Fluorescence Correlation Spectroscopy with Photobleaching Correction in Slowly Diffusing Systems

Fluorescence correlation spectroscopy (FCS) is a powerful tool to quantitatively study the diffusion of fluorescently labeled molecules. It allows in principle important questions of macromolecular transport and supramolecular aggregation in living cells to be addressed. However, the crowded environment inside the cells slows diffusion and limits the reservoir of labeled molecules, causing artifacts that arise especially from photobleaching and limit the utility of FCS in these applications. We present a method to compute the time correlation function from weighted photon arrival times, which compensates computationally during the data analysis for the effect of photobleaching. We demonstrate the performance of this method using numerical simulations and experimental data from model solutions. Using this technique, we obtain correlation functions in which the effect of photobleaching has been removed and in turn recover quantitatively accurate mean-square displacements of the fluorophores, especially when deviations from an ideal Gaussian excitation volume are accounted for by using a reference calibration correlation function. This allows quantitative FCS studies of transport processes in challenging environments with substantial photobleaching like in living cells in the future.     

Frequency-agile,rapid scanning spectroscopy: absorption sensitivity of 2 × 10−12 cm−1 Hz−1/2 with a tunable diode laser

We present ultrasensitive measurements of molecular absorption using frequency-agile rapid scanning, cavity ring-down spectroscopy with an external-cavity diode laser. A microwave source that drives an electro-optic phase modulator with a bandwidth of 20 GHz generates pairs of sidebands on the probe laser. The optical cavity provides for high sensitivity and filters the carrier and all but a single, selected sideband. Absorption spectra were acquired by stepping the tunable sideband from mode-to-mode of the ring-down cavity at a rate that was limited only by the cavity decay time. This approach allows for scanning rates of 8 kHz per cavity resonance, a minimum detectable absorption coefficient of 1.7 × 10^?11 cm^?1 after only 20 ms of averaging, and a noise-equivalent absorption coefficient of 1.7 × 10^?12 cm^?1 Hz^?1/2. By comparison with cavity-enhanced laser absorption spectrometers reported in the literature, the present system is, to the best of our knowledge, among the most sensitive and has by far the highest spectrum scanning rate.     

Measurement of H2O broadening of O2 A-band transitions and implications for atmospheric remote sensing

We present laboratory measurements of H(2)O-broadened (16)O(2) A-band (b(1)Σ(g)(+) ← X(3)Σ(g)(-)(0,0)) absorption spectra acquired with a laser-based photoacoustic spectroscopy method. This absorption band is widely used in a variety of high-precision atmospheric remote sensing applications. We report H(2)O broadening parameters for six of the strongest transitions in this band, and we show that these measured values are nominally 1.5-2 times greater than the corresponding air-broadening parameters. Simulations of atmospheric transmission spectra in the O(2) A-band that incorporate our measured H(2)O broadening parameters indicate that H(2)O present at concentrations typically found in the Earth's atmosphere can influence the column-integrated transmission relative to the dry air case. Further, because of spatial and seasonal variations in humidity, failure to account for the enhanced H(2)O pressure broadening effects can lead to concomitant biases in atmospheric O(2) A-band retrievals of quantities such as surface pressure and path length in greenhouse gas retrievals.     

Solid-supported syntheses of 3-thio-1,2,4-triazoles

Two solid-supported synthesis strategies for the preparation of 3-thio-1,2,4-triazoles are described. In the first, Rink amide resin is combined with Fmoc-protected ω-amino acids, acid hydrazides, and alkyl halides to provide diverse sets of starting materials from which numerous triazoles may be prepared. The second employs t-alkylcarbamateresin (Boc resin) which permits the use of additional pools of starting materials, including isothiocyanates and α- and ω-amino esters, resulting in triazoles with patterns of functional groups that are not possible from the initial route. The combination of multiple resins and resin attachment sites allows the preparation of a diverse library based upon the3-thio-1,2,4-triazole scaffold and avoids the pitfallof having a single linker functionality present at the same position in all library members. General synthetic procedures and representative products from each route are presented. A similarity analysis of representative sublibraries from each synthesis strategy concludes that variation of the solid-phase linker chemistry and attachment site can enhance molecular diversity of the combined triazole library. This revised version was published online in August 2006 with corrections to the Cover Date.     

Mössbauer absorption in some high Tc superconductors:170Yb in YbBa2Cu3O7−x,166Er in ErBa2Cu3O7−x,and57Fe in YBa2Cu3O7−x

For the high T_c compound YbBa₂Cu₃O_7−x, Mossbauer absorption measurements show that magnetic ordering occurs within the Yb³⁺ sublattice at 0.35K (μ_sat=1.7μ_B). For ErBa₂Cu₃O_7−x the Er³⁺ sublattice orders at 0.7K (μ_sat=4μ_B). Measurements on⁵⁷Fe diluted into YBa₂Cu₃O_7−x shows that no ordered magnetic moments exist within the Cu sublattices down to at least 4.2K. Instituto de Fisica, Porto-Alegre, Brasil (supported by CNPq)     

Baroclinic stability for a family of two‐level,semi‐implicit numerical methods for the 3D shallow water equations

The baroclinic stability of a family of two time‐level, semi‐implicit schemes for the 3D hydrostatic, Boussinesq Navier–Stokes equations (i.e. the shallow water equations), which originate from the TRIM model of Casulli and Cheng (Int. J. Numer. Methods Fluids 1992; 15 :629–648), is examined in a simple 2D horizontal–vertical domain. It is demonstrated that existing mass‐conservative low‐dissipation semi‐implicit methods, which are unconditionally stable in the inviscid limit for barotropic flows, are unstable in the same limit for baroclinic flows. Such methods can be made baroclinically stable when the integrated continuity equation is discretized with a barotropically dissipative backwards Euler scheme. A general family of two‐step predictor‐corrector schemes is proposed that have better theoretical characteristics than existing single‐step schemes. Copyright © 2006 John Wiley & Sons, Ltd.     

Temperature profiling of polypeptides in reversed-phase liquid chromatography. II. Monitoring of folding and stability of two-stranded alpha-helical coiled-coils

The present study extends the utility of reversed-phase high-performance liquid chromatography (RP-HPLC) to monitor folding and stability of de novo designed synthetic two-stranded alpha-helical coiled-coils. Thus, we have compared the effect of temperature on the RP-HPLC retention behaviour of both oxidized (two identical five-heptad alpha-helical peptides linked by a disulfide bridge) and reduced coiled-coil analogues with various amino acids substituted into the hydrophobic core of the coiled-coil. We were able to correlate the RP-HPLC retention behaviour of the oxidized analogues over the temperature range of 10 to 80 degrees C with the stability of the analogues as determined by conventional thermal and chemical denaturation approaches. In addition, the contribution of a disulfide bridge to coiled-coil stability was highlighted by comparing the elution behaviour of the oxidized and reduced analogues. Overall, we demonstrate the excellent potential of "temperature profiling" by RP-HPLC to monitor differences in oligomerization state and protein stability.