Chemical synthesis and folding pathways of large cyclic polypeptide: Studies of the cystine knot polypeptide kalata B1

Kalata B1 is a member of a new family of polypeptides, isolated from. plants, which have a cystine knot structure embedded within an amide-cyclized backbone. This family of molecules are the largest known cyclic peptides, and thus, the mechanism of synthesis and folding is of great interest. To provide information about both these phenomena, we have synthesized kalata B1 using two distinct strategies. In the first, oxidation of the cysteine residues of a linear precursor peptide to form the correct disulfide bonds results in folding of the three-dimensional structure and preorganization of the termini in close proximity for subsequent cyclization. The second approach involved cyclization prior to oxidation. In the first method, the correctly folded peptide was produced only in the presence of partially hydrophobic solvent conditions. These conditions are presumably required to stabilize the surface-exposed hydrophobic residues. However,; in the synthesis,involving cyclization prior to oxidation, the cyclic reduced peptide folded to a significant degree in the absence of hydrophobic solvents and even more efficiently in the presence of hydrophobic solvents. Cyclization clearly has a major effect on the folding pathway and facilitates formation of the correctly disulfide-bonded form in aqueous solution; In addition to facilitating folding to a compact stable structure cyclization has an important effect on biological activity as assessed by hemolytic activity.

Submarine groundwater discharge and associated chemical input to a coastal sea

This paper presents a theoretical model of flow and chemical transport processes in subterranean estuaries (unconfined brackish groundwater aquifers at the ocean-land interface). The model shows that groundwater circulation and oscillating flow, caused by wave setup and tide, may constitute up to 96% of submarine groundwater discharge (SGWD) compared with 4% due to the net groundwater discharge. While these local flow processes do not change the total amount of land-derived chemical input to the ocean over a long period (e.g., yearly), they induce fluctuations of the chemical transfer rate as the aquifer undergoes saltwater intrusion. This may result in a substantial increase in chemical fluxes to the ocean over a short period (e.g., monthly and by a factor of 20 above the averaged level), imposing a possible threat to the marine environment. These results are essentially consistent with the experimental findings of Moore [1996] and have important implications for coastal resources management.

Role of chemical cues from cotton in mediating host selection and oviposition behaviour in Helicoverpa armigera (Hubner) (Lepidoptera : Noctuidae)

We investigated the role of chemoreception in the host selection and oviposition behaviour of Helicoverpa armigera in the laboratory using five cotton genotypes and synthetic volatile terpenes. Female moths oviposited on substrates treated with methanol, ethanol, acetone and pentane extracts of leaves, squares and flowers of the cotton genotypes. Phytochemicals soluble in pentane were the most efficient in eliciting oviposition behaviour. In a two-way bioassay, pentane extracts of leaves or squares of a Multiple Host-plant Resistance genotype (MHR11), Deltapine commercial (DP90), and Smith Red Leaf (SRL) received significantly more eggs than solvent-treated controls. Extracts of squares of the native genotype Gossypium nelsonii did not receive more eggs. Females preferred DP90 and MHR11 to SRL and G. nelsonii. Female moths also laid more eggs on pentane extracts of MHR11 flowers than MHR11 leaves from preflowering, early flowering and peak-flowering plants. In a flight chamber, female moths used olfactory cues at short range to mediate oviposition and discrimination between host plants. Egg-laying, mated females were attracted at a distance (1.5 m) to volatile compounds released by whole plants and odours emanating from filter papers treated with synthetic volatile terpenes. Individually, the terpenes did not stimulate any significant oviposition response. However, there was a significant oviposition response to a mixture of equal volumes of the terpenes (trans-beta-caryophyllene, alpha-pinene, beta-pinene, myrcene, beta-bisabolol, and alpha-humulene). Conversely, antennectomised (moths with transected antennae), egg-laying, mated females did not stimulate any significant oviposition response. The significance of these findings in relation to H. armigera hostplant selection are discussed.

