoxia and hypercapnia, without adding significant effects in combination. This suggests dominant effect hypercapnia, hypoxia compared in neuroprotection mechanisms related to protein S-100B, but not the protein VEGF, hypercapnia and potentiate the neuroprotective efficacy of hypoxia-related protein HSP-70.

Elements of Conjunctive Use Water Supply.

DTIC Science & Technology

1988-03-01

180 ENVIRONMENTAL EFFECTS ............ oee-eesessese..........182 EFFECTS OF FACILITIES...184 EFFECTS OF APPLICATION OF WATER .................. 191 EFFECTS OF GROUNDWATER PUMPING ........................ 197 AIR QUALITY, NOISE...those involved in conjunctive use planning to more effectively and quickly focus on the necessary tasks. The major elements are described and important

77 FR 57066 - Proposed Flood Elevation Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-17

... River, Irwin Creek (backwater effects from Green River), Isaacs Creek (backwater effects from Green... River, Irwin Creek (backwater effects from Green River), Isaacs Creek (backwater effects from Green... miles +403 +404 upstream of CSX Railroad. Irwin Creek (backwater effects from From the Isaacs Creek None...

The Expertise Reversal Effect Concerning Instructional Explanations

ERIC Educational Resources Information Center

Rey, Gunter Daniel; Fischer, Andreas

2013-01-01

The expertise reversal effect occurs when learner's expertise moderates design principles derived from cognitive load theory. Although this effect is supported by numerous empirical studies, indicating an overall large effect size, the effect was never tested by inducing expertise experimentally and using instructional explanations in a…

Effective Instructor Feedback: Perceptions of Online Graduate Students

ERIC Educational Resources Information Center

Getzlaf, Beverley; Perry, Beth; Toffner, Greg; Lamarche, Kimberley; Edwards, Margaret

2009-01-01

This descriptive study explored online graduate students' perceptions of effective instructor feedback. The objectives of the study were to determine the students' perceptions of the content of effective instructor feedback ("what should be included in effective feedback?") and the process of effective instructor feedback ("how…

Assessing Spurious Interaction Effects in Structural Equation Modeling

ERIC Educational Resources Information Center

Harring, Jeffrey R.; Weiss, Brandi A.; Li, Ming

2015-01-01

Several studies have stressed the importance of simultaneously estimating interaction and quadratic effects in multiple regression analyses, even if theory only suggests an interaction effect should be present. Specifically, past studies suggested that failing to simultaneously include quadratic effects when testing for interaction effects could…

Improving Conditions for Principal Effectiveness: Policy Implications of Research on Effective Principals.

ERIC Educational Resources Information Center

Manasse, A. Lorri

This paper reviews principal effectiveness research and suggests measures that might promote effective principalship. The first section discusses principals' behavior patterns and conditions bearing on their effectiveness. Topics examined include role ambiguity, goal setting behavior, leadership and initiative, management behaviors, instructional…

14 CFR 372.32 - Effective period.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Aeronautics and Space OFFICE OF THE SECRETARY, DEPARTMENT OF TRANSPORTATION (AVIATION PROCEEDINGS) SPECIAL... operating authorization shall be effective upon the date specified therein, and shall continue in effect... remain in effect, or if issued for a limited period of time, shall continue in effect until the...

Is there a common mechanism underlying genomic instability, bystander effects and other nontargeted effects of exposure to ionizing radiation?

NASA Technical Reports Server (NTRS)

Morgan, William F.

2003-01-01

A number of nontargeted and delayed effects associated with radiation exposure have now been described. These include radiation-induced genomic instability, death-inducing and bystander effects, clastogenic factors and transgenerational effects. It is unlikely that these nontargeted effects are directly induced by cellular irradiation. Instead, it is proposed that some as yet to be identified secreted factor can be produced by irradiated cells that can stimulate effects in nonirradiated cells (death-inducing and bystander effects, clastogenic factors) and perpetuate genomic instability in the clonally expanded progeny of an irradiated cell. The proposed factor must be soluble and capable of being transported between cells by cell-to-cell gap junction communication channels. Furthermore, it must have the potential to stimulate cellular cytokines and/or reactive oxygen species. While it is difficult to imagine a role for such a secreted factor in contributing to transgenerational effects, the other nontargeted effects of radiation may all share a common mechanism.

