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At least 433 records · Page 24Linked to original sources
PubMed2005

Prenylflavonoids and phloroglucinol derivatives from hops (Humulus lupulus).

The ethyl acetate soluble fraction of hops (Humulus lupulus) showed potent inhibitory activity on the production of nitric oxide (NO) induced by a combination of LPS and IFN-gamma. Four known prenylflavonoids (1-4) and a new prenylflavonoid (5), hulupinic acid (6), lupulone (7), and its six new derivatives (8-13) were isolated from the active fraction. The structures were determined on the basis of physiochemical properties and spectroscopic analysis. Their inhibitory activities on the production of NO in macrophage RAW 264.7 cells were examined.

Animals↗
PubMed2003

Effect of green manure on the incidence of cyanogenic Pseudomonas strains in hop garden soils.

Incidence of cyanogenic Pseudomonas strains in hop garden soils in relation to the kind of fertilization was studied. Incidence differed with respect to the fertilization treatment and the age of the plantation. Amendment of soil with rye and with white mustard as green manures limited the number of cyanogenic Pseudomonas strains relative to farmyard manures and NPK fertilization. Among all fertilization treatments, cyanogenic Pseudomonas spp. strains had lowest populations in soils amended with white mustard.

Fertilizers↗
PubMed2005

Prevention of diet-induced obesity by dietary isomerized hop extract containing isohumulones, in rodents.

OBJECTIVE: Isomerized hop extract (IHE), which consists mainly of isohumulones and is required in the beer brewing process, was investigated for its effects on diet-induced obesity in two strains of mice. DESIGN: C57BL/6N and KK-A(y) mice were fed a standard or high-fat diet containing IHE and their body and tissue weights were measured at various time points. Oral glucose tolerance tests (OGTT) and insulin tolerance tests (ITT) were carried out in high-fat diet-fed C57BL/6N mice. The effects of IHE on intestinal lipid absorption were examined in Wistar rats using a plasma triacylglycerol assay after oral administration of a lipid emulsion. Fecal lipid levels were also measured in these animals after they were fed a high-fat diet containing IHE for 15 days. The effects of IHE on pancreatic lipase activity and the expression of genes involved in hepatic lipid metabolism were also examined using an in vitro assay and quantitative RT-PCR, respectively. RESULTS: Supplementation of high-fat-containing chow with IHE reduced body weight gain and improved glucose tolerance in our experimental mice. A reduction in body weight gain was also observed in C57BL/6N mice fed a standard diet containing IHE. Wistar rats fed a high-fat diet containing IHE showed reduced plasma triacylglycerol levels and an increase in their fecal lipid excretion. Similarly, their pancreatic lipase activity was inhibited and their elevation in plasma triacylglycerol levels seen after the oral administration of lipid emulsion was significantly suppressed. IHE-fed mice showed an increased expression in their lipid oxidation genes and a decreased expression in genes involved in triacylglycerol biosynthesis. CONCLUSION: The inhibition of intestinal dietary fat absorption may be the mechanism by which IHE induces its weight-lowering effects in high-fat diet-fed mice. The modulatory effect of IHE on lipid metabolism may also, at least partly, be responsible for its beneficial effects on body weight gain. These results suggest that IHE may be helpful in humans in preventing diet-induced obesity and perhaps even metabolic syndrome, the latter of which is known to be associated with obesity.

Animals↗
PubMed2001

Hopping, jumping and looping by restriction enzymes.

Type II restriction endonucleases recognize specific DNA sequences and cleave both strands of the DNA at fixed locations at or near their recognition sites. Many of these enzymes are dimeric proteins that recognize, in symmetrical fashion, palindromic DNA sequences. They generally catalyse independent reactions at each recognition site on the DNA, although in some cases they act processively; cutting the DNA first at one site, then translocating along the DNA to another site and cutting that before leaving the DNA. The way in which the degree of processivity varies with the length of DNA between the sites can reveal the mechanism of translocation. In contrast with the common view that proteins move along DNA by 'sliding', the principal mode of transfer of the EcoRV endonuclease is by 'hopping' and 'jumping', i.e. the dissociation of the protein from one site followed by its re-association with another site in the same DNA molecule, either close to or distant from the original site. Other type II restriction enzymes require two copies of their recognition sites for their DNA cleavage reactions. Many of these enzymes, such as SfiI, are tetramers with two DNA-binding surfaces. SfiI has no activity when bound to just one recognition site, and instead both DNA-binding surfaces have to be filled before it becomes active. Although the two sites can be on separate DNA molecules, SfiI acts optimally with two sites on the same DNA, where it traps the DNA between the sites in a loop. SfiI thus constitutes a test system for the analysis of DNA looping.

