Virtual screening for ligands of the insect molting hormone receptor

Insect growth is regulated by the orchestrated event of ecdysteroids and their receptor proteins. Agonists/antagonists of ecdysteroid receptor are predicted to disrupt normal growth, providing good candidates of new insecticides. A database of over 2 million compounds was subjected to a shape-based virtual screening cascade to identify novel nonsteroidal hits similar to the known EcR ligand ponasterone A. Testing revealed micromolar hits against two strains of insect cells. Docking experiments against EcR were used to support the predicted binding mode of these ligands based on their overlay to ponasterone A.     

Mild solution synthesis of plate-like and rod-like ZnO crystals

Micro-disks and micro-rods of ZnO were successfully synthesized by a mild solution process using zinc chloride as starting material. The morphology of the ZnO crystals changed substantially, depending on the concentrations of the Zn²⁺ ion and organic additives in the solution. A plate-like Zn₅(OH)₈Cl₂·H₂O precursor with a layered structure could be produced in solutions with high concentrations of chloride ions. The thermal stability, including phase composition and morphology, of the as-prepared Zn₅(OH)₈Cl₂·H₂O in air and water was investigated.     

Spontaneous Formation of Microgroove Arrays on the Surface of p‐Type Porous Silicon Induced by a Turing Instability in Electrochemical Dissolution

Self‐organization plays an imperative role in recent materials science. Highly tunable, periodic structures based on dynamic self‐organization at micrometer scales have proven difficult to design, but are desired for the further development of micropatterning. In the present study, we report a microgroove array that spontaneously forms on a p‐type silicon surface during its electrodissolution. Our detailed experimental results suggest that the instability can be classified as Turing instability. The characteristic scale of the Turing‐type pattern is small compared to self‐organized patterns caused by the Turing instabilities reported so far. The mechanism for the miniaturization of self‐organized patterns is strongly related to the semiconducting property of silicon electrodes as well as the dynamics of their surface chemistry.     

Sulfonate group-modified FePtCu nanoparticles as a selective probe for LDI-MS analysis of oligopeptides from a peptide mixture and human serum proteins

The availability of robust methods for the species-specific detection of meat and bone meal (MBM) in compound feedingstuffs is an important prerequisite to enforce current and upcoming European legislation on the use of processed animal proteins in animal nutrition. Among possible methods, those based on DNA turned out to be a reliable tool for this aim, since DNA is a quite thermostable molecule able to resist severe heat treatments applied in the manufacturing of animal meals. The application of such methods by control laboratories implies that the method has been validated including an assessment of its robustness. Successful transferability between laboratories is considered an important robustness criterion of the method. However, corresponding guidelines regarding the design of such a study relevant to this field are missing. Here, we demonstrate the feasibility of an alternative concept that was applied to check for the transferability of a qualitative assay for the detection of banned MBM in feedingstuffs at trace level based on real-time PCR. The concept was based on an experimental nested design applying analysis of variance (ANOVA) that was conducted independently in two laboratories and which allows for establishing major factors influencing the result of analysis. Statistical assessment of the results confirmed the importance of the DNA extraction/purification step utilised, whereas the PCR step turned out to be a minor factor regarding the overall variability of the results. Furthermore, blind samples comprised of compound feed adulterated with MBM at 0.1 % and blank compound feed were correctly classified as "positive" or "negative" samples, thus confirming fitness of purpose for the method. This approach can be of interest for other research groups working in the development of real-time PCR methods and in their use by control laboratories. Nested design of the study to check for the transferability of the real-time PCR method     

Autonomous DNA computing machine based on photochemical gate transition

We report the construction of a one-pot autonomous DNA computing machine based on photochemical gate transition (photocleavage, hybridization, and photoligation), and we performed binary digit additions using this machine. In our method, both photochemical DNA manipulations previously reported, photoligation via 5-carboxyvinyldeoxyuridene (cvU) containing ODN and photocleavage via carbazole-modified ODN, were employed. The binary digit additions were autonomously carried out by one-time irradiation at 366 nm in the single test tube. The fluorescence readout by the DNA chip was in good agreement with the correct answer of binary digit additions. We believe that this system is easily applicable to correlation analysis between SNPs as well as other binary digit processing, such as subtraction.     

