Study of DNA Origami Dimerization and Dimer Dissociation Dynamics and of the Factors that Limit Dimerization

Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single‐molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted. Reactions kinetics and yields are investigated at different origami and ion concentrations, for different ion types, for different lengths of bridging strands, and for the “sticky end” and “weaving welding” attachment techniques. Dimerization yields are never higher than 86%, which is typical for such systems. Analysis of the dynamic data shows that the low yield cannot be explained by thermodynamic instability or structural imperfections of the origami constructs. Atomic force microscopy and gel electrophoresis evidence reveal self‐dimerization of the origami monomers, likely via blunt‐end interactions made possible by the presence of bridging strands. It is suggested that this mechanism is the major factor that inhibits correct dimerization and means to overcome it are discussed.     

Seamless vertical handoff using modified weed optimization algorithm for heterogeneous wireless networks

In the global scenario, a variety of wireless access networks are available. Different types of applications such as real time, nonreal time, and high bandwidth availability are used for heterogeneous wireless networks. Therefore, it is necessary for a service provider to make an appropriate connection support. For better performance, connections are to be exchanged among the different networks using seamless vertical handoff (VHO). The proposed algorithm shows the effect of optimization technique, which involves handoff decision process using vertical handoff triggering and selection of the network. The handoff triggering is initiated by using the received signal strength (RSS). In traditional method, handoff triggering is initiated by using RSS only. This method, modified weed optimization (M-WO) algorithm, reduces the unnecessary handoff by considering both RSS and velocity of the mobile node in handoff triggering. The parameters such as battery lifetime, handoff call dropping rate, load, dynamic weights adaptation and so on are to be considered individually or combined to make an effective network selection process. This paper highlights a novel effect ofM-WOalgorithm for decision making during the VHO. Our effort is to essentially optimize the system load, so that it reduces the handoff call dropping rate and the battery power consumption of the mobile node (MN). Weight of each QoS metrics is adjusted along with the networks changing conditions to trace the M-WO. Therefore, the novel VHO decision-making algorithm is superior to the existing SSF and OPTG methods. The simulation results show that the performance ofM-WOalgorithm is far better than SSF andOPTGmethods in terms of load, handoff call dropping rate and battery lifetime of MN.     

School readiness among children with varying histories of language difficulties.

This study tested the hypotheses that (a) persistent language difficulties during childhood would predict lower school readiness and (b) language difficulties present just prior to school entry would predict lower school readiness beyond any effects of persistence. The study involved examining indicators of school readiness collected at kindergarten for children exhibiting various histories of language ability based on language measures collected at 15, 24, 36, and 54 months by the National Institute of Child Health and Human Development's Early Child Care Research Network. Children (N = 1,064) were classified according to whether they exhibited expressive or receptive language difficulties at each time point measured. The relation between persistence and timing of these difficulties to each kindergarten outcome was studied through a common factor approach for categorical outcomes. Persistence of language difficulties was not generally related to kindergarten outcomes. However, a robust effect was found for timing of language difficulties: Children who exhibited language difficulties at 54 months exhibited significantly depressed performance on measures of school readiness. Findings are discussed in terms of current policy and research concerning kindergarten readiness for children exhibiting risk. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Conscious worst case definition for risk assessment, part I: A knowledge mapping approach for defining most critical risk factors in integrative risk management of chemicals and nanomaterials

This paper helps bridge the gap between scientists and other stakeholders in the areas of human and environmental risk management of chemicals and engineered nanomaterials. This connection is needed due to the evolution of stakeholder awareness and scientific progress related to human and environmental health which involves complex methodological demands on risk management. At the same time, the available scientific knowledge is also becoming more scattered across multiple scientific disciplines. Hence, the understanding of potentially risky situations is increasingly multifaceted, which again challenges risk assessors in terms of giving the ‘right’ relative priority to the multitude of contributing risk factors. A critical issue is therefore to develop procedures that can identify and evaluate worst case risk conditions which may be input to risk level predictions. Therefore, this paper suggests a conceptual modelling procedure that is able to define appropriate worst case conditions in complex risk management. The result of the analysis is an assembly of system models, denoted the Worst Case Definition (WCD) model, to set up and evaluate the conditions of multi-dimensional risk identification and risk quantification. The model can help optimize risk assessment planning by initial screening level analyses and guiding quantitative assessment in relation to knowledge needs for better decision support concerning environmental and human health protection or risk reduction. The WCD model facilitates the evaluation of fundamental uncertainty using knowledge mapping principles and techniques in a way that can improve a complete uncertainty analysis. Ultimately, the WCD is applicable for describing risk contributing factors in relation to many different types of risk management problems since it transparently and effectively handles assumptions and definitions and allows the integration of different forms of knowledge, thereby supporting the inclusion of multifaceted risk components in cumulative risk management.     

Influence of verbal and nonverbal references to print on preschoolers' visual attention to print during storybook reading.

