Design and structural analysis of hairpin-TFO for transcriptional activation of genes in S-cerevisiae

Triplex forming oligonucleotides (TFOs) have the potential to modulate gene expression. While most of the experiments are directed towards triplex mediated inhibition of gene expression the strategy potentially could be used for gene specific activation. In an attempt to design a strategy for gene specific activation in vivo applicable to a large number of genes we have designed a TFO based activator-target system which may be utilized in Saccharomyces cerevisiae or any other system where Gal4 protein is ectopically expressed. The total genome sequence of Saccharomyces cerevisiae and expression profiles were used to select the target genes with upstream poly (pu/py) sequences. We have utilized the paradigm of Gal4 protein and its binding site. We describe here the selection of target genes and design of hairpin-TFO including the targeting sequences containing polypurine stretch found in the upstream promoter regions of weakly expressed genes. We demonstrate, the formation of hairpin-TFO, its binding to Gal4 protein, its ability to form triplex with the target duplex in vitro, the effect of polyethylenimine on complex formation and discuss the implication on in vivo transcription activation.

Method for Creative Behavioral Design Based on Analogy and Blending from Natural Things

In the near future, robots and CG (computer graphics) will be required to exhibit creative behaviors that reflect designers’ abstract images and emotions. However, there are no effective methods to develop abstract images and emotions and support designers in designing creative behaviors that reflect their images and emotions. Analogy and blending are two methods known to be very effective for designing creative behaviors. The aim of this study is to propose a method for developing designers’ abstract behavioral images and emotions and giving shape to them by constructing a computer system that supports a designer in the creation of the desired behavior. This method focuses on deriving inspiration from the behavioral aspects of natural phenomena rather than simply mimicking it. We have proposed two new methods for developing abstract behavioral images and emotions by which a designer can use analogies from natural things such as animals and plants even when there is a difference in the number of joints between the natural object and the design target. The first method uses visual behavioral images, the second uses rhythmic behavioral images. We have demonstrated examples of designed behaviors to verify the effectiveness of the proposed methods.

Polymer microfabrication by scanning based microstereolithography: Optical design and material functionality

Several research groups have attempted to optimize photopolymerization parameters to increase the throughput of scanning based microstereolithography (MSL) systems through modified beam scanning techniques. Efforts in reducing the curing line width have been implemented through high numerical aperture (NA) optical setups. However, the intensity contour symmetry and the depth of field of focus have led to grossly non-vertical and non-uniform curing profiles. This work tries to review the photopolymerization process in a scanning based MSL system from the aspect of material functionality and optical design. The focus has been to exploit the rich potential of photoreactor scanning system in achieving desired fabrication modalities (minimum curing width, uniform depth profile, and vertical curing profile) even with a reduced NA optical setup and a single movable stage. The present study tries to manipulate to its advantage the effect of optimized lower c] (photoinitiator (PI) concentration) in reducing the minimum curing width to similar to 10-20 mu m even with a higher spot size (similar to 21.36 mu m) through a judiciously chosen ``monomer-PI'' system. Optimization on grounds of increasing E-max (maximum laser exposure energy at surface) by optimizing the scan rate provides enough time for the monomer or resin to get cured across the entire resist thickness (surface to substrate similar to 10-100 mu m), leading to uniform depth profiles along the entire scan lengths. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4750975]

Contrasting fire regimes in a seasonally dry tropical forest and a savanna ecosystem in the western Ghats, India

Tropical dry forests and savannas constitute more than half of all tropical forests and grasslands, but little is known about forest fire regimes within these two extensive types of ecosystems. Forest fire regimes in a predominantly dry forest in India, the Nilgiri landscape, and a predominantly savanna ecosystem in the Sathyamangalam landscape, were examined. Remote sensing data were applied to delineate burned areas, determine fire size characteristics, and to estimate fire-rotation intervals. Belt transects (0.5 ha) were used to estimate forest structure, diversity, and fuel loads. Mean area burned, mean number of fires, and mean fire size per year were substantially higher in the Nilgiri landscape compared to the Sathyamangalam landscape. Mean fire-rotational interval was 7.1 yr in the Nilgiri landscape and 44.1 yr in the Sathyamangalam landscape. Tree (>= 10 cm diameter at breast height) species diversity, tree density, and basal area were significantly higher in the Nilgiri landscape compared to the Sathyamangalam landscape. Total fuel loads were significantly higher in tropical dry and moist deciduous forests in the Nilgiri landscape, but total fuel loads were higher in the tropical dry thorn forests of the Sathyamangalam landscape. Thus, the two landscapes revealed contrasting fire regimes and forest characteristics, with more and four-fold larger fires in the Nilgiri landscape. The dry forests and savannas could be maintained by a combination of factors, such as fire, grazing pressures, and herbivore populations. Understanding the factors maintaining these two ecosystems will be critical for their conservation.

