De novo sequencing of a 21-kDa cytochrome c4 from Thiocapsa roseopersicina by nanoelectrospray ionization ion-trap and Fourier-transform ion-cyclotron resonance mass spectrometry

We have determined the primary structure of cytochrome c(4) from Thiocapsa roseopersicina by de novo protein sequencing using the 'bottom up' approach. Three different enzymes (trypsin, endoproteinase Lys-C, and endoproteinase Glu-C) were employed to prepare four different sets of proteolytic digests. The digestion strategy was designed to permit a gradual buildup of smaller peptides into larger ones that were overlapped to yield the complete protein sequence. In this way we countered the main problem: peptides larger than about 1500 Da were difficult to sequence fully by tandem mass spectrometry. Direct infusion and online liquid chromatography were used on a linear ion trap Fourier-transform ion-cyclotron resonance hybrid instrument. The high resolving power, high mass accuracy and the availability of electron capture dissociation and collision-induced dissociation were essential to achieve full sequence coverage. The software DeNovoX complemented by manual interpretation was used to generate sequence information from tandem mass spectra. The predominantly automated nature of data acquisition and handling allowed for a relatively straightforward and fast procedure, which could compete with the mainstream alternative of nucleotide sequence determination.     

Iron (Fe) speciation in xylem sap by XANES at a high brilliant synchrotron X-ray source: opportunities and limitations

The development of highly brilliant synchrotron facilities all around the world is opening the way to new research in biological sciences including speciation studies of trace elements in plants. In this paper, for the first time, iron (Fe) speciation in xylem sap has been assessed by X-ray absorption near-edge structure (XANES) spectroscopy at the highly brilliant synchrotron PETRA III, beamline P06. Both standard organic Fe-complexes and xylem sap samples of Fe-deficient tomato plants were analyzed. The high photon flux provided by this X-ray synchrotron source allows on one side to obtain good XANES spectra in a reasonable amount of time (approx. 15 min for 200 eV scan) at low Fe concentrations (sub parts-per-million), while on the other hand may cause radiation damage to the sample, despite the sample being cooled by a stream of liquid nitrogen vapor. Standard Fe-complexes such as Fe(III)-succinate, Fe(III)-α-ketoglutarate, and Fe(III)-nicotianamine are somehow degraded when irradiated with synchrotron X-rays and Fe(III) can undergo photoreduction. Degradation of the organic molecules was assessed by HPLC-UV/Vis analyses on the same samples investigated by X-ray absorption spectroscopy (XAS). Fe speciation in xylem sap samples revealed Fe(III) to be complexed by citrate and acetate. Nevertheless, artifacts created by radiation damage cannot be excluded. The use of highly brilliant synchrotrons as X-ray sources for XAS analyses can dramatically increase the sensitivity of the technique for trace elements thus allowing their speciation in xylem sap. However, great attention must be paid to radiation damage, which can lead to biased results.

Living Cationic Sequential Block Copolymerization of Isobutylene with 4‐tert‐Butoxystyrene: Synthesis and Characterization of Poly(p‐hydroxystyrene‐b‐isobutylene‐b‐p‐hydroxystyrene) Triblock Copolymers