How much do preschool children look at print within storybooks when adults read to them? This study sought to answer this question as well as to examine the effects of adult verbal and nonverbal references to print on children's visual attention to print during storybook reading. Forty-four preschool-aged children participated in this study designed to determine the amount of visual attention children paid to print in 4 planned variations of storybook reading. Children's visual attention to print was examined when adults commented and questioned about print (verbal print condition) or pointed to and tracked the print (nonverbal print condition), relative to 2 comparison conditions (verbatim reading and verbal picture conditions). Results showed that children rarely look at print, with about 5%-6% of their fixations allocated to print in verbatim and verbal picture reading conditions. However, preschoolers' visual attention to print increases significantly when adults verbally and nonverbally reference print; both reading styles exerted similar effects. The authors conclude that explicit referencing of print is 1 way to increase young children's contacts with print during shared storybook reading. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Role of Ribes khorassanicum in the biosynthesis of AgNPs and their antibacterial properties

Silver nanoparticles (AgNPs) have been biosynthesised through the extracts of Ribes khorassanicum fruits, which served as the reducing agents and capping agents. Biosynthesised AgNPs have been found to be ultraviolet–visible (UV–vis) absorption spectra since they have displayed one surface plasmon resonance peak at 438 nm, attesting the formation of spherical NPs. These particles have been characterised by UV–vis, field‐emission scanning electron microscopy, energy‐dispersive X‐ray spectroscopy, X‐ray diffraction, Fourier transform infrared spectroscopy, and transmission electron microscopy analysis. The formation of AgNPs at 1.0 mM concentration of AgNO₃ has resulted in NPs that contained mean diameters in a range of 20–40 nm. The green‐synthesised AgNPs have demonstrated high antibacterial effect against pathogenic bacteria (i.e. Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa). Biosynthesising metal NPs through plant extracts can serve as the facile and eco‐friendly alternative for chemical and/or physical methods that are utilised for large‐scale nanometal fabrication in various medical and industrial applications.Inspec keywords: X‐ray diffraction, X‐ray chemical analysis, nanofabrication, surface plasmon resonance, nanoparticles, antibacterial activity, microorganisms, scanning electron microscopy, silver, nanomedicine, visible spectra, ultraviolet spectra, transmission electron microscopy, Fourier transform infrared spectra, field emission scanning electron microscopy, biomedical materialsOther keywords: antibacterial properties, silver nanoparticles, reducing agents, capping agents, surface plasmon resonance peak, spherical NPs, field‐emission scanning electron microscopy, energy‐dispersive X‐ray spectroscopy, X‐ray diffraction, transmission electron microscopy analysis, plant extracts, ultraviolet‐visible absorption spectra, Fourier transform infrared spectroscopy, antibacterial effect, Ribes khorassanicum fruits, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, surface plasmon resonance, AgNO₃ , Ag     

Self‐Assembly of DNA Origami Heterodimers in High Yields and Analysis of the Involved Mechanisms

Efficient fabrication of structurally and functionally diverse nanomolecular devices and machines by organizing separately prepared DNA origami building blocks into a larger structure is limited by origami attachment yields. A general method that enables attachment of origami building blocks using ‘sticky ends' at very high yields is demonstrated. Two different rectangular origami monomers are purified using agarose gel electrophoresis conducted in solute containing 100 × 10^?3 m NaCl, a treatment that facilitates the dissociation of most of the incorrectly hybridized origami structures that form through blunt‐end interactions during the thermal annealing process and removes these structures as well as excess strands that otherwise interfere with the desired heterodimerization reaction. Heterodimerization yields of gel‐purified monomers are between 98.6% and 99.6%, considerably higher than that of monomers purified using the polyethylene glycol (PEG) method (88.7–96.7%). Depending on the number of PEG purification rounds, these results correspond to about 4‐ to 25‐fold reduction in the number of incorrect structures observed by atomic force microscopy. Furthermore, the analyses of the incorrect structures observed before and after the heterodimerization reactions and comparison of the purification methods provide valuable information on the reaction mechanisms that interfere with heterodimerization.     

Conceptual modeling for identification of worst case conditions in environmental risk assessment of nanomaterials using nZVI and C60 as case studies

Conducting environmental risk assessment of engineered nanomaterials has been an extremely challenging endeavor thus far. Moreover, recent findings from the nano-risk scientific community indicate that it is unlikely that many of these challenges will be easily resolved in the near future, especially given the vast variety and complexity of nanomaterials and their applications. As an approach to help optimize environmental risk assessments of nanomaterials, we apply the Worst-Case Definition (WCD) model to identify best estimates for worst-case conditions of environmental risks of two case studies which use engineered nanoparticles, namely nZVI in soil and groundwater remediation and C₆₀ in an engine oil lubricant. Results generated from this analysis may ultimately help prioritize research areas for environmental risk assessments of nZVI and C₆₀ in these applications as well as demonstrate the use of worst-case conditions to optimize future research efforts for other nanomaterials. Through the application of the WCD model, we find that the most probable worst-case conditions for both case studies include i) active uptake mechanisms, ii) accumulation in organisms, iii) ecotoxicological response mechanisms such as reactive oxygen species (ROS) production and cell membrane damage or disruption, iv) surface properties of nZVI and C₆₀, and v) acute exposure tolerance of organisms. Additional estimates of worst-case conditions for C₆₀ also include the physical location of C₆₀ in the environment from surface run-off, cellular exposure routes for heterotrophic organisms, and the presence of light to amplify adverse effects. Based on results of this analysis, we recommend the prioritization of research for the selected applications within the following areas: organism active uptake ability of nZVI and C₆₀ and ecotoxicological response end-points and response mechanisms including ROS production and cell membrane damage, full nanomaterial characterization taking into account detailed information on nanomaterial surface properties, and investigations of dose-response relationships for a variety of organisms.