Effect of modified atmosphere packaging (MAP) and UC-C irradiation on postharvest quality of red raspberries

Red raspberries (Rubus idaeus L.) are highly appreciated by consumers. However, their postharvest shelf life scarcely exceeds 5 d under the refrigeration temperatures usually applied during commercialization, due to their high susceptibility to dehydration, softening and rot incidence. Thus, the objective of this study was to investigate the ability of UV-C radiation (UV1: 2 kJ m-2 and UV2: 4 kJ m-2 ), passive modified atmosphere packaging (MAP) with transmission rates (TR) for O2 and CO2 of 1805 mL d-1 and 1570 mL d-1 (MAP1), and 902 mL d-1 and 785 mL d-1 (MAP2), respectively, and the combination of both technologies to prolong raspberries’ shelf life at 6¿ C. Their influence on respiration, physicochemical parameters, and microbiological and nutritional quality was assessed during 12 d of storage. The combination of 4 kJ m-2 UV-C radiation and a packaging film with O2 and CO2 transmission rates of 902 mL d-1 and 785 mL d-1, respectively, produced a synergistic effect against rot development, delaying senescence of the fruit. The UV2MAP2 and MAP2 samples only showed 1.66% rot incidence after 8 d of storage. The UV2MAP2 samples also had higher bioactive content (1.76 g kg-1 of gallic acid equivalents (GAE), 1.08 g kg-1 of catechin equivalents (CE) and 0.32 g kg-1 of cyanidin 3-O-glucoside equivalents (CGE)) than the control samples at the end of their shelf life. Moreover, the mass loss was minimal (0.56%), and fruit color and firmness were maintained during shelf life. However, the rest of the batches were not suitable for commercialization after 4 d due to excessive mold development. © 2021 by the authors. Licensee MDPI, Basel, Switzerland

Dynamics of Quintessence Models of Dark Energy with Exponential Coupling to the Dark Matter

We explore quintessence models of dark energy which exhibit non-minimal coupling between the dark matter and the dark energy components of the cosmic fluid. The kind of coupling chosen is inspired in scalar-tensor theories of gravity. We impose a suitable dynamics of the expansion allowing to derive exact Friedmann-Robertson-Walker solutions once the coupling function is given as input. Self-interaction potentials of single and double exponential types emerge as result of our choice of the coupling function. The stability and existence of the solutions is discussed in some detail. Although, in general, models with appropriated interaction between the components of the cosmic mixture are useful to handle the coincidence problem, in the present study the coincidence can not be evaded due to the choice of the solution generating ansatz.Comment: 10 pages, 7 figure

UOLO - automatic object detection and segmentation in biomedical images

We propose UOLO, a novel framework for the simultaneous detection and segmentation of structures of interest in medical images. UOLO consists of an object segmentation module which intermediate abstract representations are processed and used as input for object detection. The resulting system is optimized simultaneously for detecting a class of objects and segmenting an optionally different class of structures. UOLO is trained on a set of bounding boxes enclosing the objects to detect, as well as pixel-wise segmentation information, when available. A new loss function is devised, taking into account whether a reference segmentation is accessible for each training image, in order to suitably backpropagate the error. We validate UOLO on the task of simultaneous optic disc (OD) detection, fovea detection, and OD segmentation from retinal images, achieving state-of-the-art performance on public datasets.Comment: Publised on DLMIA 2018. Licensed under the Creative Commons CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0

DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein

[EN] Single-stranded DNA-binding proteins (SSBs) play a key role in genome maintenance, binding and organizing single-stranded DNA (ssDNA) intermediates. Multimeric SSBs, such as the human mitochondrial SSB (HmtSSB), present multiple sites to interact with ssDNA, which has been shown in vitro to enable them to bind a variable number of single-stranded nucleotides depending on the salt and protein concentration. It has long been suggested that different binding modes might be used selectively for different functions. To study this possibility, we used optical tweezers to determine and compare the structure and energetics of long, individual HmtSSB¿DNA complexes assembled on preformed ssDNA and on ssDNA generated gradually during `in situ¿ DNA synthesis. We show that HmtSSB binds to preformed ss-DNA in two major modes, depending on salt and protein concentration. However, when protein binding was coupled to strand-displacement DNA synthesis, only one of the two binding modes was observed under all experimental conditions. Our results reveal a key role for the gradual generation of ssDNA in modulating the binding mode of a multimeric SSB protein and consequently, in generating the appropriate nucleoprotein structure for DNA synthetic reactions required for genome maintenance.We are grateful to Prof. M. Salas laboratory (CBMSO-CSIC) for generously providing the Phi29 DNA polymerase and to Juan P. García Villaluenga (UCM) for useful discussions. Spanish Ministry of Economy and Competitiveness [MAT2015-71806-R to J.R.A-G, FIS2010-17440, FIS2015-67765-R to F.J.C., BFU2012-31825, BFU2015-63714-R to B.I.]; Spanish Ministry of Education, Culture and Sport [FPU13/02934 to J.J., FPU13/02826 to E.B-H.]; National Institutes of Health [GM45925 to L.S.K.]; University of Tampere (to G.L.C.); Programa de Financiacion Universidad Complutense de Madrid-Santander Universidades [CT45/15-CT46/15 to F.C.]. Funding for open access charge: Spanish Ministry of Economy and Competitiveness [BFU2015-63714-R].Morin, J.; Cerrón, F.; Jarillo, J.; Beltran-Heredia, E.; Ciesielski, G.; Arias-Gonzalez, JR.; Kaguni, L.... (2017). DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein. Nucleic Acids Research. 45(12):7237-7248. https://doi.org/10.1093/nar/gkx395S723772484512Shereda, R. D., Kozlov, A. G., Lohman, T. M., Cox, M. M., & Keck, J. L. (2008). SSB as an Organizer/Mobilizer of Genome Maintenance Complexes. Critical Reviews in Biochemistry and Molecular Biology, 43(5), 289-318. doi:10.1080/10409230802341296Flynn, R. L., & Zou, L. (2010). Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians. Critical Reviews in Biochemistry and Molecular Biology, 45(4), 266-275. doi:10.3109/10409238.2010.488216Murzin, A. G. (1993). OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. The EMBO Journal, 12(3), 861-867. doi:10.1002/j.1460-2075.1993.tb05726.xKozlov, A. G., Weiland, E., Mittal, A., Waldman, V., Antony, E., Fazio, N., … Lohman, T. M. (2015). Intrinsically Disordered C-Terminal Tails of E. coli Single-Stranded DNA Binding Protein Regulate Cooperative Binding to Single-Stranded DNA. Journal of Molecular Biology, 427(4), 763-774. doi:10.1016/j.jmb.2014.12.020Kuznetsov, S. V., Kozlov, A. G., Lohman, T. M., & Ansari, A. (2006). Microsecond Dynamics of Protein–DNA Interactions: Direct Observation of the Wrapping/Unwrapping Kinetics of Single-stranded DNA around the E.coli SSB Tetramer. Journal of Molecular Biology, 359(1), 55-65. doi:10.1016/j.jmb.2006.02.070Lohman, T. M., & Ferrari, M. E. (1994). Escherichia Coli Single-Stranded DNA-Binding Protein: Multiple DNA-Binding Modes and Cooperativities. Annual Review of Biochemistry, 63(1), 527-570. doi:10.1146/annurev.bi.63.070194.002523Maier, D., Farr, C. L., Poeck, B., Alahari, A., Vogel, M., Fischer, S., … Schneuwly, S. (2001). Mitochondrial Single-stranded DNA-binding Protein Is Required for Mitochondrial DNA Replication and Development in Drosophila melanogaster. Molecular Biology of the Cell, 12(4), 821-830. doi:10.1091/mbc.12.4.821Ruhanen, H., Borrie, S., Szabadkai, G., Tyynismaa, H., Jones, A. W. E., Kang, D., … Yasukawa, T. (2010). 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(1997). Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 Å resolution. Nature Structural Biology, 4(2), 153-157. doi:10.1038/nsb0297-153Raghunathan, S., Ricard, C. S., Lohman, T. M., & Waksman, G. (1997). Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution. Proceedings of the National Academy of Sciences, 94(13), 6652-6657. doi:10.1073/pnas.94.13.6652CURTH, U., URBANKE, C., GREIPEL, J., GERBERDING, H., TIRANTI, V., & ZEVIANI, M. (1994). Single-stranded-DNA-binding proteins from human mitochondria and Escherichia coli have analogous physicochemical properties. European Journal of Biochemistry, 221(1), 435-443. doi:10.1111/j.1432-1033.1994.tb18756.xOverman, L. B., & Lohman, T. M. (1994). Linkage of pH, Anion and Cation Effects in Protein-Nucleic Acid Equilibria. Journal of Molecular Biology, 236(1), 165-178. doi:10.1006/jmbi.1994.1126Bhattacharyya, B., George, N. P., Thurmes, T. M., Zhou, R., Jani, N., Wessel, S. R., … Keck, J. L. (2013). Structural mechanisms of PriA-mediated DNA replication restart. Proceedings of the National Academy of Sciences, 111(4), 1373-1378. doi:10.1073/pnas.1318001111Carlini, L. E., Porter, R. D., Curth, U., & Urbanke, C. (1993). Viability and preliminary in vivo characterization of site directed mutants of Escherichia coli single-stranded DNA-binding protein. Molecular Microbiology, 10(5), 1067-1075. doi:10.1111/j.1365-2958.1993.tb00977.xGriffith, J. D., Harris, L. D., & Register, J. (1984). Visualization of SSB-ssDNA Complexes Active in the Assembly of Stable RecA-DNA Filaments. Cold Spring Harbor Symposia on