New mechanisms that regulate Saccharomyces cerevisiae short peptide transporter achieve balanced intracellular amino acid concentrations

The budding yeast Saccharomyces cerevisiae is able to take up large quantities of amino acids in the form of di‐ and tripeptides via a short peptide transporter, Ptr2p. It is known that PTR2 can be induced by certain peptides and amino acids, and the mechanisms governing this upregulation are understood at the molecular level. We describe two new opposing mechanisms of regulation that emphasize potential toxicity of amino acids: the first is upregulation of PTR2 in a population of cells, caused by amino acid secretion that accompanies peptide uptake; the second is loss of Ptr2p activity, due to transporter internalization following peptide uptake. Our findings emphasize the importance of proper amino acid balance in the cell and extend understanding of peptide import regulation in yeast. Copyright © 2015 John Wiley & Sons, Ltd.     

Efficient schema-based XML-to-Relational data mapping

Storing and querying XML documents using a RDBMS is a challenging problem since one needs to resolve the conflict between the hierarchical, ordered nature of the XML data model and the flat, unordered nature of the relational data model. This conflict can be resolved by the following XML-to-Relational mappings: schema mapping, data mapping and query mapping. In this paper, we propose: (i) a lossless schema mapping algorithm to generate a database schema from a DTD, which makes several improvements over existing algorithms, (ii) two linear data mapping algorithms based on DOM and SAX, respectively, to map ordered XML data to relational data. To our best knowledge, there is no published linear schema-based data mapping algorithm for mapping ordered XML data to relational data. Experimental results are presented to show that our algorithms are efficient and scalable.     

Electrical Excitation of Long-Range Surface Plasmons in PC/OLED Structure with Two Metal Nanolayers

A current-driven source of long-range surface plasmons(LRSPs)on a duplex metal nanolayer is reported.Electrical excitation of LRSPs was experimentally observed in a planar structure,where an organic light-emitting film was sandwiched between two metal nanolayers that served as electrodes.To achieve the LRSP propagation in these metal nanolayers at the interface with air,the light-emitting structure was bordered by a one-dimensional photonic crystal(PC)on the other side.The dispersion of the light emitted by such a hybrid PC/organic-light-emitting-diode structure(PC/OLED)comprising two thin metal electrodes was obtained,with a clearly identified LRSP resonance peak.     

Imaging and strain analysis of nano-scale SiGe structures by tip-enhanced Raman spectroscopy

The spatial resolution and high sensitivity of tip-enhanced Raman spectroscopy allows the characterization of surface features on a nano-scale. This technique is used to visualize silicon-based structures, which are similar in width to the transistor channels in present leading-edge CMOS devices. The reduction of the intensive far-field background signal is crucial for detecting the weak near-field contributions and requires beside a careful alignment of laser polarization and tip axis also the consideration of the crystalline sample orientation. Despite the chemical identity of the investigated sample surface, the structures can be visualized by the shift of the Raman peak positions due to the patterning induced change of the stress distribution within lines and substrate layer. From the measured peak positions the intrinsic stress within the lines is calculated and compared with results obtained by finite element modeling. The results demonstrate the capability of the tip-enhanced Raman technique for strain analysis on a sub-50 nm scale.     

Terahertz Switching Focuser Based on Thin Film Vanadium Dioxide Zone Plate

In this paper, we propose a switchable focuser device based on a Fresnel zone plate (FZP) structure for terahertz (THz) applications. Each FZP contains seven rings, etched in thin VO₂ film with the designed focal lengths of 50 and 100 mm for 3.7-THz frequency. Temperature-induced VO₂ phase transition leads to the change in dielectric susceptibility of the material, which allows one to switch on and off the focusing properties of the device. The devices were tested with radiation of 3.1 and 3.7 THz emitted by quantum cascade lasers. Experimental results were compared with numerical simulations. In this article, we compare the FZP based on VO₂ films with different properties and show that a thicker VO₂ film reveals higher focusing efficiency, while a thinner one reveals a higher modulation ratio for the peak intensity at the focal point of FZP. We demonstrate experimentally the near-diffraction-limited size of the beam in the focal point of the device. Switching between two phase states of the VO₂ films results in up to the 38-fold change of intensity in the focal point.     

Wave field reconstruction from multiple plane intensity-only data: augmented lagrangian algorithm

A complex-valued wave field is reconstructed from intensity-only measurements given at multiple observation planes parallel to the object plane. The phase-retrieval algorithm is obtained from the constrained maximum likelihood approach provided that the additive noise is gaussian. The forward propagation from the object plane to the measurement plane is treated as a constraint in the proposed variational setting of reconstruction. The developed iterative algorithm is based on an augmented lagrangian technique. An advanced performance of the algorithm is demonstrated by numerical simulations.     

