Using genetic variability available in the breeder's pool to engineer fruit quality

8 páginas, 1 figura, 2 tablas.-- This article is open-access.We substantiate here the opinion that experts in biotechnology and natural biodiversity can work together on the production of successive waves of next-gen GM fruit crops to improve organoleptic and nutritional quality and therefore generate wider public acceptance. In this scenario genetic engineering becomes a faster and more precise way of transferring genes of interest to fruit crop plants from the same or sexually compatible species (intra- or cisgenesis) than more traditional methods, such as MASPB. The availability of complete genome sequences for an increasing number of crop plants, as well as the results from genomics studies, can assist in the identification of gene-to-trait association. The next wave of GM crops will be able to take full advantage of a Synthetic Biology-based strategy in the development of new fruit varieties by using DNA not necessarily present in the breeder's pool for a wide range of applications. There are still a number of challenges which require attention, such as identifying genes and allelic forms associated with traits of interest and improving the precision and stability of the transferred DNA, etc.Peer reviewe

Traveling Material↔Semiotic Environments of Disability, Rehabilitation, and Physical Activity

In this article, we apply narrative dialogism and new materialism to health research. We examine how material↔semiotic environments (MSEs) affect the rehabilitation process of Patrick, a man who exercised with the aim to recover from spinal cord injury. The MSEs are considered embedded subcases within the overall holistic case of Patrick. Three MSEs were identified: the hospital gym, the personal gym, and the adapted gym. These are examined using the analytical lens of assemblages. First, the mutually affecting components of each MSE are described. Second, a larger environmental assemblage is identified, which is termed exercise-is-restitution assemblage. This composite assemblage illuminates the associations between the three MSEs, and reveals how restitution resonated across time and space. The article contributes to the literature by reconceptualizing restitution. It highlights the importance of the materiality of health-related narratives, and it reveals the potential of MSE for transforming rehabilitation and improving exercise promotion and maintenance

A Nonlocal Elasto-Plastic Model for Structured Soils at Large Strains for the Particle Finite Element Method

This work presents a robust and mesh-independent implementation of an elasto-plastic constitutive model at large strains, appropriate for structured soils, into a Particle Finite Element code specially developed for geotechnical simulations. The constitutive response of structured soils is characterized by softening and, thus, leading to strain localization. Strain localization poses two numerical challenges: mesh dependence of the solution and computability of the solution. The former is mitigated by employing a non-local integral type regularization whereas an Implicit-Explicit integration scheme is used to enhance the computability. The good performance of these techniques is highlighted in the simulation of the cone penetration test in undrained conditions.Peer ReviewedPostprint (published version

An in-depth view of the microscopic dynamics of Ising spin glasses at fixed temperature

Using the dedicated computer Janus, we follow the nonequilibrium dynamics of the Ising spin glass in three dimensions for eleven orders of magnitude. The use of integral estimators for the coherence and correlation lengths allows us to study dynamic heterogeneities and the presence of a replicon mode and to obtain safe bounds on the Edwards-Anderson order parameter below the critical temperature. We obtain good agreement with experimental determinations of the temperature-dependent decay exponents for the thermoremanent magnetization. This magnitude is observed to scale with the much harder to measure coherence length, a potentially useful result for experimentalists. The exponents for energy relaxation display a linear dependence on temperature and reasonable extrapolations to the critical point. We conclude examining the time growth of the coherence length, with a comparison of critical and activated dynamics.Comment: 38 pages, 26 figure

Matching microscopic and macroscopic responses in glasses

We first reproduce on the Janus and Janus II computers a milestone experiment that measures the spin-glass coherence length through the lowering of free-energy barriers induced by the Zeeman effect. Secondly we determine the scaling behavior that allows a quantitative analysis of a new experiment reported in the companion Letter [S. Guchhait and R. Orbach, Phys. Rev. Lett. 118, 157203 (2017)]. The value of the coherence length estimated through the analysis of microscopic correlation functions turns out to be quantitatively consistent with its measurement through macroscopic response functions. Further, non-linear susceptibilities, recently measured in glass-forming liquids, scale as powers of the same microscopic length.Comment: 6 pages, 4 figure

High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping

Background: Cucurbita pepo is amember of the Cucurbitaceae family, the second-most important horticultural family in terms of economic importance after Solanaceae. The ¿summer squash¿ types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species. The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). Results: We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species¿ two subspecies: Zucchini (subsp. pepo) ¿ Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. Conclusion: Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps an performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in the coding regions of genes involved in different physiological processes. The platform will also be useful for future mapping and diversity studies, and will be essential in order to accelerate the process of breeding new and better adapted squash varieties.This research was funded by the INIA projects RTA2008-00035-C02-01/02 and RTA2011-00044-C02-1/2 of the Spanish Instituto Nacional de Investigacion y Tecnologia Agraria and FEDER funds (EU). The NVD grant was supported by the Programa de Formacion del Personal Tecnico e Investigador from IFAPA, co-financed with European Social Funds. The authors wish to thank P. Salas and E. Martinez Perez for their technical assistance in the fruit characterization. We are thankful for the kindly suggestions of Dr. Harry Paris for the F2 C. pepo mapping population.Esteras Gómez, C.; Gómez, P.; Monforte Gilabert, AJ.; Blanca Postigo, JM.; Vicente-Dolera, N.; Roig Montaner, MC.; Nuez Viñals, F.... (2012). High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping. BMC Genomics. 13(80):1-21. https://doi.org/10.1186/1471-2164-13-80S121138

The three dimensional Ising spin glass in an external magnetic field: the role of the silent majority

We perform equilibrium parallel-tempering simulations of the 3D Ising Edwards-Anderson spin glass in a field. A traditional analysis shows no signs of a phase transition. Yet, we encounter dramatic fluctuations in the behaviour of the model: Averages over all the data only describe the behaviour of a small fraction of it. Therefore we develop a new approach to study the equilibrium behaviour of the system, by classifying the measurements as a function of a conditioning variate. We propose a finite-size scaling analysis based on the probability distribution function of the conditioning variate, which may accelerate the convergence to the thermodynamic limit. In this way, we find a non-trivial spectrum of behaviours, where a part of the measurements behaves as the average, while the majority of them shows signs of scale invariance. As a result, we can estimate the temperature interval where the phase transition in a field ought to lie, if it exists. Although this would-be critical regime is unreachable with present resources, the numerical challenge is finally well posed.Comment: 42 pages, 19 figures. Minor changes and added figure (results unchanged

Critical Behavior of Three-Dimensional Disordered Potts Models with Many States

We study the 3D Disordered Potts Model with p=5 and p=6. Our numerical simulations (that severely slow down for increasing p) detect a very clear spin glass phase transition. We evaluate the critical exponents and the critical value of the temperature, and we use known results at lower $p$ values to discuss how they evolve for increasing p. We do not find any sign of the presence of a transition to a ferromagnetic regime.Comment: 9 pages and 9 Postscript figures. Final version published in J. Stat. Mec