Improved Stabilities of Labeling Probes for the Selective Modification of Endogenous Proteins in Living Cells and In Vivo

To date, various affinity-based protein labeling probes have been developed and applied in biological research to modify endogenous proteins in cell lysates and on the cell surface. However, the reactive groups on the labeling probes are also the cause of probe instability and nonselective labeling in a more complex environment, e. g., intracellular and in vivo. Here, we show that labeling probes composed of a sterically stabilized difluorophenyl pivalate can achieve efficient and selective labeling of endogenous proteins on the cell surface, inside living cells and in vivo. As compared with the existing protein labeling probes, probes with the difluorophenyl pivalate exhibit several advantages, including long-term stability in stock solutions, resistance to enzymatic hydrolysis and can be customized easily with diverse fluorophores and protein ligands. With this probe design, endogenous hypoxia biomarker in living cells and nude mice were successfully labeled and validated by in vivo, ex vivo, and immunohistochemistry imaging.     

Cluster fusion-fission dynamics in the Singapore stock exchange

In this paper, we investigate how the cross-correlations between stocks in the Singapore stock exchange (SGX) evolve over 2008 and 2009 within overlapping one-month time windows. In particular, we examine how these cross-correlations change before, during, and after the Sep–Oct 2008 Lehman Brothers Crisis. To do this, we extend the complete-linkage hierarchical clustering algorithm, to obtain robust clusters of stocks with stronger intracluster correlations, and weaker intercluster correlations. After we identify the robust clusters in all time windows, we visualize how these change in the form of a fusion-fission diagram. Such a diagram depicts graphically how the cluster sizes evolve, the exchange of stocks between clusters, as well as how strongly the clusters mix. From the fusion-fission diagram, we see a giant cluster growing and disintegrating in the SGX, up till the Lehman Brothers Crisis in September 2008 and the market crashes of October 2008. After the Lehman Brothers Crisis, clusters in the SGX remain small for few months before giant clusters emerge once again. In the aftermath of the crisis, we also find strong mixing of component stocks between clusters. As a result, the correlation between initially strongly-correlated pairs of stocks decay exponentially with average life time of about a month. These observations impact strongly how portfolios and trading strategies should be formulated.     

Template‐Free Hydrothermal Synthesis of Mesoporous MgO Nanostructures and Their Applications in Water Treatment

The controlled synthesis of Mg(OH)₂ nanowires and microflowers composed of nanoplates was successfully achieved by a template‐free hydrothermal synthetic method. It was found that the reaction medium played a crucial role in the morphological control of the precursor nanostructures. The high polarity of water molecules favored the polar growth of the precursor, resulting in the formation of nanowires with a diameter of 80 nm, whereas a mixed water/ethanol medium with a lower degree of polarity led to the formation of microflowers. Moreover, mesoporous MgO nanostructures could be obtained by further annealing these as‐prepared precursors in air at 500 °C for 2 h. During thermal treatment, the wire‐ and flower‐like morphologies were retained. Porosity formation was due to thermal decomposition of Mg(OH)₂ and release of H₂O. Both the mesoporous MgO nanowires and microflowers showed superior ability of adsorbing the organic dye methyl orange, and thus they are promising candidates for polluted water treatment.     

Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides

We have broadened the utility of the SEQUEST computer algorithms to permit correlation of uninterpreted high-energy collision-induced dissociation spectra of peptides with all sequences in a database. SEQUEST now allows for the additional fragment ion types observed under high-energy conditions. We analyzed spectra from peptides isolated following trypsin digestion of 13 proteins. SEQUEST ranked the correct sequence first for 90% (18/20) of the spectra in searches of the OWL database, without constraint by enzyme cleavage specificity or species of origin. All false-positives were flagged by the scoring system. SEQUEST searches databases for sequences that correspond to the precursor ion mass ±0.5 u. Preliminary ranking of the top 500 candidates is done by calculation of fragment ion masses for each sequence, and comparison to the measured ion masses on the basis of ion series continuity, summed ion intensity, and immonium ion presence. Final ranking is done by construction of model spectra for the 500 candidates and constructing/performing of a cross-correlation analysis with the actual spectrum. Given the need to relate mounting genome sequence information with corresponding suites of proteins that comprise the cellular molecular machinery, tandem mass spectrometry appears destined to play the leading role in accelerating protein identification on the large scale required.     