Base Sequence↗
PubMed1999

Biosynthesis of bitter acids in hops. A (13)C-NMR and (2)H-NMR study on the building blocks of humulone.

The biosynthesis of humulone, an antibacterial bitter acid from hops, was studied by isotope-incorporation experiments using (13)C-labelled glucose or (2)H(2)O. (13)C enrichments, (2)H enrichments and (13)C(13)C coupling patterns identify isovaleryl-CoA, malonyl-CoA and dimethylallyl pyrophosphate as precursors for humulone. Dimethylallyl pyrophosphate, which serves as a building block for the bitter acid, is generated via the deoxyxylulose pathway of terpenoid biosynthesis. The data confirm that a symmetrical intermediate is involved in humulone formation.

Acyl Coenzyme A↗
PubMed2004

Army ants algorithm for rare event sampling of delocalized nonadiabatic transitions by trajectory surface hopping and the estimation of sampling errors by the bootstrap method.

The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory surface hopping (TSH) calculations is the so-called anteater algorithm, which is inefficient for sampling low-probability nonadiabatic events. We present a new sampling scheme (called the army ants algorithm) for carrying out TSH calculations that is applicable to systems with any strength of coupling. The army ants algorithm is a form of rare event sampling whose efficiency is controlled by an input parameter. By choosing a suitable value of the input parameter the army ants algorithm can be reduced to the anteater algorithm (which is efficient for strongly coupled cases), and by optimizing the parameter the army ants algorithm may be efficiently applied to systems with low-probability events. To demonstrate the efficiency of the army ants algorithm, we performed atom-diatom scattering calculations on a model system involving weakly coupled electronic states. Fully converged quantum mechanical calculations were performed, and the probabilities for nonadiabatic reaction and nonreactive deexcitation (quenching) were found to be on the order of 10(-8). For such low-probability events the anteater sampling scheme requires a large number of trajectories ( approximately 10(10)) to obtain good statistics and converged semiclassical results. In contrast by using the new army ants algorithm converged results were obtained by running 10(5) trajectories. Furthermore, the results were found to be in excellent agreement with the quantum mechanical results. Sampling errors were estimated using the bootstrap method, which is validated for use with the army ants algorithm.

Journal Article↗
PubMed2004

Minima hopping: an efficient search method for the global minimum of the potential energy surface of complex molecular systems.

A method is presented that can find the global minimum of very complex condensed matter systems. It is based on the simple principle of exploring the configurational space as fast as possible and of avoiding revisiting known parts of this space. Even though it is not a genetic algorithm, it is not based on thermodynamics. The efficiency of the method depends strongly on the type of moves that are used to hop into new local minima. Moves that find low-barrier escape-paths out of the present minimum generally lead into low energy minima.

Journal Article↗
PubMed2004

Path-integral Monte Carlo simulations for electronic dynamics on molecular chains. I. Sequential hopping and super exchange.

An improved real-time quantum Monte Carlo procedure is presented and applied to describe the electronic transfer dynamics along molecular chains. The model consists of discrete electronic sites coupled to a thermal environment which is integrated out exactly within the path integral formulation. The approach is numerically exact and its results reduce to known analytical findings (Marcus theory, golden rule) in proper limits. Special attention is paid to the role of superexchange and sequential hopping at lower temperatures in symmetric donor-bridge-acceptor systems. In contrast to previous approximate studies, superexchange turns out to play a significant role only for extremely high-lying bridges where the transfer is basically frozen or for extremely low temperatures where for weaker dissipation a description in terms of rate constants is no longer feasible. For bridges with increasing length an algebraic decrease of the yield is found for short as well as for long bridges. The approach can be extended to electronic systems with more complicated topologies including impurities and in presence of external time-dependent forces.