Chemical synthesis, antibacterial activity and conformation of diptericin, an 82-mer peptide originally isolated from insects

The small amounts of antibacterial peptides that can be isolated from insects do not allow detailed studies of their range of activity, side-chain sugar requirements, or their conformation, factors that frequently play roles in the mode of action. In this paper, we report the solid-phase step-by-step synthesis of diptericin, an 82-mer peptide, originally isolated from Phormia terranovae. The unglycosylated peptide was purified to homogeneity by conventional reversed-phase high performance liquid chromatography, and its activity spectrum was compared to that Of synthetic unglycosylated drosocin, which shares strong sequence homology with diptericin's N-terminal domain. Diptericin appeared to have antibacterial activity:for only a limited number of Gram-negative bacteria. Diptericin's submicromolar potency against Escherichia coli strains indicated that, in a manner similar to drosocin, the presence of the carbohydrate side chain is not,necessary to kill bacteria. Neither the N-terminal, drosocin-analog fragment, nor the C-terminal, glycine-rich attacin-analog region was active against any of the bacterial strains studied, regardless of whether the Gal-GalNAc disaccharide units were attached. This suggested that the active site of diptericin fell outside the drosocin or attacin homology domains. In addition, the conformation of diptericin did not seem to play a role in the antibacterial activity, as was demonstrated by the complete lack of ordered structure by two-dimensional nuclear magnetic resonance spectroscopy and circular dichroism. Diptericin completely killed bacteria within I h, considerably faster than drosocin and the attacins; unlike some other, fast-acting antibacterial peptides, diptericin did not lyse normal mammalian cells. Taken together, these data suggest diptericin does not belong to any known class of antibacterial peptides.

Chemical synthesis, characterization and activity of RK-1, a novel alpha-defensin-related peptide

The 32-residue peptide, RK-1, a novel kidney-derived three disulfide-bonded member of the antimicrobial alpha-defensin family, was synthesized by the continuous now Fmoc-solid phase method. The crude, cleaved and S-reduced Linear peptide was both efficiently folded and oxidized in an acidic solution of aqueous dimethyl sulfoxide. Following purification of the resulting product, it was shown by a variety of analytical techniques, including matrix assisted laser desorption time of flight mass spectrometry, to possess a very high degree of purity. The disulfide bond pairing of the synthetic peptide was determined by H-1-NMR spectroscopy and confirmed to be a Cys(1)-Cys(6), Cys(2)-Cys(4), Cys(3)-Cys(5) arrangement similar to other mammalian alpha-defensin peptides. The synthetic RK-1 was also shown to inhibit the growth of Escherichia coli type strain NCTC 10418, Copyright (C) 2000 European Peptide Society and John Wiley & Sons, Ltd.

Changes in quantum efficiency of Photosystem II of symbiotic dinoflagellates of corals after heat stress, and of bleached corals sampled after the 1998 Great Barrier Reef mass bleaching event Ross J. Jones , Selina Ward, Affendi Yang Amri and Ove Hoegh-Guldberg

Pulse-amplitude-modulation chlorophyll fluorometry was used to examine changes in dark-adapted F-v/F-m of endosymbiotic dinoflagellate microalgae within the tissues of the temperate coral Plesiastrea versipora exposed to elevated seawater temperature. The F-v/F-m was markedly reduced following exposure of corals to 28 degrees C for 48 h. When corals were returned to ambient (24 degrees C) conditions, F-v/F-m increased in an initial rapid and then secondary slower phase. Tissue discolouration (coral bleaching), caused by a significant decrease in the density of algae, was observed during the first 2-3 days of the recovery period. After 14 days, F-v/F-m was still significantly lower than in control corals. The recovery of F-v/F-m is discussed in terms of repair processes within the symbiotic algae, division of healthy algae and also the selective removal of photo-damaged dinoflagellates. Under field conditions, bleached corals sampled at Heron Island Reef during a bleaching event had significantly lower F-v/F-m than non-bleached colonies; four months after the bleaching event, there were no differences in F-v/F-m or algal density in corals marked as having bleached or having shown no signs of colour loss. The results of this laboratory and field study are consistent with the hypothesis that an impairment of photosynthesis occurs during heat-stress, and is the underlying cause of coral bleaching.