Sensitivity studies of different aerosol indirect effects in mixed-phase clouds

NASA Astrophysics Data System (ADS)

Lohmann, U.; Hoose, C.

2009-11-01

Aerosols affect the climate system by changing cloud characteristics. Using the global climate model ECHAM5-HAM, we investigate different aerosol effects on mixed-phase clouds: The glaciation effect, which refers to a more frequent glaciation due to anthropogenic aerosols, versus the de-activation effect, which suggests that ice nuclei become less effective because of an anthropogenic sulfate coating. The glaciation effect can partly offset the indirect aerosol effect on warm clouds and thus causes the total anthropogenic aerosol effect to be smaller. It is investigated by varying the parameterization for the Bergeron-Findeisen process and the threshold coating thickness of sulfate (SO4-crit), which is required to convert an externally mixed aerosol particle into an internally mixed particle. Differences in the net radiation at the top-of-the-atmosphere due to anthropogenic aerosols between the different sensitivity studies amount up to 0.5 W m-2. This suggests that the investigated mixed-phase processes have a major effect on the total anthropogenic aerosol effect.

Sensitivity studies of different aerosol indirect effects in mixed-phase clouds

NASA Astrophysics Data System (ADS)

Lohmann, U.; Hoose, C.

2009-07-01

Aerosols affect the climate system by changing cloud characteristics. Using the global climate model ECHAM5-HAM, we investigate different aerosol effects on mixed-phase clouds: The glaciation effect, which refers to a more frequent glaciation due to anthropogenic aerosols, versus the de-activation effect, which suggests that ice nuclei become less effective because of an anthropogenic sulfate coating. The glaciation effect can partly offset the indirect aerosol effect on warm clouds and thus causes the total anthropogenic aerosol effect to be smaller. It is investigated by varying the parameterization for the Bergeron-Findeisen process and the threshold coating thickness of sulfate (SO4-crit), which is required to convert an externally mixed aerosol particle into an internally mixed particle. Differences in the net radiation at the top-of-the-atmosphere due to anthropogenic aerosols between the different sensitivity studies amount up to 0.5 W m-2. This suggests that the investigated mixed-phase processes have a major effect on the total anthropogenic aerosol effect.

The effective propagation constants of SH wave in composites reinforced by dispersive parallel nanofibers

NASA Astrophysics Data System (ADS)

Qiang, FangWei; Wei, PeiJun; Li, Li

2012-07-01

In the present paper, the effective propagation constants of elastic SH waves in composites with randomly distributed parallel cylindrical nanofibers are studied. The surface stress effects are considered based on the surface elasticity theory and non-classical interfacial conditions between the nanofiber and the host are derived. The scattering waves from individual nanofibers embedded in an infinite elastic host are obtained by the plane wave expansion method. The scattering waves from all fibers are summed up to obtain the multiple scattering waves. The interactions among random dispersive nanofibers are taken into account by the effective field approximation. The effective propagation constants are obtained by the configurational average of the multiple scattering waves. The effective speed and attenuation of the averaged wave and the associated dynamical effective shear modulus of composites are numerically calculated. Based on the numerical results, the size effects of the nanofibers on the effective propagation constants and the effective modulus are discussed.

Neither fixed nor random: weighted least squares meta-analysis.

PubMed

Stanley, T D; Doucouliagos, Hristos

2015-06-15

This study challenges two core conventional meta-analysis methods: fixed effect and random effects. We show how and explain why an unrestricted weighted least squares estimator is superior to conventional random-effects meta-analysis when there is publication (or small-sample) bias and better than a fixed-effect weighted average if there is heterogeneity. Statistical theory and simulations of effect sizes, log odds ratios and regression coefficients demonstrate that this unrestricted weighted least squares estimator provides satisfactory estimates and confidence intervals that are comparable to random effects when there is no publication (or small-sample) bias and identical to fixed-effect meta-analysis when there is no heterogeneity. When there is publication selection bias, the unrestricted weighted least squares approach dominates random effects; when there is excess heterogeneity, it is clearly superior to fixed-effect meta-analysis. In practical applications, an unrestricted weighted least squares weighted average will often provide superior estimates to both conventional fixed and random effects. Copyright © 2015 John Wiley & Sons, Ltd.