The living polymerization of p‐tert‐butoxystyrene (tBuOS) was studied in methylcyclohexane (MeChx)/methylchloride (MeCl) 60/40 v/v solvent mixture at –80°C. The model initiator 1,1,‐ditolylethylene (DTE) capped 2‐chloro‐2,4,4‐trimethylpentane (TMPCl) was formed in situ in conjunction with TiCl₄. Lowering the Lewis acidity by the addition of Ti(OIp)₄ was necessary to induce a rapid and controlled polymerization of tBuOS. Well‐defined polymers with controlled molecular weights, however, were only obtained at a narrow [Ti(OIp)₄]/[TiCl₄]=0.83–0.86 ratio. Above this ratio, the polymerization of tBuOS was slow and became absent at [Ti(OIp)₄]/[TiCl₄]≥1.18. At ratios lower than 0.83, the polymerization was too rapid and the initiator efficiency was lower than 100%. The living polymerization of tBuOS was also studied with SnBr₄ as Lewis acid. After capping TMPCl with DTE, Ti(OIp)₄ was added to reach [Ti(OIp)₄]/[TiCl₄]=1.2, followed by the addition of tBuOS and SnBr₄. SnBr₄ induced a well‐controlled living polymerization approximately first order in [SnBr₄], and the polymers exhibited close to theoretical M _ns and low polydispersity indices (PDI<1.2). The success of the method was also demonstrated by the clean synthesis of poly(isobutylene‐b‐p‐tert‐butoxystyrene) PIB‐b‐PtBuOS diblock copolymers. PtBuOS‐b‐PIB‐b‐PtBuOS triblock copolymer thermoplastic elastomers were prepared by employing 5‐tert‐butyl‐1,3‐bis(1‐methoxy‐1‐methylethyl)benzene (DCE) as a difunctional initiator for the living polymerization of IB followed by capping with DTE and substitution of TiCl₄ with SnBr₄ for the polymerization of tBuOS. Deprotection of the triblock copolymer in the presence of catalytic amount of HCl yielded poly(p‐hydroxystyrene‐b‐isobutylene‐b‐p‐hydroxystyrene) (PHOS‐b‐PIB‐b‐PHOS). PHOS‐b‐PIB‐b‐PHOS with 39.3 wt% p‐hydroxystyrene content exhibited typical characteristic of a thermoplastic elastomers (TPEs) with tensile strength of 18 MPa and ultimate elongation of 300%.     

Electron Transfer Dissociation of Photolabeled Peptides. Backbone Cleavages Compete with Diazirine Ring Rearrangements

Gas-phase conformations and electron transfer dissociations of pentapeptide ions containing the photo-Leu residue (L*) were studied. Exhaustive conformational search including molecular dynamics force-field, semi-empirical, ab initio, and density functional theory calculations established that the photo-Leu residue did not alter the gas-phase conformations of (GL*GGK? + ?2H)²⁺ and (GL*GGK-NH₂?+?H)⁺ ions, which showed the same conformer energy ranking as the unmodified Leu-containing ions. This finding is significant in that it simplifies conformational analysis of photo-labeled peptide ions. Electron transfer dissociation mass spectra of (GL*GGK? + ?2H)²⁺, (GL*GGK-NH₂?+?2H)²⁺,(GL*GGKK?+?2H)²⁺, (GL*GLK?+?2H)²⁺, and (GL*LGK?+?2H)²⁺ showed 16 %–21 % fragment ions originating by radical rearrangements and cleavages in the diazirine ring. These side-chain dissociations resulted in eliminations of N₂H₃, N₂H₄, [N₂H₅], and [NH₄O] neutral fragments and were particularly abundant in long-lived charge-reduced cation-radicals. Deuterium labeling established that the neutral hydrazine molecules mainly contained two exchangeable and two nonexchangeable hydrogen atoms from the peptide and underwent further H/D exchange in an ion–molecule complex. Electron structure calculations on the charge-reduced ions indicated that the unpaired electron was delocalized between the diazirine and amide π* electronic systems in the low electronic states of the cation-radicals. The diazirine moiety in GL*GGK-NH₂was calculated to have an intrinsic electron affinity of 1.5 eV, which was further increased by the Coulomb effect of the peptide positive charge. Mechanisms are proposed for the unusual elimination of hydrazine from the photo-labeled peptide ions.

Directed flow from global symmetry and initial state Fluctuations

Collective flow is studied in a 3+1D fluid dynamical model with globally symmetric, peripheral initial conditions, taking into account the shear flow. At $\sqrt {s_{NN} } $ = 2.76 TeV in semi-peripheral Pb+Pb collisions this leads to rotation, while at more peripheral collisions with high resolution and low numerical viscosity, the initial development of a Kelvin-Helmholz instability is observed. This effect provides a precision tool for studying the viscosity of Quark-Gluon Plasma.     