Quantum controlled-NOT gate with 'hot' trapped ions

We present a novel method of performing quantum logic gates in trapped ion quantum computers which does not require the ions to be cooled down to the ground state of their vibrational modes, thereby avoiding one of the principal experimental difficulties encountered in realizing this technology. Our scheme employs adiabatic passages and a phase shift conditional on the phonon number state.

A new approach to current and noise in double quantum dot systems

We use a quantum master equation to describe transport in double-dot devices. The coherent dot-to-dot coupling affects the noise spectra strongly. For phonon-assisted tunneling, the calculated current spectra are consistent with those of experiments. The model shows that quantum stochastic theory may he applied to some advantage in mesoscopic electronic systems. (C) 2000 Elsevier Science B.V. All rights reserved.

Response of a two-level atom to a narrow-bandwidth squeezed-vacuum excitation

Using the coupled-system approach we calculate the optical spectra of the fluorescence and transmitted fields of a two-level atom driven by a squeezed vacuum of bandwidths smaller than the natural atomic linewidth. We find that in this regime of squeezing bandwidths the spectra exhibit unique features, such as a hole burning and a three-peak structure, which do not appear for a broadband excitation. We show that the features are unique to the quantum nature of the driving squeezed vacuum field and donor appear when the atom is driven by a classically squeezed field. We find that a quantum squeezed-vacuum field produces squeezing in the emitted fluorescence field which appears only in the squeezing spectrum while there is no squeezing in the total field. We also discuss a nonresonant excitation and find that depending on the squeezing bandwidth there is a peak or a hole in the spectrum at a frequency corresponding to a three-wave-mixing process. The hole appears only for a broadband excitation and results from the strong correlations between squeezed-vacuum photons.

Finite element modelling of dissipative structures for nonequilibrium chemical reactions in fluid-saturated porous media

We use the finite element method to model and predict the dissipative structures of chemical species for a nonequilibrium chemical reaction system in a fluid-saturated porous medium. In particular, we explore the conditions under which dissipative structures of the species may exist in the Brusselator type of nonequilibrium chemical reaction. Since this is the first time the finite element method and related strategies have been used to study the chemical instability problems in a fluid-saturated porous medium, it is essential to validate the method and strategies before they are put into application. For this purpose, we have rigorously derived the analytical solutions for dissipative structures of chemical species in a benchmark problem, which geometrically is a square. Comparison of the numerical solutions with the analytical ones demonstrates that the proposed numerical method and strategy are robust enough to solve chemical instability problems in a fluid-saturated porous medium. Finally, the related numerical results from two application examples indicate that both the regime and the magnitude of pore-fluid flow have significant effects on the nature of the dissipative structures that developed for a nonequilibrium chemical reaction system in a fluid-saturated porous medium. The motivation for this study is that self-organization under conditions of pore-fluid flow in a porous medium is a potential mechanism of the orebody formation and mineralization in the upper crust of the Earth. (C) 2000 Elsevier Science S.A. All rights reserved.

Exactly solvable quantum spin ladders associated with the orthogonal and symplectic Lie algebras

We extend the results of spin ladder models associated with the Lie algebras su(2(n)) to the case of the orthogonal and symplectic algebras o(2(n)), sp(2(n)) where n is the number of legs for the system. Two classes of models are found whose symmetry, either orthogonal or symplectic, has an explicit n dependence. Integrability of these models is shown for an arbitrary coupling of XX-type rung interactions and applied magnetic field term.

