Heterogeneous photobleaching in confocal microscopy

Photobleaching was studied during recording of confocal scanning laser microscopy. Studies on fluorescent gels of FITC-labeled dextran were used to evaluate differential bleaching along thez-axis. Differential bleaching along the z-axis was observed and it was seen that this was related to the numerical aperture of the objective in use. This points to the conclusion that photon energy flux density is an important parameter in photobleaching. To check if photon energy flux density heterogeneity is affected by local variation in the refractive index of the sample, photobleaching rates were calculated for different fluorescent objects (sections of seeds, animal cells stained with nuclear stains, immunocytochemistry preparations) and a pronounced similarity was found between photobleaching rates and DIC images.     

Synthesis and characterization of poly(ethylene oxide‐co‐ethylene carbonate) macromonomers and their use in the preparation of crosslinked polymer electrolytes

Methacrylate‐functionalized poly(ethylene oxide‐co‐ethylene carbonate) macromonomers were prepared in two steps by the anionic ring‐opening polymerization of ethylene carbonate at 180 °C, with potassium methoxide as the initiator, followed by the reaction of the terminal hydroxyl groups of the polymers with methacryloyl chloride. The molecular weight of the polymer went through a maximum after approximately 45 min of polymerization, and the content of ethylene carbonate units in the polymer decreased with the reaction time. A polymer having a number‐average molecular weight of 2650 g mol^?1 and an ethylene carbonate content of 28 mol % was selected and used to prepare a macromonomer, which was subsequently polymerized by UV irradiation in the presence of different concentrations of lithium bis(trifluoromethanesulfonyl)imide salt. The resulting self‐supportive crosslinked polymer electrolyte membranes reached ionic conductivities of 6.3 × 10^?6 S cm^?1 at 20 °C. The coordination of the lithium ions by both the ether and carbonate oxygens in the polymer structure was indicated by Fourier transform infrared spectroscopy. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 2195–2205, 2006     

Proteomics study of anthrax lethal toxin-treated murine macrophages

The anthrax lethal toxin (LeTx) is composed of two proteins, protective antigen and lethal factor, which bind and enter the cell through a host receptor termed the anthrax toxin receptor (ATR). In the cell, LeTx targets p38, part of the MAP kinase signaling pathway. The toxin appears to initiate an apoptotic pathway in infected cells, indicating additional downstream targets of the toxin. We have applied a proteomics approach to investigate these downstream targets and the affected processes. In this study we have used an improved strategy for fractionation based on protein pI, off-gel electrophoresis, employed in conjunction with relative quantitation using the mass labeling approach. In our survey, 67 proteins were observed and quantified from the cytosol of RAW 264.7 cells with respect to control versus toxin-treated cells. Many of these proteins are involved in the oxidative stress response, as well as apoptosis, and thus likely to be relevant to the effects of anthrax in infected cells. Our results indicate that the tumor necrosis factor-alpha-mediated pathway is compromised in intoxicated cells. The knowledge of such changes and the pathways leading to the changes should be of great value in understanding and combating this disease.     

Real‐time Probing the Formation of [M(2,2‐bipyridine)2(NO3)3] (M = Ce,La, Tb) Complexes and Influence of Synthesis Parameters

Despite the strong technological importance of lanthanide complexes, their formation processes are rarely investigated. This work is dedicated to determining the influence of synthesis parameters on the formation of [Ce(bipy)₂(NO₃)₃] as well as Ce³⁺‐ and Tb³⁺‐substituted [La(bipy)₂(NO₃)₃] (bipy = 2,2′‐bipyridine) complexes. To this end, we performed in situ luminescence measurements, synchrotron‐based X‐ray diffraction (XRD) analysis, infrared spectroscopy (IR), and measured pH value and/or ion conductivity during their synthesis process under real reaction conditions. For the [Ce(bipy)₂(NO₃)₃] complex, the in situ luminescence measurements initially presented a broad emission band at 490 nm, assigned to the 5d→4f Ce³⁺ ions within the ethanolic solvation shell. Upon the addition of bipy, a red shift to 700 nm was observed. This shift was attributed to the changes in the environment of the Ce³⁺ ions, indicating their desolvation and incorporation into the [Ce(bipy)₂(NO₃)₃] complex. The induction time was reduced from 8 to 3.5 min, by increasing the reactant concentration by threefold. In contrast, [La(bipy)₂(NO₃)₃] crystallized within days instead of minutes, unless influenced by high Ce³⁺ and Tb³⁺ concentrations. Monitoring and controlling the influence of the reaction parameters on the structure of emissive complexes is important for the development of rational synthesis approaches and optimization of their structure‐related properties like luminescence.     

