Identification of Thioflavin T Binding Modes to DNA: A Structure-Specific Molecular Probe for Lasing Applications

The binding mechanism of thioflavin T (ThT) to DNA was studied using polarized light spectroscopy and fluorescence-based techniques in solutions and in solid films. Linear dichroism measurements showed that ThT binds to DNA duplex by intercalation. Time-resolved fluorescence studies revealed a second binding mode which is the external binding to the DNA phosphate groups. Both binding modes represent the nonspecific type of interactions. The studies were complemented with the analysis of short oligonucleotides having DNA cavities. The results indicate that the interplay between three binding modes-intercalation, external binding, and binding inside DNA cavities-determines the effective fluorescence quantum yield of the dye in the DNA structures. External binding was found to be responsible for fluorescence quenching because of energy transfer between intercalated and externally bound molecules. Finally, amplified spontaneous emission (ASE) was successfully generated in the ThT-stained films and used for detecting different DNA structures. ASE measurements show that ThT-stained DNA structures can be used for designing bioderived microlasers

A multiply substituted G-H loop from foot-and-mouth disease virus in complex with a neutralizing antibody: A role for water molecules

The crystal structure of a 15 amino acid synthetic peptide, corresponding to the sequence of the major antigenic site A (G-H loop of VP1) from a multiple variant of foot-and-mouth disease virus (FMDV), has been determined at 2·3 resolution. The variant peptide includes four amino acid substitutions in the loop relative to the previously studied peptide representing FMDV C-S8c1 and corresponds to the loop of a natural FMDV isolate of subtype C1. The peptide was complexed with the Fab fragment of the neutralizing monoclonal antibody 4C4. The peptide adopts a compact fold with a nearly cyclic conformation and a disposition of the receptor-recognition motif Arg-Gly-Asp that is closely related to the previously determined structure for the viral loop, as part of the virion, and for unsubstituted synthetic peptide antigen bound to neutralizing antibodies. New structural findings include the observation that well-defined solvent molecules appear to play a major role in stabilizing the conformation of the peptide and its interactions with the antibody. Structural results are supported by molecular-dynamic simulations. The multiply substituted peptide developed compensatory mechanisms to bind the antibody with a conformation very similar to that of its unsubstituted counterpart. One water molecule, which for steric reasons could not occupy the same position in the unsubstituted antigen, establishes hydrogen bonds with three peptide amino acids. The constancy of the structure of an antigenic domain despite multiple amino acid substitutions has implications for vaccine design

Root transcriptional responses of two melongenotypes with contrasting resistance toMonosporascus cannonballus (Pollack et Uecker)infection

Background: Monosporascus cannonballus is the main causal agent of melon vine decline disease. Several studies have been carried out mainly focused on the study of the penetration of this pathogen into melon roots, the evaluation of symptoms severity on infected roots, and screening assays for breeding programs. However, a detailed molecular view on the early interaction between M. cannonballus and melon roots in either susceptible or resistant genotypes is lacking. In the present study, we used a melon oligo-based microarray to investigate the gene expression responses of two melon genotypes, Cucumis melo ¿Piel de sapo¿ (¿PS¿) and C. melo ¿Pat 81¿, with contrasting resistance to the disease. This study was carried out at 1 and 3 days after infection (DPI) by M. cannonballus. Results: Our results indicate a dissimilar behavior of the susceptible vs. the resistant genotypes from 1 to 3 DPI. ¿PS¿ responded with a more rapid infection response than ¿Pat 81¿ at 1 DPI. At 3 DPI the total number of differentially expressed genes identified in ¿PS¿ declined from 451 to 359, while the total number of differentially expressed transcripts in ¿Pat 81¿ increased from 187 to 849. Several deregulated transcripts coded for components of Ca2+ and jasmonic acid (JA) signalling pathways, as well as for other proteins related to defence mechanisms. Transcriptional differences in the activation of the JA-mediated response in ¿Pat 81¿ compared to ¿PS¿ suggested that JA response might be partially responsible for their observed differences in resistance. Conclusions: As a result of this study we have identified for the first time a set of candidate genes involved in the root response to the infection of the pathogen causing melon vine decline. This information is useful for understanding the disease progression and resistance mechanisms few days after inoculation.Roig Montaner, MC.; Fita, A.; Rios, G.; Hammond, JP.; Nuez Viñals, F.; Picó Sirvent, MB. (2012). 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An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.). BMC Genomics, 10(1), 467. doi:10.1186/1471-2164-10-467Reddy, V. S. (2003). Plant Molecular Biology, 52(1), 143-159. doi:10.1023/a:1023993713849Reddy, A. S. N., Ali, G. S., Celesnik, H., & Day, I. S. (2011). Coping with Stresses: Roles of Calcium- and Calcium/Calmodulin-Regulated Gene Expression. The Plant Cell, 23(6), 2010-2032. doi:10.1105/tpc.111.084988Tena, G., Boudsocq, M., & Sheen, J. (2011). Protein kinase signaling networks in plant innate immunity. Current Opinion in Plant Biology, 14(5), 519-529. doi:10.1016/j.pbi.2011.05.006Eulgem, T., & Somssich, I. E. (2007). Networks of WRKY transcription factors in defense signaling. Current Opinion in Plant Biology, 10(4), 366-371. doi:10.1016/j.pbi.2007.04.020Li, J., Brader, G., Kariola, T., & Tapio Palva, E. (2006). 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Life Cycle Assessment of Novel Aircraft Interior Panels Made from Renewable or Recyclable Polymers with Natural Fiber Reinforcements and Non-Halogenated Flame Retardants

