In silico design of small RNA switches

The discovery of natural RNA sensors that respond to a change in the environment by a conformational switch can be utilized for various biotechnological and nanobiotechnological advances. One class of RNA sensors is the riboswitch: an RNA genetic control element that is capable of sensing small molecules, responding to a deviation in ligand concentration with a structural change. Riboswitches are modularly built from smaller components. Computational methods can potentially be utilized in assembling these building block components and offering improvements in the biochemical design process. We describe a computational procedure to design RNA switches from building blocks with favorable properties. To achieve maximal throughput for genetic control purposes, future designer RNA switches can be assembled based on a computerized preprocessing buildup of the constituent domains, namely the aptamer and the expression platform in the case of a synthetic riboswitch. Conformational switching is enabled by the RNA versatility to possess two highly stable states that are energetically close to each other but topologically distinct, separated by an energy barrier between them. Initially, computer simulations can produce a list of short sequences that switch between two conformers when trigerred by point mutations or temperature. The short sequences should possess an additional desirable property; when these selected small RNA switch segments are attached to various aptamers, the ligand binding mechanism should replace the aforementioned event triggers, which will no longer be effective for crossing the energy barrier. In the assembled RNA sequence, energy minimization folding predictions should then show no difference between the folded structure of the entire sequence relative to the folded structure of each of its constituents. Moreover, energy minimization methods applied on the entire sequence could aid at this preprocessing stage by exhibiting high mutational robustness to capture the stability of the formed hairpin in the expression platform. The above computer-assisted assembly procedure together with application specific considerations may further be tailored for therapeutic gene regulation. Index Terms-Design of RNA switches, energy minimization methods, RNA folding predictions.     

Fatigue assessment of offshore wind turbines on monopile foundations using multi‐band modal expansion

Offshore wind turbines (OWTs) are subjected to both quasi‐static loads originating from variations in the thrust force and dynamic loads linked to turbulence, waves and turbine dynamics. Both types of loads contribute to fatigue life progression and thus define the turbine's age. As a structural health monitoring solution, one could thus directly measure the stress history at fatigue critical locations. However, for OWTs on monopile foundations some fatigue critical locations are located below the seabed. Installing strain sensors at these hotspots is therefore impossible for existing wind turbines. This measurement restriction is overcome by reconstructing the full‐field response of the structure based on the limited number of accelerometers and strain sensors (installed at a few easily accessible locations) and a calibrated finite element model of the system. The system model uses a multi‐band modal expansion approach constituted of the quasi‐static and dynamic contributions. These contributions are superimposed to reconstruct the stress history at all degrees of freedom of the finite element model, and the subsequent assess fatigue life consumption at all fatigue hot spots of the OWT. In this paper, the proposed virtual sensing technique is validated by predicting the stresses in the transition piece with 12 days of consecutive measurements from an operational OWT. The data set contains both variations in environmental and operating conditions as well as extreme events. Finally, a full‐field strain assessment in the tower and foundation system of the OWT is demonstrated. Copyright © 2017 John Wiley & Sons, Ltd.     

A TRNSYS-based simulation framework for the analysis of solar thermal and heat pump systems

The modeling and simulation of combined solar and heat pump (SHP) systems is a challenging task as it requires expert knowledge in modeling as well as in the behavior of the real systems. As an example of a SHP system, this work considers parallel solar thermal and heat pump systems with ground or air source heat pumps for the efficient energy supply of buildings. An introduction to SHP systems and the considered system concepts is given and the challenges in designing new models within the simulation environment TRNSYS are described. Finally, a TRNSYS-based stand-alone tool (SHP-SimFrame) ispresented which enables users to analyze predefined SHP concepts with hardly any knowledge in modeling and simulation itself.     

Subsecond voltammetric separation between dopamine and serotonin in the presence of ascorbate

Although voltammetry has proved an important tool for unraveling the dynamics of specific neurotransmitter molecules during the past decade, it has been very difficult to monitor more than one neurotransmitter simultaneously. In this work, we present a voltammetric methodology that allows discrimination between dopamine and serotonin, two important neurotransmitter molecules with very similar electrochemical properties, in the presence of high concentrations of ascorbate. We combined the application of a novel large-amplitude/high-frequency voltage excitation with signal processing techniques valid for the analysis of nonstationary and nonlinear phenomena. This allows us to minimize the contribution from capacitance and preserve the faradaic features of the voltammetric response providing us with excellent voltammetric detail. Using appropriate voltage excitation parameters and defining specific regions in the voltage space, so-called voltage windows, we can measure the concentrations of dopamine and serotonin separately or independently in mixed solutions even in the presence of high concentrations of ascorbate. Because of the enhanced voltammetric detail of this new technique, it is also possible to explore effects attributed to interfacial phenomena such as adsorption/desorption and electrode fouling.     

Electroanalytical performance of nitrogen-containing tetrahedral amorphous carbon thin-film electrodes

Tetrahedral amorphous carbon (ta-C) consists of a mixture of sp(3)- and sp(2)-bonded carbon ranging from 60 to 40% (sp(3)/sp(3)+sp(2)) depending on the deposition conditions. The physical, chemical, and electrochemical properties depend on the sp(2)/sp(3) bonding ratio as well as the presence of incorporated impurities, such as hydrogen or nitrogen. The ability to grow ta-C at lower temperatures (25-100 °C) on a wider variety of substrates as compared to CVD diamond is an advantage of this material. Herein, we report on the structural and electrochemical properties of nitrogen-incorporated ta-C thin films (ta-C:N). The incorporation of nitrogen into the films decreases the electrical resistivity from 613 ± 60 (0 sccm N(2)) to 1.10 ± 0.07 Ω-cm (50 sccm N(2)), presumably by increasing the sp(2)-bonded carbon content and the connectedness of these domains. Similar to boron-doped diamond, these materials are characterized by a low background voltammetric current, a wide working potential window (~ 3 V), and relatively rapid electron-transfer kinetics for aqueous redox systems, including Fe(CN)(6)(-3/-4) and Ru(NH(3))(6)(+3/+2), without conventional pretreatment. Additionally, there is weak molecular adsorption of polar molecules (methylene blue) on the ta-C surface. Overall, the properties of the ta-C and ta-C:N electrodes are such that they could be excellent new choices for electroanalytical measurements.     