The directive of the protein: how does cytochrome P450 select the mechanism of dopamine formation?

Dopamine can be generated from tyramine via arene hydroxylation catalyzed by a cytochrome P450 enzyme (CYP2D6). Our quantum mechanical/molecular mechanical (QM/MM) results reveal the decisive impact of the protein in selecting the 'best' reaction mechanism. Instead of the traditional Meisenheimer-complex mechanism, the study reveals a mechanism involving an initial hydrogen atom transfer from the phenolic hydroxyl group of the tyramine to the iron-oxo of the compound I (Cpd I), followed by a ring-π radical rebound that eventually leads to dopamine by keto-enol rearrangement. This mechanism is not viable in the gas phase since the O-H bond activation by Cpd I is endothermic and the process does not form a stable intermediate. By contrast, the in-protein reaction has a low barrier and is exothermic. It is shown that the local electric field of the protein environment serves as a template that stabilizes the intermediate of the H-abstraction step and thereby mediates the catalysis of dopamine formation at a lower energy cost. Furthermore, it is shown that external electric fields can either catalyze or inhibit the process depending on their directionality.     

Improved Bounds for Ternary Linear Codes of Dimension 8 Using Tabu Search

In this paper, new codes of dimension 8 are presented which give improved bounds on the maximum possible minimum distance of ternary linear codes. These codes belong to the class of quasi-twisted (QT) codes, and have been constructed using a stochastic optimization algorithm, tabu search. Twenty three codes are given which improve or establish the bounds for ternary codes. In addition, a table of upper and lower bounds for d ₃(n, 8) is presented for n 200.     

Classification of Graeco‐Latin Cubes

A q‐ary code of length n, size M, and minimum distance d is called an code. An code with is said to be maximum distance separable (MDS). Here one‐error‐correcting () MDS codes are classified for small alphabets. In particular, it is shown that there are unique (5, 5³, 3)₅ and (5, 7³, 3)₇ codes and equivalence classes of (5, 8³, 3)₈ codes. The codes are equivalent to certain pairs of mutually orthogonal Latin cubes of order q, called Graeco‐Latin cubes.     

Platinum(II) and palladium(II) complexes of bisphosphine ligands bearing o-N,N-dimethylanilinyl substituents: a hint of catalytic olefin hydration

Platinum(II) and palladium(II) complexes of the potentially hexadentate P,N-donor ligand family Ar2P-X-PAr2 (X = (CH2)2 [dmape], cyclic-C5H8 [dmapcp]; Ar = o-N,N-dimethylanilinyl) are described. In CH2Cl2, the dmape complexes exist as equilibrium mixtures of MCl2(P,P'-dmape) and [MCl(P,P',N-dmape)]Cl isomers (M = Pd, Pt), governed by deltaH(o) = -19 +/- 4 kJ mol(-1) and deltaS(o) = -100 +/- 30 J mol(-1) K(-1) for M = Pt, and deltaH(o) = -11 +/- 7 kJ mol(-1) and deltaS(o) = -60 +/- 20 J mol(-1) K(-1) for M = Pd. The water-soluble dmapcp complexes exist solely in the [MCl(P,P',N-dmapcp)]Cl form, but the free and coordinated anilinyl rings in these complexes are in slow diastereoselective exchange. X-ray crystal structures for MCl2(P,P'-dmape) (M = Pd, Pt), and the [PdCl(P,P',N-dmape)]+ and [PtCl(P,P',N-dmapcp)]+ cations, are presented. Some of the complexes show marginal activity in water for the catalyzed hydration of maleic to malic acid, giving about 6-7% conversion in 24 h at 100 degrees C and substrate:catalyst loadings of 100:1. Attempts to synthesize a PdCl(P,P',N-dmapm)+ species led instead to isolation of [Pd(mu-Cl)(P,P'-dmapm)]2[PF6]2 (dmapm = Ar2PCH2Ar2).     

Solvating,manipulating, damaging,and repairing DNA in a computer

This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007