Nonadiabatic electron wavepacket dynamics of molecules in an intense optical field: an ab initio electronic state study

A theory of quantum electron wavepacket dynamics that nonadiabatically couples with classical nuclear motions in intense optical fields is studied. The formalism is intended to track the laser-driven electron wavepackets in terms of the linear combination of configuration-state functions generated with ab initio molecular orbitals. Beginning with the total quantum Hamiltonian for electrons and nuclei in the vector potential of classical electromagnetic field, we reduce the Hamiltonian into a mixed quantum-classical representation by replacing the quantum nuclear momentum operators with the classical counterparts. This framework gives equations of motion for electron wavepackets in an intense laser field through the time dependent variational principle. On the other hand, a generalization of the Newtonian equations provides a matrix form of forces acting on the nuclei for nonadiabatic dynamics. A mean-field approximation to the force matrix reduces this higher order formalism to the semiclassical Ehrenfest theory in intense optical fields. To bring these theories into a practical quantum chemical package for general molecules, we have implemented the relevant ab initio algorithms in it. Some numerical results in the level of the semiclassical Ehrenfest-type theory with explicit use of the nuclear kinematic (derivative) coupling and the velocity form for the optical interaction are presented.     

Self-modeling curve resolution (SMCR) analysis of near-infrared (NIR) imaging data of pharmaceutical tablets

The idea of quality by design (QbD) has been proposed in pharmaceutical field. QbD is a systematic approach to control the product performance based on the scientific understanding of the product quality and its manufacturing process. In the present study, near-infrared (NIR) imaging is utilized as a tool to achieve this concept. A practical use of a chemometrics technique called self-modeling curve resolution (SMCR) is demonstrated with NIR imaging analysis of pharmaceutical tablets containing two ingredients, a soluble active ingredient, pentoxifylline (PTX), and an insoluble excipient, palmitic acid. Concentration profiles obtained by SMCR reveal that the homogenous distribution of chemical ingredients strongly depends on the grinding time and that its process plays a central role in quantitative control, say sustained-release of PTX. In addition, pure component spectra by SMCR indicate a sequential change of specific NIR peak intensities following the increase of the grinding time. The spectra change shows a molecular structure change related to its crystallinity during grinding process. Accordingly, this study clearly demonstrates that NIR imaging combined with SMCR can be a powerful tool to reveal chemical or physical mechanism induced by the manufacturing process of pharmaceutical products and that it may be a solid solution for QbD of pharmaceutical products.     

Detection of the His-heme Fe2+-NO species in the reduction of NO to N2O by ba3-oxidase from thermus thermophilus

Reaction pathways in the enzymatic formation and cleavage of the N-N and N-O bonds, respectively, are difficult to verify without the structure of the intermediates, but we now have such information on the heme a(3)(2+)-NO species formed in the reaction of ba(3)-oxidase with NO from resonance Raman spectroscopy. We have identified the His-heme a(3)(2+)-NO/Cu(B)(1+) species by its characteristic Fe-NO and N-O stretching frequencies at 539 and 1620 cm(-)(1), respectively. The Fe-NO and N-O frequencies in ba(3)-oxidase are 21 and 7 cm(-)(1) lower and higher, respectively, than those observed in Mb-NO. From these results and earlier Raman and FTIR measurements, we demonstrate that the protein environment of the proximal His384 that is part of the Q-proton pathway controls the strength of the Fe-His384 bond upon ligand (CO vs NO) binding. We also show by time-resolved FTIR spectroscopy that Cu(B)(1+) has a much lower affinity for NO than for CO. We suggest that the reduction of NO to N(2)O by ba(3)-oxidase proceeds by the fast binding of the first NO molecule to heme a(3) with high-affinity, and the second NO molecule binds to Cu(B) with low-affinity, producing the temporal co-presence of two NO molecules in the heme-copper center. The low-affinity of Cu(B) for NO binding also explains the NO reductase activity of the ba(3)-oxidase as opposed to other heme-copper oxidases. With the identification of the His-heme a(3)(2+)-NO/Cu(B)(1+) species, the structure of the binuclear heme a(3)-Cu(B)(1+) center in the initial step of the NO reduction mechanism is known.