Journal Article↗
PubMed2005

Intramolecular fluorescence quenching in luminescent copolymers containing fluorenone and fluorene units: a direct measurement of intrachain exciton hopping rate.

The quenching process of fluorescence emission in polyfluorene (PF) due to the presence of intramolecular 9-fluorenone (9 FL) moieties is studied in dilute toluene solution as a function of 9 FL content in eight copolymers containing both fluorene and fluorenone units (PF/FL(x)). The absorption spectrum of PF/FL(x) copolymers clearly shows a new absorption band, redshifted relatively to the PF and 9-fluorenone absorption, which increases in intensity when the fluorenone fraction increases and also decreases with solvent polarity. Fluorescence emission spectra of PF/FL(x) show that this redshifted and unstructured emission does not coincide with the 9-fluorenone emission and, with increasing solvent polarity, it further redshifts and decreases in intensity. An isoemissive point is clearly observed on the fluorescence emission spectra of PF/FL(x) as a function of fluorenone content, showing that the new emission band is formed at the expense of PF. We propose the formation of an intramolecular charge transfer complex (ICTC) between PF units and 9-fluorenone to explain the appearance of the new emission band. Global analysis of time resolved fluorescence decays collected at 415 nm (PF emission) and 580 nm (the ICTC emission) show that three exponentials are generally needed to achieve excellent fits. Two of the components (420 ps and 6.5 ns) are independent of 9-fluorenone fraction. A further fast component is strongly dependent on fluorenone fraction and ranges between 280 and 70 ps. This component appears as a decay time at 415 nm and as a rise time at 580 nm and is ascribed to the migration of exciton to quenching sites (formation of intramolecular CT complex or exciton ionization at CT complex). A kinetic mechanism involving three different kinetic species, quenched PF units kinetically coupled with the ICTC complex, and unquenched PF units is proposed to explain the experimental data and the quenching rate constant is obtained, k(1) congruent with 10(11) s(-1). This is an experimental measurement of the intrachain exciton hopping rate.

Journal Article↗
PubMed2005

The photodynamics of ethylene: a surface-hopping study on structural aspects.

Simulations of the photodynamics of ethylene were carried out by employing the semiempirical direct trajectory with surface hopping method in order to assess quantitatively the importance of different regions of the S(2)S(1) and S(1)S(0) crossing seams. The results show that during the first 50 fs after a vertical photoexcitation to the pipi(*) state, the nonadiabatic coupling between the S(1) and the S(2) states produces a recurrence pattern of oscillation of the populations in these states. Within the first 100 fs, the S(1) state population spans a limited region of the configuration space between the initial geometries and the twisted-pyramidalized minimum on the crossing seam (MXS). Depending on the way of counting, about 50% of the S(1)-->S(0) transitions occur in the pyramidalized region of the crossing seam, but not necessarily close to the MXS. The remaining 50% occurs in the H-migration and ethylidene regions. Our analysis shows that the ethylidene region becomes more important in later stages of the dynamics when the flux of trajectories that was not effectively converted to the ground state in the pyramidalized region starts to reach this part of the configuration space. The excited-state nonadiabatic dynamics could be employed to generate suitable initial phase space distributions for the hot-ethylene ground-state kinetic studies.

Journal Article↗
PubMed2005

The triplet channel in the photodissociation of ozone in the Hartley band: classical trajectory surface hopping analysis.

The triplet channel in the photodissociation of ozone in the Hartley band, O3 + hv-->O(3P) + O2(3sigma), is investigated by means of a classical trajectory surface hopping method using ab initio diabatic potential energy surfaces for the B and the R states. Because of the strong recoil in the R state along the breaking O-O bond, O2(3sigma) is produced with a high rotational energy. The nonadiabatic transition probability depends markedly on the coordinate along the crossing seam. As a consequence a unique correlation is found between the internuclear geometry at the crossing and the final vibrational state of O2(3sigma). The calculated distribution of the translational energy is in good accord with the measured distribution.

Journal Article↗
PubMed2005

Dynamic arrest in a liquid of symmetric dumbbells: reorientational hopping for small molecular elongations.