Quantitative Biology, 49(0), 553-559. doi:10.1101/sqb.1984.049.01.062Morrical, S. W., & Cox, M. M. (1990). Stabilization of recA protein-ssDNA complexes by the single-stranded DNA binding protein of Escherichia coli. Biochemistry, 29(3), 837-843. doi:10.1021/bi00455a034Muniyappa, K., Williams, K., Chase, J. W., & Radding, C. M. (1990). Active nucleoprotein filaments of single-stranded binding protein and recA protein on single-stranded DNA have a regular repeating structure. Nucleic Acids Research, 18(13), 3967-3973. doi:10.1093/nar/18.13.3967Wessel, S. R., Marceau, A. H., Massoni, S. C., Zhou, R., Ha, T., Sandler, S. J., & Keck, J. L. (2013). PriC-mediated DNA Replication Restart Requires PriC Complex Formation with the Single-stranded DNA-binding Protein. Journal of Biological Chemistry, 288(24), 17569-17578. doi:10.1074/jbc.m113.478156Bell, J. C., Liu, B., & Kowalczykowski, S. C. (2015). Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function. eLife, 4. doi:10.7554/elife.08646Suksombat, S., Khafizov, R., Kozlov, A. G., Lohman, T. M., & Chemla, Y. R. (2015). Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways. eLife, 4. doi:10.7554/elife.08193Zhou, R., Kozlov, A. G., Roy, R., Zhang, J., Korolev, S., Lohman, T. M., & Ha, T. (2011). SSB Functions as a Sliding Platform that Migrates on DNA via Reptation. Cell, 146(2), 222-232. doi:10.1016/j.cell.2011.06.036Pant, K., Karpel, R. L., Rouzina, I., & Williams, M. C. (2004). Mechanical Measurement of Single-molecule Binding Rates: Kinetics of DNA Helix-destabilization by T4 Gene 32 Protein. Journal of Molecular Biology, 336(4), 851-870. doi:10.1016/j.jmb.2003.12.025Pant, K., Karpel, R. L., Rouzina, I., & Williams, M. C. (2005). Salt Dependent Binding of T4 Gene 32 Protein to Single and Double-stranded DNA: Single Molecule Force Spectroscopy Measurements. Journal of Molecular Biology, 349(2), 317-330. doi:10.1016/j.jmb.2005.03.065Robberson, D. L., & Clayton, D. A. (1972). Replication of Mitochondrial DNA in Mouse L Cells and Their Thymidine Kinase- Derivatives: Displacement Replication on a Covalently-Closed Circular Template. Proceedings of the National Academy of Sciences, 69(12), 3810-3814. doi:10.1073/pnas.69.12.3810Ciesielski, G. L., Bermek, O., Rosado-Ruiz, F. A., Hovde, S. L., Neitzke, O. J., Griffith, J. D., & Kaguni, L. S. (2015). Mitochondrial Single-stranded DNA-binding Proteins Stimulate the Activity of DNA Polymerase γ by Organization of the Template DNA. Journal of Biological Chemistry, 290(48), 28697-28707. doi:10.1074/jbc.m115.673707Lázaro, J. M., Blanco, L., & Salas, M. (1995). [5] Purification of bacteriophage φ29 DNA polymerase. DNA Replication, 42-49. doi:10.1016/0076-6879(95)62007-9Ibarra, B., Chemla, Y. R., Plyasunov, S., Smith, S. B., Lázaro, J. M., Salas, M., & Bustamante, C. (2009). Proofreading dynamics of a processive DNA polymerase. The EMBO Journal, 28(18), 2794-2802. doi:10.1038/emboj.2009.219Morin, J. A., Cao, F. J., Lazaro, J. M., Arias-Gonzalez, J. R., Valpuesta, J. M., Carrascosa, J. L., … Ibarra, B. (2012). Active DNA unwinding dynamics during processive DNA replication. Proceedings of the National Academy of Sciences, 109(21), 8115-8120. doi:10.1073/pnas.1204759109Smith, S. B., Cui, Y., & Bustamante, C. (2003). [7] Optical-trap force transducer that operates by direct measurement of light momentum. Biophotonics, Part B, 134-162. doi:10.1016/s0076-6879(03)61009-8Bosco, A., Camunas-Soler, J., & Ritort, F. (2013). Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions. Nucleic Acids Research, 42(3), 2064-2074. doi:10.1093/nar/gkt1089Smith, S., Finzi, L., & Bustamante, C. (1992). Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science, 258(5085), 1122-1126. doi:10.1126/science.1439819Longley, M. J., Smith, L. A., & Copeland, W. C. (2009). Preparation of Human Mitochondrial Single-Stranded DNA-Binding Protein. Mitochondrial DNA, 73-85. doi:10.1007/978-1-59745-521-3_5Li, K., & Williams, R. S. (1997). Tetramerization and Single-stranded DNA Binding Properties of Native and Mutated Forms of Murine Mitochondrial Single-stranded DNA-binding Proteins. Journal of Biological Chemistry, 272(13), 8686-8694. doi:10.1074/jbc.272.13.8686Jarillo, J., Morín, J. A., Beltrán-Heredia, E., Villaluenga, J. P. G., Ibarra, B., & Cao, F. J. (2017). Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers. PLOS ONE, 12(4), e0174830. doi:10.1371/journal.pone.0174830Bujalowski, W., & Lohman, T. M. (1986). Escherichia coli single-strand binding protein forms multiple, distinct complexes with single-stranded DNA. Biochemistry, 25(24), 7799-7802. doi:10.1021/bi00372a003Thömmes, P., Farr, C. L., Marton, R. F., Kaguni, L. S., & Cotterill, S. (1995). Mitochondrial Single-stranded DNA-binding Protein fromDrosophilaEmbryos. Journal of Biological Chemistry, 270(36), 21137-21143. doi:10.1074/jbc.270.36.21137Rodriguez, I., Lazaro, J. M., Blanco, L., Kamtekar, S., Berman, A. J., Wang, J., … de Vega, M. (2005). A specific subdomain in  29 DNA polymerase confers both processivity and strand-displacement capacity. Proceedings of the National Academy of Sciences, 102(18), 6407-6412. doi:10.1073/pnas.0500597102Kamtekar, S., Berman, A. J., Wang, J., Lázaro, J. M., de Vega, M., Blanco, L., … Steitz, T. A. (2004). Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage φ29. Molecular Cell, 16(4), 609-618. doi:10.1016/j.molcel.2004.10.019Chrysogelos, S., & Griffith, J. (1982). Escherichia coli single-strand binding protein organizes single-stranded DNA in nucleosome-like units. Proceedings of the National Academy of Sciences, 79(19), 5803-5807. doi:10.1073/pnas.79.19.5803Hamon, L., Pastre, D., Dupaigne, P., Breton, C. L., Cam, E. 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Mechanical Identities of RNA and DNA Double Helices Unveiled at the Single-Molecule Level