A comprehensive life cycle assessment of panels for aircraft interiors was conducted, including both a conventional glass fiber-reinforced panel and different novel sustainable panels. The conventional panel is made of a glass fiber-reinforced thermoset composite with halogenated flame retardant, whereas the sustainable panels are made of renewable or recyclable polymers, natural fiber reinforcements, and nonhalogenated flame retardants. Four different sustainable panels were investigated: a geopolymer-based panel; a linseed-oil–based biopolymer panel; and two thermoplastic panels, one with polypropylene (PP) and another with polylactic acid (PLA). All of the sustainable panels were developed to fulfil fire resistance requirements and to be lighter than the conventional panels in order to reduce fuel consumption and air pollutant emissions from the aircraft. The environmental impacts associated with energy consumption and air emissions were assessed, as well as other environmental impacts resulting from the extraction and processing of materials, transportation of materials and waste, panel manufacturing, use, maintenance, and end of life (EoL). All the sustainable panels showed better environmental performance than the conventional panel. The overall impacts of the sustainable panels were offset by the environmental benefits in the use stage attributed to weight reduction. One square meter of the novel panels could save to 6,000 kilograms of carbon dioxide equivalents. The break-even point (in months) at which the use of sustainable panels would yield an environmental benefit relative to the impacts arising in production and EoL was as follows: 1.2 for the geopolymer panel; 1.7 for the biopolymer panel; 10.4 for the PLA panel; and 54.5 for the PP panel.This research is part of the project CAYLEY, which was co-funded by the Eco-innovation Initiative of the European Union with contract no. ECO/10/277239

Spectroscopic and microscopic investigations of tautomerization in porphycenes: condensed phases, supersonic jets, and single molecule studies

We describe various experimental approaches that have been used to obtain a detailed understanding of double hydrogen transfer in porphycene, a model system for intramolecular hydrogen bonding and tautomerism. The emerging picture is that of a multidimensional tautomerization coordinate, with several vibrational modes acting as reaction-promoters or inhibitors through anharmonic intermode coupling. Tunnelling processes, coherent in the case of isolated molecules and incoherent in condensed phases, are found to play a major role even at elevated temperatures. Single-molecule spectroscopy studies reveal large fluctuations in hydrogen transfer rates observed over time for the same chromophore. Scanning probe microscopy is employed to directly observe the structure and tautomerization dynamics of single molecules adsorbed on metal surfaces and demonstrates how the interactions of the molecules with atoms of the supporting surface affect their static and dynamic properties: different tautomeric forms are stabilized for molecules depending on the surface structure and the reaction mechanism can also change, from a concerted to a stepwise transfer. The scanning probe microscopy studies prove that tautomerization in single molecules can be induced by different stimuli: heat, electron attachment, light, and force exerted by the microscope’s tip. Possible applications utilizing tautomerism are discussed in combination with molecular architectures on surfaces, which could pave the way for the development of single-molecule electronics

