Mismatch discrimination in oligonucleotide hybridization reactions using single strand binding protein. A surface plasmon fluorescence study

We describe the use of surface plasmon- and surface plasmon fieldenhanced fluorescence spectroscopy for the detection of hybridization reactions between surface-attached probe oligonucleotides and complement strands binding from solution. These targets, exhibiting different base mismatches relative to the probe 15-mer sequences, carry a fluorophore at their 5'-end thus allowing for sensitive detection and quantification of association, k_on, and dissociation, k_off, rate constants, as well as affinity constants, K_a. We demonstrate that by the competitive binding / replacement of single strand binding proteins the mismatch discrimination can be further enhanced.     

Atmospheric trace gas analysis with cavity ring-down spectroscopy

Cavity ring-down spectroscopy (CRDS) is a highly sensitive laser absorption method. It can be used for quantitative analysis of molecular species at the sub-ppb level. The absorption cell (cavity) is sealed by two high-reflective mirrors on each side, which results in an effective absorption path-length of some kilometers. Our experiments for atmospheric gas analysis have been carried out so far with an Excimer pumped dye laser in the UV-VIS and a CO overtone sideband laser in the wavelength region around 3 μm. Experiments with an all solid-state difference frequency laser system will follow. In the UV-VIS region, we measured trace gas molecules like SO₂, NO₂, and CH₂O. In the mid-infrared, around 3 μm, we measured hydrocarbons like CH₄, C₂H₆, and C₂H₄ with a detection limit of less than 1 ppb. The noise equivalent absorption coefficients in the MIR are in the order of 1.7·10⁻⁹ cm⁻¹. Due to the high data acquisition rate and the high sensitivity, CRDS enables real-time detection of trace gases in ambient air.     

Handling Climate Change – Establishing Waste CO2 Management A View from Biotechnology

The biggest material flows induced by industry are realized in energy production. Coal, oil and gas as raw material streams are moved from their deposits to their further converting. From there product streams are branched out. However, the biggest material flow of this industry is waste CO₂ mobilized by chemical conversion from fossil deposits and released into the atmosphere. A waste management is urgently needed to reduce the amount of this flow, to neutralize its effects on environment and to establish applications yielding a return. Natural backflow of CO₂ from the atmosphere to the biosphere waits for completion by industrial methods in order to shift it to a dimension equalizing the finally unavoidable amount of waste CO₂ flow into the atmosphere.     

Dynamic X-ray radiography for the determination of foamed bitumen bubble area distribution

Foam bitumen is highly efficient in wetting and coating the surface of mineral aggregate at lower temperature. In order to improve understanding and characterization of the bitumen foam, X-ray radiography was used to study the formation and decay of bitumen foam in 2D representation. Image segmentation analysis was used to determine the foam bubble size distribution. In addition, the main parameters influencing foam bitumen formation, water content, and temperature were also investigated. The results demonstrate the influence of the water content on morphology and expansion of foam bitumen bubbles. Adding more water in the foaming process leads to quick collapse of bubbles and intensifies coalescence of foam bitumen. Higher temperatures produces larger bubbles at early foaming stage compared to lower temperature. Moreover the morphology of bubble formation depends on the types of bitumen used. An exponential function has been implemented to represent the bubble area distribution.     

Identification and Structure–Activity Relationship Studies of Small‐Molecule Inhibitors of the Methyllysine Reader Protein Spindlin1

The methyllysine reader protein Spindlin1 has been implicated in the tumorigenesis of several types of cancer and may be an attractive novel therapeutic target. Small‐molecule inhibitors of Spindlin1 should be valuable as chemical probes as well as potential new therapeutics. We applied an iterative virtual screening campaign, encompassing structure‐ and ligand‐based approaches, to identify potential Spindlin1 inhibitors from databases of commercially available compounds. Our in silico studies coupled with in vitro testing were successful in identifying novel Spindlin1 inhibitors. Several 4‐aminoquinazoline and quinazolinethione derivatives were among the active hit compounds, which indicated that these scaffolds represent promising lead structures for the development of Spindlin1 inhibitors. Subsequent lead optimization studies were hence carried out, and numerous derivatives of both lead scaffolds were synthesized. This resulted in the discovery of novel inhibitors of Spindlin1 and helped explore the structure–activity relationships of these inhibitor series.     