We present extensive equilibrium and out-of-equilibrium molecular-dynamics simulations of a liquid of symmetric dumbbell molecules, for constant packing fraction, as a function of temperature and molecular elongation. We compute diffusion constants as well as odd and even orientational correlators. The notations odd and even refer to the parity of the order l of the corresponding Legendre l polynomial, evaluated for the orientation of the molecular axis relative to its initial position. Rotational degrees of freedom of order l are arrested if, in the long-time limit, the corresponding orientational l correlator does not decay to zero. It is found that for large elongations translational and rotational degrees of freedom freeze at the same temperature. For small elongations only the even rotational degrees of freedom remain coupled to translational motions and arrest at a finite common temperature. On the contrary, the odd rotational degrees of freedom remain ergodic at all investigated temperatures. Hence, in the translationally arrested state, each molecule remains trapped in the cage formed by its neighboring molecules, but is able to perform 180 degrees rotations, which lead to relaxation only for the odd orientational correlators. The temperature dependence of the characteristic time of these residual rotations is well described by an Arrhenius law. Finally, we discuss the evidence in favor of the presence of the type-A transition for the odd rotational degrees of freedom, as predicted by mode-coupling theory for small molecular elongations. This transition is distinct from the type-B transition, associated with the arrest of the translational and even rotational degrees of freedom for small elongations, and with all degrees of freedom for large elongations. Odd orientational correlators are computed for small elongations at very low temperatures in the translationally arrested state. The obtained results suggest that hopping events restore the ergodicity of the odd rotational degrees of freedom at temperatures far below the A transition.

Journal Article↗
PubMed2005

Simulation of the photodynamics of azobenzene on its first excited state: comparison of full multiple spawning and surface hopping treatments.

We have studied the cis-->trans and trans-->cis photoisomerization of azobenzene after n-->pi* excitation using the full multiple spawning (FMS) method for nonadiabatic wave-packet dynamics with potential-energy surfaces and couplings determined "on the fly" from a reparametrized multiconfigurational semiempirical method. We compare the FMS results with a previous direct dynamics treatment using the same potential-energy surfaces and couplings, but with the nonadiabatic dynamics modeled using a semiclassical surface hopping (SH) method. We concentrate on the dynamical effects that determine the photoisomerization quantum yields, namely, the rate of radiationless electronic relaxation and the character of motion along the reaction coordinate. The quantal and semiclassical results are in good general agreement, confirming our previous analysis of the photodynamics. The SH method slightly overestimates the rate of excited state decay, leading in this case to lower quantum yields.

Journal Article↗
PubMed2006

A surface hopping method for chemical reaction dynamics in solution described by diabatic representation: an analysis of tunneling and thermal activation.

We present a surface hopping method for chemical reaction in solution based on diabatic representation, where quantum mechanical time evolution of the vibrational state of the reacting nuclei as well as the reaction-related electronic state of the system are traced simultaneously together with the classical motion of the solvent. The method is effective in describing the system where decoherence between reactant and product states is rapid. The diabatic representation can also give a clear picture for the reaction mechanism, e.g., thermal activation mechanism and a tunneling one. An idea of molecular orbital theory has been applied to evaluate the solvent contribution to the electronic coupling which determines the rate of reactive transition between the reactant and product potential surfaces. We applied the method to a model system which can describe complex chemical reaction of the real system. Two numerical examples are presented in order to demonstrate the applicability of the present method, where the first example traces a chemical reaction proceeded by thermal activation mechanism and the second examines tunneling mechanism mimicking a proton transfer reaction.

Journal Article↗
PubMed2006

Variation of sperm head shape and tail length in a species of Australian hydromyine rodent: the spinifex hopping mouse, Notomys alexis.

In Australia, there are around 60 species of murid rodents that occur in the subfamily Hydromyinae, most of which produce highly complex, monomorphic, spermatozoa in which the head has an apical hook together with two ventral processes containing filamentous actin and a long tail of species-specific length. One of the few exceptions to this is the spinifex hopping mouse, Notomys alexis, whose spermatozoa have previously been shown to have pleiomorphic heads. In this study, the structural organisation of the sperm head has been investigated in more detail and the variability in length of the midpiece and total length of the sperm tail has been determined for this species. The findings confirm that pleiomorphic sperm heads are invariably present in these animals and that this variability is associated with that of the nucleus, although nuclear vacuoles were not evident. The total length of the sperm tail, as well as that of the midpiece, was also highly variable both within, as well as between, individual animals. The reason(s) for this high degree of variability in sperm morphology is not known but it may relate to a relaxation of the genetic control of sperm form owing to depressed levels of inter-male sperm competition.

