High dynamic range proteome imaging with the structured illumination gel imager

A current challenge for proteomics is detecting proteins over the large concentration ranges found in complex biological samples such as whole‐cell extracts. Currently, no unbiased, whole‐proteome analysis scheme is capable of detecting the full range of cellular proteins. This is due in part to the limited dynamic range of the detectors used to sense proteins or peptides. We present a new technology, structured illumination (SI) gel imager, which detects fluorescently labeled proteins in electrophoretic gels over a 1 000 000‐fold concentration range. SI uses computer‐generated masks to attenuate the illumination of highly abundant proteins, allowing for long exposures of low‐abundance proteins, thus avoiding detector saturation. A series of progressively masked gel images are assembled into a single, very high dynamic range image. We demonstrate that the SI imager can detect proteins over a concentration range of approximately 1 000 000‐fold, making it a useful tool for comprehensive, unbiased proteome‐wide surveys.     

Biomolecular Imaging with a C60-SIMS/MALDI Dual Ion Source Hybrid Mass Spectrometer: Instrumentation,Matrix Enhancement,and Single Cell Analysis

We describe a hybrid MALDI/C₆₀-SIMS Q-TOF mass spectrometer and corresponding sample preparation protocols to image intact biomolecules and their fragments in mammalian spinal cord, individual invertebrate neurons, and cultured neuronal networks. A lateral spatial resolution of 10 μm was demonstrated, with further improvement feasible to 1 μm, sufficient to resolve cell outgrowth and interconnections in neuronal networks. The high mass resolution (>13,000 FWHM) and tandem mass spectrometry capability of this hybrid instrument enabled the confident identification of cellular metabolites. Sublimation of a suitable matrix, 2,5-dihydroxybenzoic acid, significantly enhanced the ion signal intensity for intact glycerophospholipid ions from mammalian nervous tissue, facilitating the acquisition of high-quality ion images for low-abundance biomolecules. These results illustrate that the combination of C₆₀-SIMS and MALDI mass spectrometry offers particular benefits for studies that require the imaging of intact biomolecules with high spatial and mass resolution, such as investigations of single cells, subcellular organelles, and communities of cells. Graphical Abstract

?     

Rapid crack growth in a thermoelastic solid under mixed-mode thermomechanical loading

A two-dimensional steady-sate analysis of semi-infinite brittlecrack growth at a constant subcritical rate in an unboundedfully-coupled thermoelastic solid under mixed-mode thermomechanicalloading is made. The loading consists of normal and shear tractionsand heat fluxes applied as point sources (line loads in theout-of-plane direction). A related problem is solved exactly in an integral transformspace, and robust asymptotic forms used to reduce the originalproblem to a set of integral equations. The equations are partiallycoupled and exhibit operators of both Cauchy and Abel types,yet can be solved analytically. The temperature change field at a distance from the moving crackedge is then constructed, and its dominant term is found tobe controlled by the imposed heat fluxes. The role of this termis, indeed, enhanced if the heat fluxes serve to render thecrack as a net heat source/sink for the solid, as opposed tobeing a transmitter of heat across its plane. More generally,the influence of the thermoelastic coupling on this field, aswell as other functions, is found to increase with crack speed.     

Synthetic magnetic opals

We present studies of novel nanocomposites of BiNi impregnated into the structure of opals as well as inverse opals. Atomic force microscopy and high resolution elemental analyses show a highly ordered structure and uniform distribution of the BiNi filler in the matrix. These BiNi-based nanocomposites are found to exhibit distinct ferromagnetic-like ordering with transition temperature of about 675 K. As far as we know there exists no report in literature on any BiNi compound which is magnetic.     

Synthesis of substituted N-benzyl pyridones via an O- to N-alkyl migration

A new LiI-promoted O- to N-alkyl migration has been developed for the conversion of O-alkylated 2-hydroxy pyridines, quinolines, and pyrimidines to the corresponding N-alkylated heterocycles in good to excellent yields (57-99%). This method serves as an efficient means for the preparation of N-benzyl pyridones, quinolones, and pyrimidones.     

Enhanced hydrolytic stability of self-assembling alkylated two-dimensional covalent organic frameworks

The stability and bulk properties of two-dimensional boronate ester-linked covalent organic frameworks (COFs) were investigated upon exposure to aqueous environments. Enhanced stability was observed for frameworks with alkylation in the pores of the COF compared to nonalkylated, bare-pore frameworks. COF-18? and COF-5 were analyzed as "bare-pore" COFs, while COF-16? (methyl), COF-14? (ethyl), and COF-11? (propyl) were evaluated as "alkylated-pore" materials. Upon submersion in aqueous media, the porosity of alkylated COFs decreased ～25%, while the nonalkylated COFs were almost completely hydrolyzed, virtually losing all porosity. Similar trends were observed for the degree of crystallinity for these materials, with ～40% decrease for alkylated COFs and 95% decrease for nonalkylated COFs. SEM was used to probe the particle size and morphology for these hydrolyzed materials. Stability tests, using absorbance spectroscopy and (1)H NMR, monitored the release of monomers as the COF degraded. While nonalkylated COFs were stable in organic solvent, hydrolysis was rapid in aqueous environments, more so in basic compared to neutral or acidic aqueous media (minutes to hours, respectively). Notably, alkylation in the pores of COFs slows hydrolysis, exhibiting up to a 50-fold enhancement in stability for COF-11? over COF-18?.     

INTENSITY DEPENDENCE OF FLUOROPHORE PHOTOBLEACHING BY A STEPPED-INTENSITY SLOW-BLEACH EXPERIMENT

Abstract— We describe a simple method for determination of the dependence of fluorophore photo-bleaching on the intensity of the incident light. A sample of fluorophore is illuminated uniformly with an intensity which is sufficient only to bleach a small fraction of the fluorophore during a fluorescence lifetime period. The long-term decay of fluorescence due to photobleaching is monitored before and after a stepped increase in the incident intensity. The order of the photobleaching reaction is determined by taking the ratio of the logarithms of the limiting values of the slope of the fluorescence bleaching curve and the absolute fluorescence change. The method is applied to fluorescein, bound to dextran or ovalbumin, in aqueous solution, and the order of the reaction in both cases is shown to be unity.