`Universal' recession curves and their geomorphological interpretation

The study of recession flows offers fundamental insights into basin hydrological processes and, in particular, into the collective behavior of the governing dominant subsurface flows and properties. We use here an existing geomorphological interpretation of recession dynamics, which links the exponent in the classic recession curve -dQ/dt - kQ(alpha) to the geometric properties of the time-varying drainage network to study the general properties of recession curves across a wide variety of river basins. In particular, we show how the parameter k depends on the initial soil moisture state of the basin and can be made to explicitly depend on an index discharge, representative of initial sub-subsurface storage. Through this framework we obtain a non-dimensional, event-independent, recession curve. We subsequently quantify the variability of k across different basins on the basis of their geometry, and, by rescaling, collapse curves from different events and basins to obtain a generalized, or `universal', recession curve. Finally, we analyze the resulting normalized recession curves and explain their universal characteristics, lending further support to the notion that the statistical properties of observed recession curves bear the signature of the geomorphological structure of the networks producing them. (C) 2014 Elsevier Ltd. All rights reserved.

Design and Modeling of an Active Five-Axis Compliant Micromanipulator

This paper presents the design and modeling of an active five-axis compliant micromanipulator whose tip orientation can be independently controlled by large angles about two axes and the tip-position can be controlled in three dimensions. These features enable precise control of the contact point of the tip and the tip-sample interaction forces with three-dimensional nanoscale objects, including those features that are conventionally inaccessible. Control of the tip-motion is realized by means of electromagnetic actuation combined with a novel kinematic and structural design of the micromanipulator, which, in addition, also ensures compatibility with existing high-resolution motion-measurement systems. The design and analysis of the manipulator structure and those of the actuation system are first presented. Quasi-static and dynamic lumped-parameter (LP) models are then derived for the five-axis compliant micromanipulator. Finite element (FE) analysis is employed to validate these models, which are subsequently used to study the effects of tip orientation on the mechanical characteristics of the five-axis micromanipulator. Finally, a prototype of the designed five-axis manipulator is fabricated by means of focused ion-beam milling (FIB).

Design and morphology control of a thiophene derivative through electrospraying using various solvents

In the present work, electrospraying of an organic molecule is carried out using various solvents, obtaining fibril structures along with a range of distinct morphologies. Solvent characteristics play a major role in determining the morphology of the organic material. A thiophene derivative (7,9-di(thiophen-2-yl)-8H-cyclopentaa]acenaphthylen-8-one) (DTCPA) of donor-acceptor-donor (DAD) architecture is used to study this solvent effect. Seven solvents with decreasing vapour pressure are selected for experiments. Electrospraying is conducted at a solution concentration of 1.5 wt% and a constant applied voltage of 15 kV. Gradual transformation in morphology of the electrospun product from spiked-spheres to only spikes is observed. A mechanism describing this transformation is proposed based on electron micrograph analysis and XRD analysis. These data indicate that the morphological change is due to the synergistic effect of both vapour pressure and dielectric constant of the solvents. Through a reasonable control of the crystallite size and morphology along with the proposal of the transformation mechanism, this study elucidates electrospraying as a prospective method for designing architectures in organic electronics.

DESIGN REQUIREMENTS FOR DIRECT SUPERCRITICAL CARBON DIOXIDE RECEIVER DEVELOPMENT AND TESTING

This paper establishes the design requirements for the development and testing of direct supercritical carbon dioxide (sCO2) solar receivers. Current design considerations are based on the ASME Boiler and Pressure Vessel Code (BPVC). Section I (BPVC) considers typical boilers/superheaters (i.e. fired pressure vessels) which work under a constant low heat flux. Section VIII (BPVC) considers pressure vessels with operating pressures above 15 psig 2 bar] (i.e. unfired pressure vessels). Section III, Division I - Subsection NH (BPVC) considers a more detailed stress calculation, compared to Section I and Section VIII, and requires a creep-fatigue analysis. The main drawback from using the BPVC exclusively is the large safety requirements developed for nuclear power applications. As a result, a new set of requirements is needed to perform detailed thermal-structural analyses of solar thermal receivers subjected to a spatially-varying, high-intensity heat flux. The last design requirements document of this kind was an interim Sandia report developed in 1979 (SAND79-8183), but it only addresses some of the technical challenges in early-stage steam and molten-salt solar receivers but not the use of sCO2 receivers. This paper presents a combination of the ASME BPVC and ASME B31.1 Code modified appropriately to achieve the reliability requirements in sCO(2) solar power systems. There are five main categories in this requirements document: Operation and Safety, Materials and Manufacturing, Instrumentation, Maintenance and Environmental, and General requirements. This paper also includes the modeling guidelines and input parameters required in computational fluid dynamics and structural analyses utilizing ANSYS Fluent, ANSYS Mechanical, and nCode Design Life. The main purpose of this document is to serve as a reference and guideline for design and testing requirements, as well as to address the technical challenges and provide initial parameters for the computational models that will be employed for the development of sCO(2) receivers.