Animals↗
PubMed2006

NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA.

Nonspecific protein-DNA interactions are inherently dynamic and involve both diffusion of the protein along the DNA and hopping of the protein from one DNA molecule or segment to another. Understanding how gene regulatory proteins interact nonspecifically with DNA in terms of both structure and dynamics is challenging because the experimental observables are an ensemble average of many rapidly exchanging states. By using a variety of NMR spectroscopic techniques, including relaxation analysis, paramagnetic relaxation enhancement, and residual dipolar couplings, we have characterized structural and kinetic aspects of the interaction of the HoxD9 homeodomain with a nonspecific, 24-bp DNA duplex in a system in which the protein is not constrained to any particular site. The data reveal that HoxD9 binds to nonspecific DNA with the same binding mode and orientation as that observed in the specific complex. The mobility, however, of Arg side-chains contacting the DNA is increased in the nonspecific complex relative to the specific one. The kinetics of intermolecular translocation between two different nonspecific DNA molecules have also been analyzed and reveal that at high DNA concentrations (such as those present in vivo) direct transfer from one nonspecific complex to another nonspecific DNA molecule occurs without going through the intermediary of free protein. This finding provides a simple mechanism for accelerating the target search in vivo for the specific site in a sea of nonspecific sites by permitting more effective sampling of available DNA sites as the protein jumps from one segment to another.

DNA↗
PubMed1999

Long-distance charge transport in duplex DNA: the phonon-assisted polaron-like hopping mechanism.

An anthraquinone-linked duplex DNA oligomer containing 60 base pairs was synthesized by PCR. The strand complementary to the quinone-containing strand has four isolated GG steps, which serve as traps for a migrating radical cation. Irradiation of the quinone leads to electron transfer from the DNA to the quinone forming the anthraquinone radical anion and a base radical cation. The radical cation migrates through the DNA, causing reaction at GG steps revealed as strand breaks. The efficiency of strand cleavage falls off exponentially with distance from the quinone (slope = -0.02 A(-1)). This finding necessitates reinterpretation of mechanisms proposed for radical cation migration in DNA. We propose that radical cations form self-trapped polarons that migrate by thermally activated hopping.

Anthraquinones↗
PubMed2004

Isohumulones, bitter acids derived from hops, activate both peroxisome proliferator-activated receptor alpha and gamma and reduce insulin resistance.

The peroxisome proliferator-activated receptors (PPARs) are dietary lipid sensors that regulate fatty acid and carbohydrate metabolism. The hypolipidemic effects of fibrate drugs and the therapeutic benefits of the thiazolidinedione drugs are due to their activation of PPARalpha and -gamma, respectively. In this study, isohumulones, the bitter compounds derived from hops that are present in beer, were found to activate PPARalpha and -gamma in transient co-transfection studies. Among the three major isohumulone homologs, isohumulone and isocohumulone were found to activate PPARalpha and -gamma. Diabetic KK-Ay mice that were treated with isohumulones (isohumulone and isocohumulone) showed reduced plasma glucose, triglyceride, and free fatty acid levels (65.3, 62.6, and 73.1%, respectively, for isohumulone); similar reductions were found following treatment with the thiazolidinedione drug, pioglitazone. Isohumulone treatment did not result in significant body weight gain, although pioglitazone treatment did increase body weight (10.6% increase versus control group). C57BL/6N mice fed a high fat diet that were treated with isohumulones showed improved glucose tolerance and reduced insulin resistance. Furthermore, these animals showed increased liver fatty acid oxidation and a decrease in size and an increase in apoptosis of their hypertrophic adipocytes. A double-blind, placebo-controlled pilot study for studying the effect of isohumulones on diabetes suggested that isohumulones significantly decreased blood glucose and hemoglobin A1c levels after 8 weeks (by 10.1 and 6.4%, respectively, versus week 0). These results suggest that isohumulones can improve insulin sensitivity in high fat diet-fed mice with insulin resistance and in patients with type 2 diabetes.

Aged↗