In vitro recombination cloning of entire cDNA libraries in Arabidopsis thaliana and its application to the yeast two-hybrid system

In the postgenomic era many experiments rely on the availability of transcript sequence for cloning. As these clones usually originate from cDNA libraries, the quality of these libraries is crucial. If a good library is generated it is desirable to use a versatile cloning system suitable for many different kinds of applications. The cloning systems based on in vitro recombination proves fitting for this task. However, the use of this method for shuttling entire cDNA libraries between different vectors has not yet been studied in great detail. Here we describe the construction of four cDNA libraries from different tissues of Arabidopsis thaliana, the shuttling of the libraries into expression vectors, and evaluation of this method as well as its suitability for downstream applications. Libraries were constructed from seedlings, hormone treated seedlings, flowers, developing seeds and primary leaves in the ldquoentry vectorrdquo of the Gatewaytrade cloning system. After initial characterization of the libraries, they were shuttled into an expression vector (a yeast two-hybrid prey vector). To monitor for a size bias generally assumed to be inherent to in vitro recombination methods, the libraries were characterized before and after the transfer into the expression vector. However no significant difference could be detected. The functionality of the in vitro recombination system for the shuttling of entire libraries was then further tested by protein-protein interaction screens. The results of the library characterization and of the yeast two-hybrid screens and their implications for large-scale proteomic approaches are discussed

Ab-initio study of the thermopower of biphenyl-based single-molecule junctions

Employing ab-initio electronic structure calculations combined with the non-equilibrium Green's function technique, we study the dependence of the thermopower Q on the conformation in biphenyl-based single-molecule junctions. For the series of experimentally available biphenyl molecules, alkyl side chains allow us to gradually adjust the torsion angle \phi\ between the two phenyl rings from 0 to 90{\deg} and to control in this way the degree of \pi-electron conjugation. Studying different anchoring groups and binding positions, our theory predicts that the absolute values of the thermopower decrease slightly towards larger torsion angles, following an a+b*cos^{2}\phi\ dependence. The anchoring group determines the sign of Q and a,b, simultaneously. Sulfur and amine groups give rise to Q,a,b>0, while for cyano Q,a,b<0. The different binding positions can lead to substantial variations of the thermopower mostly due to changes in the alignment of the frontier molecular orbital levels and the Fermi energy. We explain our ab-initio results in terms of a \pi-orbital tight-binding model and a minimal two-level model, which describes the pair of hybridizing frontier orbital states on the two phenyl rings. The variations of the thermopower with \phi\ seem to be within experimental resolution.Comment: 8 pages, 4 figues, 3 table

Understanding the Electronic Transport Through Single Noble Gas Atoms

We present a theoretical study of the conductance of atomic junctions comprising single noble gas atoms (He, Ne, Ar, Kr, and Xe) coupled to gold electrodes. The aim is to elucidate how the presence of noble gas atoms affects the electronic transport through metallic atomic-size contacts. Our analysis, based on density functional theory and including van der Waals interactions, shows that for the lightest elements (He and Ne) no significant current flows through the noble gas atoms and their effect is to reduce the conductance of the junctions by screening the interaction between the gold electrodes. This explains the observations reported in metallic atomic-size contacts with adsorbed He atoms. Conversely, the heaviest atoms (Kr and Xe) increase the conductance due to the additional current path provided by their valence p states.Comment: 3 figure

Cluster-based density-functional approach to quantum transport through molecular and atomic contacts

We present a cluster-based density-functional approach to model charge transport through molecular and atomic contacts. The electronic structure of the contacts is determined in the framework of density functional theory, and the parameters needed to describe transport are extracted from finite clusters. A similar procedure, restricted to nearest-neighbor interactions in the electrodes, has been presented by Damle et al. [Chem. Phys. 281, 171 (2002)]. Here, we show how to systematically improve the description of the electrodes by extracting bulk parameters from sufficiently large metal clusters. In this way we avoid problems arising from the use of nonorthogonal basis functions. For demonstration we apply our method to electron transport through Au contacts with various atomic-chain configurations and to a single-atom contact of Al.Comment: 18 pages, 13 figure

Nucleon-nucleon elastic scattering analysis to 2.5 GeV

A partial-wave analysis of NN elastic scattering data has been completed. This analysis covers an expanded energy range, from threshold to a laboratory kinetic energy of 2.5 GeV, in order to include recent elastic pp scattering data from the EDDA collaboration. The results of both single-energy and energy-dependent analyses are described.Comment: 23 pages of text. Postscript files for the figures are available from ftp://clsaid.phys.vt.edu/pub/said/n

Nutritional Factors Modulating Alu Methylation inan Italian Sample from The Mark-Age StudyIncluding Offspring of Healthy Nonagenarians