Two-dimensional nonlinear dynamics of evanescent-wave guided atoms in a hollow fiber

We describe the classical and quantum two-dimensional nonlinear dynamics of large blue-detuned evanescent-wave guiding cold atoms in hollow fiber. We show that chaotic dynamics exists for classic dynamics, when the intensity of the beam is periodically modulated. The two-dimensional distributions of atoms in (x,y) plane are simulated. We show that the atoms will accumulate on several annular regions when the system enters a regime of global chaos. Our simulation shows that, when the atomic flux is very small, a similar distribution will be obtained if we detect the atomic distribution once each the modulation period and integrate the signals. For quantum dynamics, quantum collapses, and revivals appear. For periodically modulated optical potential, the variance of atomic position will be suppressed compared to the no modulation case. The atomic angular momentum will influence the evolution of wave function in two-dimensional quantum system of hollow fiber.

High-frequency acousto-electric single-photon source

We propose a single optical photon source for quantum cryptography based on the acoustoelectric effect. Surface acoustic waves (SAWs) propagating through a quasi-one-dimensional channel have been shown to produce packets of electrons that reside in the SAW minima and travel at the velocity of sound. In our scheme, the electron packets are injected into a p-type region, resulting in photon emission. Since the number of electrons in each packet can be controlled down to a single electron, a stream of single- (or N-) photon states, with a creation time strongly correlated with the driving acoustic field, should be generated.

Decoherence and coherent population transfer between two coupled systems

We show that an arbitrary system described by two dipole moments exhibits coherent superpositions of internal states that can be completely decoupled fi om the dissipative interactions (responsible for decoherence) and an external driving laser field. These superpositions, known as dark or trapping states, can he completely stable or can coherently interact with the remaining states. We examine the master equation describing the dissipative evolution of the system and identify conditions for population trapping and also classify processes that can transfer the population to these undriven and nondecaying states. It is shown that coherent transfers are possible only if the two systems are nonidentical, that is the transitions have different frequencies and/or decay rates. in particular, we find that the trapping conditions can involve both coherent and dissipative interactions, and depending on the energy level structure of the system, the population can be trapped in a linear superposition of two or more bare states, a dressed state corresponding to an eigenstate of the system plus external fields or, in some cases. in one of the excited states of the system. A comprehensive analysis is presented of the different processes that are responsible for population trapping, and we illustrate these ideas with three examples of two coupled systems: single V- and Lambda-type three-level atoms and two nonidentical tao-level atoms, which are known to exhibit dark states. We show that the effect of population trapping does not necessarily require decoupling of the antisymmetric superposition from the dissipative interactions. We also find that the vacuum-induced coherent coupling between the systems could be easily observed in Lambda-type atoms. Our analysis of the population trapping in two nonidentical atoms shows that the atoms can be driven into a maximally entangled state which is completely decoupled from the dissipative interaction.

Conotoxin TVIIA, a novel peptide from the venom of Conus tulipa - 1. Isolation, characterization and chemical synthesis

A novel conotoxin belonging to the 'four-loop' structural class has been isolated from the venom of the piscivorous cone snail Conus tulipa. It was identified using a chemical-directed strategy based largely on mass spectrometric techniques. The new toxin, conotoxin TVIIA, consists of 30 amino-acid residues and contains three disulfide bonds. The amino-acid sequence was determined by Edman analysis as SCSGRDSRCOOVCCMGLMCSRGKCVSIYGE where O = 4-transl-hydroxyproline. Two under-hydroxylated analogues, [Pro10]TVIIA and [Pro10,11]TVIIA, were also identified in the venom of C. tulipa. The sequences of TVIIA and [Pro10]TVIIA were further verified by chemical synthesis and coelution studies with native material. Conotoxin TVIIA has a six cysteine/four-loop structural framework common to many peptides from Conus venoms including the omega-, delta- and kappa-conotoxins. However, TVIIA displays little sequence homology with these well-characterized pharmacological classes of peptides, but displays striking sequence homology with conotoxin GS, a peptide from Conus geographus that blocks skeletal muscle sodium channels. These new toxins and GS share several biochemical features and represent a distinct subgroup of the four-loop conotoxins.