[EN] Double-stranded (ds) RNA is the genetic material of a variety of viruses and has been recently recognized as a relevant molecule in cells for its regulatory role. Despite that the elastic response of dsDNA has been thoroughly characterized in recent years in single-molecule stretching experiments, an equivalent study with dsRNA is still lacking. Here, we have engineered long dsRNA molecules for their individual characterization contrasting information with dsDNA molecules of the same sequence. It is known that dsRNA is an A-form molecule unlike dsDNA, which exhibits B-form in physiological conditions. These structural types are distinguished at the single-molecule level with atomic force microscopy (AFM) and are the basis to understand their different elastic response. Force¿extension curves of dsRNA with optical and magnetic tweezers manifest two main regimes of elasticity, an entropic regime whose end is marked by the A-form contour- length and an intrinsic regime that ends in a low-cooperative overstretching transition in which the molecule extends to 1.7 times its A-form contour-length. DsRNA does not switch between the A and B conformations in the presence of force. Finally, dsRNA presents both a lower stretch modulus and overstretching transition force than dsDNA, whereas the electrostatic and intrinsic contributions to the persistence length are larger.This work was supported by grants from the Spanish Ministry of Science and Innovation (BFU2011-29038 and BFU2010-15703) and the Comunidad de Madrid (S2009/MAT/1507). IRA.-G. acknowledges a Ramon y Cajal contract from the Spanish Ministry of Science and Innovation (RYC-2007-01765). Work in the F.M.-H. laboratory was supported by a Starting Grant from the European Research Council (no. 206117) and a grant from the Spanish Ministry of Science and Innovation (FIS2011-24638). We thank M. S. Dillingham for kindly providing the pSP73-JY0 plasmid, M. Menendez for access to a spectropolarimeter, A. Monserrate for polylysine-AFM control experiments, and B. Ibarra for fruitful discussions.Herrero-Galán, E.; Fuentes-Perez. M.E.; Carrasco, C.; Valpuesta, J.; Carrascosa, J.; Moreno-Herrero, F.; Arias-Gonzalez, JR. (2013). Mechanical Identities of RNA and DNA Double Helices Unveiled at the Single-Molecule Level. Journal of the American Chemical Society. 135(1):122-131. https://doi.org/10.1021/ja3054755S122131135