Sex-differential heterologous (non-specific) effects of vaccines: an emerging public health issue that needs to be understood and exploited.

PubMed

Flanagan, Katie L; Plebanski, Magdalena

2017-01-01

Vaccines have heterologous effects on the immune system, leading to altered susceptibility to a range of pathogens, and possibly allergy and autoimmunity. Effects are often sex-differential. This review discusses the evidence, mechanisms and public health implications of the non-specific effects of vaccines (NSEs). Areas covered: This article firstly discusses the World Health Organization systematic review of the evidence for sex-differential heterologous effects of vaccines, and further PubMed indexed studies on NSEs on susceptibility to infectious diseases, allergy, autoimmunity and malignancy in animals and humans. Potential immunological mechanisms are evaluated, including sex-differential effects. Finally it describes how advances in systems biology might be applied to study such effects. Expert commentary: This section points out the need to understand immune mechanisms in order to exploit beneficial vaccine effects, and diminish deleterious ones. It suggests analysis of vaccine effects by sex is important, and discusses the future for personalised vaccines that take these effects into account.

Are adverse effects incorporated in economic models? An initial review of current practice.

PubMed

Craig, D; McDaid, C; Fonseca, T; Stock, C; Duffy, S; Woolacott, N

2009-12-01

To identify methodological research on the incorporation of adverse effects in economic models and to review current practice. Major electronic databases (Cochrane Methodology Register, Health Economic Evaluations Database, NHS Economic Evaluation Database, EconLit, EMBASE, Health Management Information Consortium, IDEAS, MEDLINE and Science Citation Index) were searched from inception to September 2007. Health technology assessment (HTA) reports commissioned by the National Institute for Health Research (NIHR) HTA programme and published between 2004 and 2007 were also reviewed. The reviews of methodological research on the inclusion of adverse effects in decision models and of current practice were carried out according to standard methods. Data were summarised in a narrative synthesis. Of the 719 potentially relevant references in the methodological research review, five met the inclusion criteria; however, they contained little information of direct relevance to the incorporation of adverse effects in models. Of the 194 HTA monographs published from 2004 to 2007, 80 were reviewed, covering a range of research and therapeutic areas. In total, 85% of the reports included adverse effects in the clinical effectiveness review and 54% of the decision models included adverse effects in the model; 49% included adverse effects in the clinical review and model. The link between adverse effects in the clinical review and model was generally weak; only 3/80 (< 4%) used the results of a meta-analysis from the systematic review of clinical effectiveness and none used only data from the review without further manipulation. Of the models including adverse effects, 67% used a clinical adverse effects parameter, 79% used a cost of adverse effects parameter, 86% used one of these and 60% used both. Most models (83%) used utilities, but only two (2.5%) used solely utilities to incorporate adverse effects and were explicit that the utility captured relevant adverse effects; 53% of those models that included utilities derived them from patients on treatment and could therefore be interpreted as capturing adverse effects. In total, 30% of the models that included adverse effects used withdrawals related to drug toxicity and therefore might be interpreted as using withdrawals to capture adverse effects, but this was explicitly stated in only three reports. Of the 37 models that did not include adverse effects, 18 provided justification for this omission, most commonly lack of data; 19 appeared to make no explicit consideration of adverse effects in the model. There is an implicit assumption within modelling guidance that adverse effects are very important but there is a lack of clarity regarding how they should be dealt with and considered in modelling. In many cases a lack of clear reporting in the HTAs made it extremely difficult to ascertain what had actually been carried out in consideration of adverse effects. The main recommendation is for much clearer and explicit reporting of adverse effects, or their exclusion, in decision models and for explicit recognition in future guidelines that 'all relevant outcomes' should include some consideration of adverse events.

Cross-Cultural Generalizability of Year in School Effects: Negative Effects of Acceleration and Positive Effects of Retention on Academic Self-Concept

ERIC Educational Resources Information Center

Marsh, Herbert W.

2016-01-01

Given that the Big-Fish-Little-Pond-Effect, the negative effect of school-average achievement on academic self-concept, is one of the most robust findings in educational psychology (Marsh, Seaton et al., 2007), this research extends the theoretical model, based on social comparison theory, to study relative year in school effects (e.g., being 1…