Probing Ag nanoparticle surface oxidation in contact with (in)organics: an X‐ray scattering and fluorescence yield approach

Characterizing interfacial reactions is a crucial part of understanding the behavior of nanoparticles in nature and for unlocking their functional potential. Here, an advanced nanostructure characterization approach to study the corrosion processes of silver nanoparticles (Ag‐Nps), currently the most highly produced nanoparticle for nanotechnology, is presented. Corrosion of Ag‐Nps under aqueous conditions, in particular in the presence of organic matter and halide species common to many natural environments, is of particular importance because the release of toxic Ag⁺ from oxidation/dissolution of Ag‐Nps may strongly impact ecosystems. In this context, Ag‐Nps capped with polyvinolpyrrolidone (PVP) in contact with a simple proxy of organic matter in natural waters [polyacrylic acid (PAA) and Cl^? in solution] has been investigated. A combination of synchrotron‐based X‐ray standing‐wave fluorescence yield‐ and X‐ray diffraction‐based experiments on a sample consisting of an approximately single‐particle layer of Ag‐Nps deposited on a silicon substrate and coated by a thin film of PAA containing Cl revealed the formation of a stable AgCl corrosion product despite the presence of potential surface stabilizers (PVP and PAA). Diffusion and precipitation processes at the Ag‐Nps–PAA interface were characterized with a high spatial resolution using this new approach.     

Copper as an electron trap in GaAs0.6P0.4

An electron trap having an energy level of 0.14 eV from the conduction band edge was found in the bulk of copper-diffused VPE-grown n-GaAs_0.6P_0.4 by conventional DLTS measurements and by pulse-duration dependent capacitance amplitude measurements. The capture cross section at room temperature is about 1.0×10^–21 cm² and has a weak temperature dependence. These properties are attributed to a non-repulsive center having a capturing mechanism which involves multiphonon emission processes with hardly any lattice relaxation. Evolution of the spatial distributions of the traps with time under junction electric field were studied. The results suggest that the trap is positively charged and has a high diffusivity under electric field. The center can thus be identified as positively charged interstitial copper ion rather than some form of copper complexes.     

Functionalization of Polyethyleneimine with Hollow Cyclotriveratrylene and Its Subsequent Supramolecular Interaction with Doxorubicin

In this paper, a modified Cyclotriveratrylene was synthesized and linked to a branched Polyethylenimine, and this unique polymeric material was subsequently examined as a potential supramolecular carrier for Doxorubicin. Spectroscopic analysis in different solvents had shown that Doxorubicin was coordinated within the hollow-shaped unit of the armed Cyclotriveratrylene, and the nature of the host–guest complex revealed intrinsic Van der Waals interactions and hydrogen bonding between the host and guest. The strongest interaction was detected in water because of the hydrophobic effect shared between the aromatic groups of the Doxorubicin and Cyclotriveratrylene unit. Density functional theory calculations had also confirmed that in the most stable coordination of Doxorubicin with the cross-linked polymer, the aromatic rings of the Doxorubicin were localized toward the Cyclotriveratrylene core, while its aliphatic chains aligned closer with amino groups, thus forming a compact supramolecular assembly that may confer a shielding effect on Doxorubicin. These observations had emphasized the importance of supramolecular considerations when designing a novel drug delivery platform.     

Generalization of Strang's Preconditioner with Applications to Toeplitz Least Squares Problems

In this paper, we propose a method to generalize Strang's circulant preconditioner for arbitrary n-by-n matrices A_n. The th column of our circulant preconditioner Sn is equal to the th column of the given matrix A_n. Thus if A_n is a square Toeplitz matrix, then Sn is just the Strang circulant preconditioner. When Sn is not Hermitian, our circulant preconditioner can be defined as . This construction is similar to the forward-backward projection method used in constructing preconditioners for tomographic inversion problems in medical imaging. We show that if the matrix A_n has decaying coefficients away from the main diagonal, then is a good preconditioner for An. Comparisons of our preconditioner with other circulant-based preconditioners are carried out for some 1-D Toeplitz least squares problems: min ∥ b - Ax∥₂. Preliminary numerical results show that our preconditioner performs quite well, in comparison to other circulant preconditioners. Promising test results are also reported for a 2-D deconvolution problem arising in ground-based atmospheric imaging.     

Three-dimensional visualization of diffusion flame shapes under acoustic excitation using stereoscopic imaging and reconstruction technique

Stereoscopic imaging and reconstruction technique is introduced to reconstruct the flame structures that are subject to acoustic excitation. The laminar diffusion flame under investigation was created in a cylindrical tube and excited by a loudspeaker. Stereo images were taken at a shutter speed of 1/10000^th second using a ‘stereo camera’ and the depth cue of the flame structures along the camera viewing direction were then computed using machine vision methodology. By visualizing the computed three-dimensional flame models, as well as judging the corresponding attribute such as surface gradient, the understanding of the flame and acoustic wave interaction could be improved.