4‐Biphenylalanine‐ and 3‐Phenyltyrosine‐Derived Hydroxamic Acids as Inhibitors of the JumonjiC‐Domain‐Containing Histone Demethylase KDM4A

Overexpression of the histone lysine demethylase KDM4A, which regulates H3K9 and H3K36 methylation states, has been related to the pathology of several human cancers. We found that a previously reported hydroxamate‐based histone deacetylase (HDAC) inhibitor (SW55) was also able to weakly inhibit this demethylase with an IC₅₀ value of 25.4 μm . Herein we report the synthesis and biochemical evaluations, with two orthogonal in vitro assays, of a series of derivatives of this lead structure. With extensive chemical modifications on the lead structure, also by exploiting the versatility of the radical arylation with aryldiazonium salts, we were able to increase the potency of the derivatives against KDM4A to the low‐micromolar range and, more importantly, to obtain demethylase selectivity with respect to HDACs. Cell‐permeable derivatives clearly showed a demethylase‐inhibition‐dependent antiproliferative effect against HL‐60 human promyelocytic leukemia cells.     

Fourier‐Transform Rheology of Unvulcanized,Carbon Black Filled Styrene Butadiene Rubber

Rubber materials filled with reinforcing fillers display nonlinear rheological behavior at small strain amplitudes below γ₀ < 0.1. Nevertheless, rheological data are analyzed mostly in terms of linear parameters, such as shear moduli (G′, G″), which loose their physical meaning in the nonlinear regime. In this work styrene butadiene rubber filled with carbon black (CB) under large amplitude oscillatory shear (LAOS) is analyzed in terms of the nonlinear parameter I_3/1. Three different CB grades are used and the filler load is varied between 0 and 70 phr. It is found that I_3/1(φ) is most sensitive to changes of the total accessible filler surface area at low strain amplitudes (γ₀ = 0.32). The addition of up to 70 phr CB leads to an increase of I_3/1(φ) by a factor of more than ten. The influence of the measurement temperature on I_3/1 is pronounced for CB levels above the percolation threshold.

     

Gallium gradients in Cu(In,Ga)Se2 thin‐film solar cells

The gallium gradient in Cu(In,Ga)Se₂ (CIGS) layers, which forms during the two industrially relevant deposition routes, the sequential and co‐evaporation processes, plays a key role in the device performance of CIGS thin‐film modules. In this contribution, we present a comprehensive study on the formation, nature, and consequences of gallium gradients in CIGS solar cells. The formation of gallium gradients is analyzed in real time during a rapid selenization process by in situ X‐ray measurements. In addition, the gallium grading of a CIGS layer grown with an in‐line co‐evaporation process is analyzed by means of depth profiling with mass spectrometry. This gallium gradient of a real solar cell served as input data for device simulations. Depth‐dependent occurrence of lateral inhomogeneities on the µm scale in CIGS deposited by the co‐evaporation process was investigated by highly spatially resolved luminescence measurements on etched CIGS samples, which revealed a dependence of the optical bandgap, the quasi‐Fermi level splitting, transition levels, and the vertical gallium gradient. Transmission electron microscopy analyses of CIGS cross‐sections point to a difference in gallium content in the near surface region of neighboring grains. Migration barriers for a copper‐vacancy‐mediated indium and gallium diffusion in CuInSe₂ and CuGaSe₂ were calculated using density functional theory. The migration barrier for the In_Cu antisite in CuGaSe₂ is significantly lower compared with the Ga_Cu antisite in CuInSe₂, which is in accordance with the experimentally observed Ga gradients in CIGS layers grown by co‐evaporation and selenization processes. Copyright © 2014 John Wiley & Sons, Ltd.