Reflections from polished single mode fiber ends

When the end of a single mode fiber is polished and placed in an index-matching liquid, a reflection will occur. Its amplitude depends on two factors: (1) the difference between the liquid's refractive index and that of the fiber, and (2) the polishing procedure used. By proper choice of both, the end-reflection can be reduced to below -60 dB. When two well-polished fiber ends are joined together with a small, liquid-filled gap between them, the resulting reflection will be the coherent addition of the two individual end-reflections. By adjusting the gap, this reflection can be made greater than or less than the individual end-reflections.     

The preparation of novel 4,4'- and N,N'-linked pipecolic acid derivatives

Routes used for the preparation of the novel 4,4'- and N,N'-linked pipecolic acids (1a,band 2b,c) are described and discussed together with the characterisation of the products and intermediates.     

Determination of the size distribution of sonoluminescence bubbles in a pulsed acoustic field

A simple method is described for determining the size of sonoluminescence bubbles generated by acoustic cavitation. The change in the intensity of sonoluminescence, from 4 ms pulses of 515 kHz ultrasound, as a function of the "off" time between acoustic pulses, is the basis of the method. The bubble size determined in water was in the range of 2.8-3.7 mum.     

Zinc-porphyrin Solvation in folded and unfolded states of Zn-cytochrome c

After a brief review of the use of photochemical triggers and heme metal substitution to probe the folding dynamics of cytochrome c, we present new results on the photophysics and photochemistry of folded and unfolded states of the zinc-substituted protein (Zn-cyt c). Our measurements of Zn-cyt c triplet state decay kinetics reveal a systematic isotope effect on lifetimes: the decay in the folded protein (tau(H)2(O) approximately 10 ms) is only modestly affected by isotopically substituted buffers (k(H)2(O)/k(D)2(O) = 1.2), whereas a reduced triplet lifetime (approximately 1.3 ms) and greater isotope effect (1.4) were found for the chemically denatured, fully unfolded protein. The shortest lifetime (0.1-0.4 ms) and greatest isotope effect (1.5) were found for a fully exposed model compound, zinc-substituted N-acetyl-microperoxidase-8 (ZnAcMP8), implying that the unfolded protein provides some protection to the Zn-porphyrin group even under fully denaturing conditions. Further evidence for partial structure in unfolded Zn-cyt c comes from bimolecular quenching experiments using Ru(NH(3))(6)(3+) as an external Zn-porphyrin triplet state quencher. In the presence of quencher, partially unfolded protein at midpoint guanidinium chloride (GdmCl) and urea concentrations exhibits biphasic triplet decay kinetics, a fast component corresponding to an extended, solvent-exposed state (6.6 x 10(8) M(-1) s(-1) in GdmCl, 6.3 x 10(8) M(-1) s(-1) in urea) and a slow component attributable to a compact, relatively solvent-inaccessible, state (5.9 x 10(7) M(-1) s(-1) in GdmCl, 8.6 x 10(6) M(-1) s(-1) in urea). The variation in Zn-porphyrin solvation for the compact states in the two denaturants reveals that the cofactor in the partially unfolded protein is better protected in urea solutions.     

Ultraviolet resonance Raman spectroscopy of folded and unfolded states of an integral membrane protein

The vibrational structure of native anchoring tryptophan (Trp) and tyrosine residues in an integral membrane protein, bacterial outer membrane protein A (OmpA), have been investigated using UV resonance Raman (UVRR) spectroscopy for the first time. Spectra of native OmpA, a single-Trp mutant, and a Trp-less mutant were recorded in folded and unfolded states, and reveal significant changes in tryptophan structure and local environment. Salient alterations upon folding include loss of hydrogen-bonding character of indole N1H, evidenced by a shift in W17 frequency from 874 and 878 cm(-1), and growth in hydrophobicity of the local tryptophan environment, supported by increase in the ratio I1361/I1340. In addition to these site-specific changes in a single tryptophan residue, modification of the vibrational structure of the remaining native tryptophan and tyrosine amino acids is also evident. Finally, the UVRR data presented here indicate that the structures of OmpA folded in vesicle and folded in detergent may differ, and provide important foundations for ongoing studies of membrane protein folding.     

The range of ambient radius for an active bubble in sonoluminescence and sonochemical reactions

Numerical simulations of nonequilibrium chemical reactions inside an air bubble in liquid water irradiated by ultrasound have been performed for various ambient bubble radii. The intensity of sonoluminescence (SL) has also been calculated taking into account electron-atom bremsstrahlung, radiative attachment of electrons to neutral molecules, radiative recombination of electrons and ions, chemiluminescence of OH, molecular emission from nitrogen, etc. The lower bound of ambient radius for an active bubble in SL and sonochemical reactions nearly coincides with the Blake threshold for transient cavitation. The upper bound is in the same order of magnitude as that of the linear resonance radius. In actual experiments, however, the distribution of ambient radius for active bubbles may be narrow at around the threshold ambient radius for the shape instability. The threshold peak temperature inside an air bubble for nitrogen burning is higher than that for oxidant formation. The threshold peak temperatures depend on ultrasonic frequency and acoustic amplitude because chemical reactions inside a bubble are in nonequilibrium. The dominant emission mechanism in SL is electron-atom bremsstrahlung except at a lower bubble temperature than 2000 K, for which molecular emissions may be dominant.     

Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions

Formaldehyde cross-linking of proteins is emerging as a novel approach to study protein-protein interactions in living cells. It has been shown to be compatible with standard techniques used in functional proteomics such as affinity-based protein enrichment, enzymatic digestion, and mass spectrometric protein identification. So far, the lack of knowledge on formaldehyde-induced protein modifications and suitable mass spectrometric methods for their targeted detection has impeded the identification of the different types of cross-linked peptides in these samples. In particular, it has remained unclear whether in vitro studies that identified a multitude of amino acid residues reacting with formaldehyde over the course of several days are suitable substitutes for the much shorter reaction times of 10-20 min used in cross-linking experiments in living cells. The current study on model peptides identifies amino-termini as well as lysine, tryptophan, and cysteine side chains, i.e. a small subset of those modified after several days, as the major reactive sites under such conditions, and suggests relative position in the peptide sequence as well as sequence microenvironment to be important factors that govern reactivity. Using MALDI-MS, mass increases of 12 Da on amino groups and 30 Da on cysteines were detected as the major reaction products, while peptide fragment ion analysis by tandem mass spectrometry was used to localize the actual modification sites on a peptide. Non-specific cross-linking was absent, and could only be detected with low yield at elevated peptide concentrations. The detailed knowledge on the constraints and products of the formaldehyde reaction with peptides after short incubation times presented in this study is expected to facilitate the targeted mass spectrometric analysis of proteins after in vivo formaldehyde cross-linking.