Alu hypomethylation promotes genomic instability and is associated with aging and age-related diseases. Dietary factors affect global DNA methylation, leading to changes in genomic stability and gene expression with an impact on longevity and the risk of disease. This preliminary study aims to investigate the relationship between nutritional factors, such as circulating trace elements, lipids and antioxidants, and Alu methylation in elderly subjects and offspring of healthy nonagenarians. Alu DNA methylation was analyzed in sixty RASIG (randomly recruited age-stratified individuals from the general population) and thirty-two GO (GeHA offspring) enrolled in Italy in the framework of the MARK-AGE project. Factor analysis revealed a different clustering between Alu CpG1 and the other CpG sites. RASIG over 65 years showed lower Alu CpG1 methylation than those of GO subjects in the same age class. Moreover, Alu CpG1 methylation was associated with fruit and whole-grain bread consumption, LDL2-Cholesterol and plasma copper. The preserved Alu methylation status in GO, suggests Alu epigenetic changes as a potential marker of aging. Our preliminary investigation shows that Alu methylation may be affected by food rich in fibers and antioxidants, or circulating LDL subfractions and plasma copper

Quality of human-computer interaction - results of a national usability survey of hospital-IT in Germany

<p>Abstract</p> <p>Background</p> <p>Due to the increasing functionality of medical information systems, it is hard to imagine day to day work in hospitals without IT support. Therefore, the design of dialogues between humans and information systems is one of the most important issues to be addressed in health care. This survey presents an analysis of the current quality level of human-computer interaction of healthcare-IT in German hospitals, focused on the users' point of view.</p> <p>Methods</p> <p>To evaluate the usability of clinical-IT according to the design principles of EN ISO 9241-10 the IsoMetrics Inventory, an assessment tool, was used. The focus of this paper has been put on suitability for task, training effort and conformity with user expectations, differentiated by information systems. Effectiveness has been evaluated with the focus on interoperability and functionality of different IT systems.</p> <p>Results</p> <p>4521 persons from 371 hospitals visited the start page of the study, while 1003 persons from 158 hospitals completed the questionnaire. The results show relevant variations between different information systems.</p> <p>Conclusions</p> <p>Specialised information systems with defined functionality received better assessments than clinical information systems in general. This could be attributed to the improved customisation of these specialised systems for specific working environments. The results can be used as reference data for evaluation and benchmarking of human computer engineering in clinical health IT context for future studies.</p

Nanooptics of molecular-shunted plasmonic nanojunctions.

Gold nanoparticles are separated above a planar gold film by 1.1 nm thick self-assembled molecular monolayers of different conductivities. Incremental replacement of the nonconductive molecules with a chemically equivalent conductive version differing by only one atom produces a strong 50 nm blue-shift of the coupled plasmon. With modeling this gives a conductance of 0.17G(0) per biphenyl-4,4'-dithiol molecule and a total conductance across the plasmonic junction of 30G(0). Our approach provides a reliable tool quantifying the number of molecules in each plasmonic hotspot, here <200.We acknowledge financial support from EPSRC grant EP/ G060649/1, EP/I012060/1, EP/L027151/1, EP/K028510/1, ERC grant LINASS 320503. F.B. acknowledges support from the Winton Programme for the Physics of Sustainability. C.T. and J.A. acknowledge financial support from Project FIS2013- 41184-P from MINECO, ETORTEK 2014-15 of the Basque Department of Industry and IT756-13 from the Basque consolidated groups.This paper was originally published in Nano Letters under a CC-BY licence (F Benz, C Tserkezis, LO Herrmann, B de Nijs, A Sanders, DO Sigle, L Pukenas, SD Evans, J Aizpurua, JJ Baumberg, Nano Letters 2015, 15, 669−674

Chemical PARP Inhibition Enhances Growth of Arabidopsis and Reduces Anthocyanin Accumulation and the Activation of Stress Protective Mechanisms

Poly-ADP-ribose polymerase (PARP) post-translationally modifies proteins through the addition of ADP-ribose polymers, yet its role in modulating plant development and stress responses is only poorly understood. The experiments presented here address some of the gaps in our understanding of its role in stress tolerance and thereby provide new insights into tolerance mechanisms and growth. Using a combination of chemical and genetic approaches, this study characterized phenotypes associated with PARP inhibition at the physiological level. Molecular analyses including gene expression analysis, measurement of primary metabolites and redox metabolites were used to understand the underlying processes. The analysis revealed that PARP inhibition represses anthocyanin and ascorbate accumulation under stress conditions. The reduction in defense is correlated with enhanced biomass production. Even in unstressed conditions protective genes and molecules are repressed by PARP inhibition. The reduced anthocyanin production was shown to be based on the repression of transcription of key regulatory and biosynthesis genes. PARP is a key factor for understanding growth and stress responses of plants. PARP inhibition allows plants to reduce protection such as anthocyanin, ascorbate or Non-Photochemical-Quenching whilst maintaining high energy levels likely enabling the observed enhancement of biomass production under stress, opening interesting perspectives for increasing crop productivity