Raymond J. Corsini (1914–2008).

Presents an obituary for Raymond J. Corsini, one of psychology’s most prolific authors and editors. Ray’s most important contributions include editing an award-winning four-volume encyclopedia of psychology (1994, Wiley), a dictionary of psychology (1999, Brunner/ Mazel), and one of the leading graduate texts on psychotherapy (Corsini & Wedding, 8th ed., 2008, Cengage), which was translated into more than a dozen languages. However, Ray took the greatest pride in the development of the Corsini 4-R system (also known as Individual Education), an innovative approach to school system reform reform based on democratic principles and Adlerian psychology. (The four Rs were responsibility, respect, resourcefulness, and responsiveness.) Corsini died in Honolulu on November 8, 2008. He is survived by his physician wife, Kleona Rigney, and his social worker daughter, Evelyn Anne Corsini. Both share Ray’s passionate commitment to Adlerian social interest. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Development of a smart packaging for the monitoring of fish spoilage

There is much interest from the fisheries industry in developing rapid methods to evaluate real-time freshness of fish and seafood products. Emphasis is on the ones that would reflect and account for the products history and their storage conditions from “harvest-to-home”. The development of a “smart packaging” that monitors the microbial breakdown products in the headspace of packaged fish is described. When fish spoils it releases a variety of basic volatile amines which are detectable with appropriate pH indicating sensors. These are prepared by entrapping within a polymer matrix a pH sensitive dye that responds, through visible color changes to the spoilage volatile compounds that contribute to a quantity known as total volatile basic nitrogen (TVB-N). Laboratory trials on fresh fish filets showed that the sensor accurately tracks the increase in amines concentration in the package headspace. The response was also found to correlate to changing microbial populations (total viable count or TVC and Pseudomonas spp.). In addition, leaching of the dye was assessed over time to assess the suitability of the sensor formulation for food packaging application.     

Self‐Assembly: I‐Motif Nanospheres: Unusual Self‐Assembly of Long Cytosine Strands (Small 8/2011)

The synthesis and characterization of novel DNA structures based on tetraplex cytosine (C) arrangements, known as i‐motifs or i‐tetraplexes, is reported. Atomic force microscopy (AFM) investigation shows that long C‐strands in mild acidic conditions form compact spherically shaped nanostructures. The DNA nanospheres are characterized by a typical uniform shape and narrow height distribution. Electrostatic force microscopy (EFM) measurements performed on the i‐motif spheres clearly show their electrical polarizability. Further investigations by scanning tunneling microscopy (STM) at ultrahigh vacuum reveals that the structures exhibit an average voltage gap of 1.9 eV, which is narrower than the voltage gap previously measured for poly(dG)–poly(dC) molecules in similar conditions.     

UV Absorption microspectrophotometry and digestibility of cell types of bermudagrass internodes at different stages of maturity

The walls of sclerenchyma, vascular bundle sheaths, and parenchyma at different maturities (internodes 2, 5, and 7 from the apex) of bermudagrass [Cynodon dactylon (L) Pers] were analyzed by UV absorption microspectrophotometry, and the results were related to wall digestibility. Sclerenchyma walls from internode 2 were degraded by rumen microorganisms, with only the middle lamella remaining. Undegraded sclerenchyma walls gave a UV absorption spectrum similar to that of p-coumaroyl and feruloyl arabinoxylo-trisaccharides isolated from bermudagrass cell walls. Absorption maxima occurred at ? 245 and 320 nm, together with a shoulder at ? 280 nm. Sclerenchyma from the older internodes 5 and 7 showed only partial degradation of the secondary wall adjacent to the lumen. Spectra of undegraded walls from these internodes showed absorption maxima at ? 245 and 285 nm with a shoulder at ? 320 nm. Spectra of sclerenchyma walls that included the middle lamellae gave a higher absorption at ? 320 nm than did wall layers excluding the middle lamellae. Vascular bundle sheaths generally were similar in digestion patterns and spectra to those of sclerenchyma. Parenchyma cells in internode 2, which were totally degradable, gave low absorbance. Parenchyma cell walls from internodes 5 and 7 were degraded except for the middle lamellae in cells nearest to the sclerenchyma; parenchyma cells nearest to the stem centre were totally degraded. Spectra of parenchyma wall regions that included middle lamellae were similar to the p-coumaroyl and feruloyl arabinoxylo-trisaccharides, and absorbance values were low compared with sclerenchyma and vascular walls. Results suggested that esteror ether-linked phenolic acids accounted for most of the UV absorption in young sclerenchyma and young and old parenchyma; lignin-like aromatics increased in older, poorly digested sclerenchyma as ester/ether-type compounds decreased. An estimation of the amount of ‘ferulic acid equivalents’ of the walls was made assuming all the absorbance at ? λ_max 320 nm was due to ferulic acid; older sclerenchyma walls had the highest values (160 mg g^?1 walls) and parenchyma walls the lowest (11 mg g^?1 walls).