Femtosecond to second studies of a water-soluble porphyrin derivative in chemical and biological nanocavities

The interactions of 5,10,15,20-tetrakis(4-sulfonatophenyl)-porphyrin (TSPP) with a quaternary ammonium modified β-cyclodextrin (QA-β-CD) and human serum albumin (HSA) protein in aqueous solutions at pH 7 were studied using steady-state, stopped-flow, and femtosecond to millisecond spectroscopy. TSPP forms 1:1 and 1:2 complexes with QA-β-CD (K(1) = 1.9 × 10(5) M(-1) and K(2) = 7 × 10(3) M(-1)) at 293 K, whereas with the HSA protein only 1:1 complex (K(1) = 1.7 × 10(6) M(-1)) has been found. The chemical and biological nanocavities have notable effects on the fluorescence lifetimes of the Q(x) state (from 9.3 to 11.1 ns in QA-β-CD and 11.6 ns in HSA). Furthermore, the rotational times (400 ps for the free TSPP, 1.6 and 19 ns for QA-β-CD and HSA protein complexes, respectively) clearly indicate the robustness of the formed entities. The confined environment does not affect much the fs dynamics (0.1-0.2 ps) of the encapsulated molecule. However, it clearly affect the ps one (1-2 ps (H(2)O) and 5-10 ps (QA-β-CD and HSA)). The effect of O(2) on the relaxation of the triplet state of the free and encapsulated TSPP is also studied and the obtained results are discussed in light of the shielding effect provided by the chemical and biological cavities. The observed difference, longer triplet lifetime upon encapsulation, might be relevant to the efficiency of this porphyrin in photodynamic therapy. The presteady-state kinetics of the TSPP:HSA has been studied by the stopped-flow spectrometer, and a two-step model was proposed for the complexation processes. The results show the importance of the initial association step for the overall ligand recognition process. This first step occurs with rate constant of ~4 × 10(5) M(-1) s(-1), which is about 5 orders of magnitude larger than the rate constant of the consecutive relaxation processes. We believe that our observations of molecular interaction between TSPP, QA-β-CD, and HSA protein from femtosecond to second at both ground and electronically first excited state give detailed information to improve our understanding of this kind of system and thus for a better design of drug delivery nanocarriers.     

PUVA treatment of the nasal cavity improves the clinical symptoms of allergic rhinitis and inhibits the immediate-type hypersensitivity reaction in the skin

We earlier reported that intranasal irradiation with the 308 nm xenon chloride (XeCl) ultraviolet-B laser and irradiation with a combination of ultraviolet-B (UVB), ultraviolet-A (UVA) and visible light (VIS) is highly effective in the treatment of allergic rhinitis and inhibit the immediate-type hypersensitivity reaction in the skin. Since photochemotherapy with 8-methoxypsoralen (8-MOP) plus UVA light (PUVA) is widely used in the treatment of different inflammatory skin disorders due to its immunosuppressive effect, in the present study we investigated the efficacy of intranasal PUVA treatment in allergic rhinitis and the effect of PUVA treatment on the skin prick test (SPT) reaction. An open study was performed in 17 patients with hay fever. Intranasal PUVA therapy was given four times weekly for 3 weeks. The treatment was started with a fluence of 0.5x of the individual minimal phototoxic dose (MPD) and the dosages were gradually increased. Evaluation was based on the symptom scores. The effect of PUVA treatment on the allergen-induced wheal formation was also studied in the SPT. PUVA treatment of the nasal cavity significantly decreased the nasal symptoms of the patients with allergic rhinitis. Treatment of the skin with PUVA also significantly suppressed the allergen-induced wheal formation in the SPT reaction. These data suggest that intranasal PUVA phototherapy is also an effective modality in the treatment of allergic rhinitis.     

Correlation between hue angle and lightness of light irradiated wood

The objective of this study was to investigate irradiation characteristics of Beech (Fagus crenata Blume), black locust (Robinia pseudoacacia L.), Japanese cedar (Cryptomeria japonica D. Don) and spruce (Picea abies Karst.) wood samples by sunlight, xenon light and mercury vapour light. The colour change of the samples was evaluated by CIE L*a*b* and L*h*c* colour co-ordinate systems. It was found that the samples showed a rapid colour change at the initial period of treatment but the rate of change decreased with treatment time. It was determined that neither xenon nor mercury lamp light can accurately simulate sunlight. A wide range of colour changes were caused by the applied light sources. In spite of this wide colour range a good linear correlation was found between the lightness and the colour hue. The coefficients of determination (R²) are between 0.7 and 0.96. Accordingly, this linear correlation gives the possibility of following the colour change during photodegradation by measuring only the lightness.     

Subcarrier Domain of Multicarrier Continuous-Variable Quantum Key Distribution

Journal of Statistical Physics - The subcarrier domain of multicarrier continuous-variable quantum key distribution (CVQKD) is defined. In a multicarrier CVQKD scheme, the information is granulated...