Modulation of Aptamer–Ligand-Binding by Complementary Oligonucleotides: A G-Quadruplex Anti-Ochratoxin A Aptamer Case Study

Short oligonucleotides are widely used for the construction of aptamer-based sensors and logical bioelements to modulate aptamer–ligand binding. However, relationships between the parameters (length, location of the complementary region) of oligonucleotides and their influence on aptamer–ligand interactions remain unclear. Here, we addressed this task by comparing the effects of short complementary oligonucleotides (ssDNAs) on the structure and ligand-binding ability of an aptamer and identifying ssDNAs’ features that determine these effects. Within this, the interactions between the OTA-specific G-quadruplex aptamer 1.12.2 (5′-GATCGGGTGTGGGTGGCGTAAAGGGA GCATCGGACA-3′) and 21 single-stranded DNA (ssDNA) oligonucleotides complementary to different regions of the aptamer were studied. Two sets of aptamer–ssDNA dissociation constants were obtained in the absence and in the presence of OTA by isothermal calorimetry and fluorescence anisotropy, respectively. In both sets, the binding constants depend on the number of hydrogen bonds formed in the aptamer–ssDNA complex. The ssDNAs’ having more than 23 hydrogen bonds with the aptamer have a lower aptamer dissociation constant than for aptamer–OTA interactions. The ssDNAs’ having less than 18 hydrogen bonds did not affect the aptamer–OTA affinity. The location of ssDNA’s complementary site in the aptamer affeced the kinetics of the interaction and retention of OTA-binding in aptamer–ssDNA complexes. The location of the ssDNA site in the aptamer G-quadruplex led to its unfolding. In the presence of OTA, the unfolding process was longer and takes from 20 to 70 min. The refolding in the presence of OTA was possible and depends on the length and location of the ssDNA’s complementary site. The location of the ssDNA site in the tail region led to its rapid displacement and wasn’t affecting the G-qaudruplex’s integrity. It makes the tail region more perspective for the development of ssDNA-based tools using this aptamer.     

Optimized Heterologous Expression and Efficient Purification of a New TRAIL-Based Antitumor Fusion Protein SRH–DR5-B with Dual VEGFR2 and DR5 Receptor Specificity

In the last two decades, bifunctional proteins have been created by genetic and protein engineering methods to increase therapeutic effects in various diseases, including cancer. Unlike conventional small molecule or monotargeted drugs, bifunctional proteins have increased biological activity while maintaining low systemic toxicity. The recombinant anti-cancer cytokine TRAIL has shown a limited therapeutic effect in clinical trials. To enhance the efficacy of TRAIL, we designed the HRH–DR5-B fusion protein based on the DR5-selective mutant variant of TRAIL fused to the anti-angiogenic synthetic peptide HRHTKQRHTALH. Initially low expression of HRH–DR5-B was enhanced by the substitution of E. coli-optimized codons with AT-rich codons in the DNA sequence encoding the first 7 amino acid residues of the HRH peptide. However, the HRH–DR5-B degraded during purification to form two adjacent protein bands on the SDS-PAGE gel. The replacement of His by Ser at position P2 immediately after the initiator Met dramatically minimized degradation, allowing more than 20 mg of protein to be obtained from 200 mL of cell culture. The resulting SRH–DR5-B fusion bound the VEGFR2 and DR5 receptors with high affinity and showed increased cytotoxic activity in 3D multicellular tumor spheroids. SRH–DR5-B can be considered as a promising candidate for therapeutic applications.     

Understanding the High Voltage Behavior of LiNiO2 Through the Electrochemical Properties of the Surface Layer

Nickel-rich layered oxides are adopted as electrode materials for EV's. They suffer from a capacity loss when the cells are charged above 4.15 V versus Li/Li⁺. Doping and coating can lead to significant improvement in cycling. However, the mechanisms involved at high voltage are not clear. This work is focused on LiNiO₂ to overcome the effect of M cations. Galvanostatic intermittent titration technique (GITT) and in situ X-ray diffraction (XRD) experiments are performed at very low rates in various voltage ranges (3.8–4.3 V,). On the “4.2–4.3 V” plateau the R2 phase is transformed simultaneously in R3, R3 with H4 stacking faults and H4. As the charge proceeds above 4.17 V cell polarization increases, hindering Li deintercalation. In discharge, such polarization decreases immediately. Upon cycling, the polarization increases at each charge above 4.17 V. In discharge, the capacity and dQ/dV features below 4.1 V remain constant and unaffected, suggesting that the bulk of the material do not undergo significant structural defect. This study shows that the change in polarization results from the electrochemical behavior of the grain surface having very low conductivity above 4.17 V and high conductivity below this threshold. This new approach can explain the behavior observed with dopants like tungsten.