Photoluminescence Activation of Organic Dyes via Optically Trapped Quantum Dots

This document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Nano, copyright © American Chemical Society after peer review and technical editing by the publisher.[EN] Laser tweezers afford quantum dot (QD) manipulation for use as localized emitters. Here, we demonstrate fluorescence by radiative energy transfer from optically trapped colloidal QDs (donors) to fluorescent dyes (acceptors). To this end, we synthesized silica-coated QDs of different compositions and triggered their luminescence by simultaneous trapping and two-photon excitation in a microfluidic chamber filled with dyes. This strategy produces a near-field light source with great spatial maneuverability, which can be exploited to scan nanostructures. In this regard, we demonstrate induced photoluminescence of dye-labeled cells via optically trapped silica-coated colloidal QDs placed at their vicinity. Allocating nanoscale donors at controlled distances from a cell is an attractive concept in fluorescence microscopy because it dramatically reduces the number of excited dyes, which improves resolution by preventing interferences from the whole sample, while prolonging dye luminescence lifetime due to the lower power absorbed from the QDs.H.R.-R. is supported by an FPI-UAM 2015 fellowship (BES-2009-027909). Authors acknowledge funding from the Spanish Ministry of Economy and Competitiveness through MAT2017-85617-R and MAT2015-71806-R. B.H.J. acknowledges financial support from the Spanish Ministry of Economy and Competitiveness, through the Maria de Maeztu (IFIMAC) and Severo Ochoa (IMDEA Nanoscience) Programmes for Units of Excellence in R&D.Rodríguez-Rodríguez, H.; Acebrón, M.; Iborra, F.; Arias-Gonzalez, JR.; Juárez, B. (2019). Photoluminescence Activation of Organic Dyes via Optically Trapped Quantum Dots. ACS Nano. 13(6):7223-7230. https://doi.org/10.1021/acsnano.9b02835S7223723013