Electrical switching of a chiral lasing from polariton condensate in a Rashba-Dresselhaus regime

Efficient optical classical and quantum information processing imposes on light novel requirements: chirality with low threshold non-linearities. In this work we demonstrate a chiral lasing from an optical modes due to emerging photonic Rashba-Dresselhaus spin-orbit coupling (SOC). For this purpose we developed a new electrically tunable device based on an optical cavity filled with birefringent liquid crystal (LC) and perovskite crystals. Our novel method for the growth of single crystals of CsPbBr$_3$ inorganic perovskite in polymer templates allows us to reach a strong light-matter coupling regime between perovskite excitons and cavity modes, and induce polariton condensation. The sensitivity of the LC to external electric fields lets us to tune the condensate energy in situ and induce synthetic SOC. This shapes the condensate between a single linearly polarized or two circularly polarized separated in momentum, emitting coherent light. The difference in the condensation thresholds between the two SOC regimes can be used to switch on and off the chiral condensate emission with a voltage.Comment: 8 pages, 5 figure

Organising multi-dimensional biological image information: The BioImage Database

Nowadays it is possible to unravel complex information at all levels of cellular organization by obtaining multi-dimensional image information. at the macromolecular level, three-dimensional (3D) electron microscopy, together with other techniques, is able to reach resolutions at the nanometer or subnanometer level. The information is delivered in the form of 3D volumes containing samples of a given function, for example, the electron density distribution within a given macromolecule. The same situation happens at the cellular level with the new forms of light microscopy, particularly confocal microscopy, all of which produce biological 3D volume information. Furthermore, it is possible to record sequences of images over time (videos), as well as sequences of volumes, bringing key information on the dynamics of living biological systems. It is in this context that work on bioimage started two years ago, and that its first version is now presented here. In essence, Bioimage is a database specifically designed to contain multi-dimensional images, perform queries and interactively work with the resulting multi-dimensional information on the World Wide Web, as well as accomplish the required cross-database links. Two sister home pages of bioimage can be accessed at http://www.bioimage.org and http://www-embl.bioimage.or

Angolan vegetable crops have unique genotypes of potential value for future breeding programmes

[EN] A survey was carried out in Angola with the aim of collecting vegetable crops. Collecting expeditions were conducted in Kwanza-Sul, Benguela, Huila and Namibe Provinces and a total of 80 accessions belonging to 22 species was collected from farmers and local markets. Species belonging to the Solanaceae (37 accessions) and Cucurbitaceae (36 accessions) families were the most frequently found with pepper and eggplant being the predominant solanaceous crops collected. Peppers were sold in local markets as a mixture of different types, even different species: Capsicum chinense, C. baccatum, C. frutescens and C. pubescens. Most of the eggplant accessions collected belonged to Solanum aethiopicum L. Gilo Group, the so-called 'scarlet eggplant'. Cucurbita genus was better represented than the other cucurbit crops. A high morphological variation was present in the Cucurbita maxima and C. moschata accessions. A set of 22 Cucurbita accessions from Angola, along with 32 Cucurbita controls from a wide range of origins, was cultivated in Valencia, Spain and characterised based on morphology and molecularity using a set of 15 microsatellite markers. A strong dependence on latitude was found in most of the accessions and as a result, many accessions did not set fruit. The molecular analysis showed high molecular variability and uniqueness in the collected accessions, as shown by their segregation from the set of global controls. In summary, the material collected is quite valuable because of its uniqueness and the potential of the breeding characteristics it possesses.This work, project A1/039611/11, was funded by the Agencia Espanola de Cooperacion Internacional para el Desarrollo (Spanish Agency of International Cooperation for the Development).Domingos, J.; Fita, A.; Picó Sirvent, MB.; Sifres Cuerda, AG.; Daniel, IH.; Salvador, J.; Pedro, J.... (2016). Angolan vegetable crops have unique genotypes of potential value for future breeding programmes. South African Journal of Science. 112(3):114-125. http://hdl.handle.net/10251/97771S114125112