The influence of road networks on brown bear spatial distribution and habitat suitability in a human-modified landscape

Roads are human infrastructure that heavily affect wildlife, often with marked impacts on carnivores, including brown bears Ursus arctos. Here, we assessed the potential impact of road networks on the distribution of brown bears in the small, isolated and endangered Cantabrian population of north-western Spain. To ascertain whether local road networks affect brown bear spatial distribution, we first assessed potential influences on the distance of bear locations to roads using candidate models which included topographic variables, landcover types, bear age and reproductive status, traffic volume and road visibility. Then, we built two sets of habitat suitability models, both with and without roads, to discern the possible loss of habitat suitability caused by roads. The mean distance of bear locations to the nearest road was 968 804 m and the closest road was a low traffic road in 72.5% of cases. Candidate models showed little influence of our variables on bear distance to the nearest road, with the exception of elevation. Habitat suitability models revealed that road networks in our study area seem to have almost no effect on brown bear habitat suitability, except for females with yearlings during the denning season. However, this result may also be a consequence of the fact that only a small proportion (16.5%) of the cells classified as suitable bear habitats were crossed by roads, that is, most of the roads are primarily located in unsuitable bear habitats in the Cantabrian Mountains. Compared to previous studies conducted in other populations, mainly North American ones, our findings might suggest a different response of Eurasian brown bears to roads due to a longer bear-human coexistence in Europe versus North America. However, the indirect approach used in our study does not exclude other detrimental effects, for example, road mortality, increased stress and movement pattern disruption, only detectable by more direct approaches such as telemetry

Functional over-redundancy and high functional vulnerability in global fish faunas on tropical reefs

When tropical systems lose species, they are often assumed to be buffered against declines in functional diversity by the ability of the species-rich biota to display high functional redundancy: i.e., a high number of species performing similar functions. We tested this hypothesis using a ninefold richness gradient in global fish faunas on tropical reefs encompassing 6,316 species distributed among 646 functional entities (FEs): i.e., unique combinations of functional traits. We found that the highest functional redundancy is located in the Central Indo-Pacific with a mean of 7.9 species per FE. However, this overall level of redundancy is disproportionately packed into few FEs, a pattern termed functional over-redundancy (FOR). For instance, the most speciose FE in the Central Indo-Pacific contains 222 species (out of 3,689) whereas 38% of FEs (180 out of 468) have no functional insurance with only one species. Surprisingly, the level of FOR is consistent across the six fish faunas, meaning that, whatever the richness, over a third of the species may still be in overrepresented FEs whereas more than one third of the FEs are left without insurance, these levels all being significantly higher than expected by chance. Thus, our study shows that, even in high-diversity systems, such as tropical reefs, functional diversity remains highly vulnerable to species loss. Although further investigations are needed to specifically address the influence of redundant vs. vulnerable FEs on ecosystem functioning, our results suggest that the promised benefits from tropical biodiversity may not be as strong as previously thought

Evolution of density perturbations in double exponential quintessence models

In this work we investigate the evolution of matter density perturbations for quintessence models with a self-interaction potential that is a combination of exponentials. One of the models is based on the Einstein theory of gravity, while the other is based on the Brans-Dicke scalar tensor theory. We constrain the parameter space of the models using the determinations for the growth rate of perturbations derived from data of the 2-degree Field Galaxy Redshift Survey.Comment: 5 pages, 3 eps figure