Recurrent backpropagation and the dynamical approach to adaptive neural computation

Error backpropagation in feedforward neural network models is a popular learning algorithm that has its roots in nonlinear estimation and optimization. It is being used routinely to calculate error gradients in nonlinear systems with hundreds of thousands of parameters. However, the classical architecture for backpropagation has severe restrictions. The extension of backpropagation to networks with recurrent connections will be reviewed. It is now possible to efficiently compute the error gradients for networks that have temporal dynamics, which opens applications to a host of problems in systems identification and control

Connecting mitochondrial dynamics and life-or-death events via Bcl-2 family proteins

International audienceThe morphology of a population of mitochondria is the result of several interacting dynamical phenomena, including fission, fusion, movement, elimination and biogenesis. Each of these phenomena is controlled by underlying molecular machinery, and when defective can cause disease. New understanding of the relationships between form and function of mitochondria in health and disease is beginning to be unraveled on several fronts. Studies in mammals and model organisms have revealed that mitochondrial morphology, dynamics and function appear to be subject to regulation by the same proteins that regulate apoptotic cell death. One protein family that influences mitochondrial dynamics in both healthy and dying cells is the Bcl-2 protein family. Connecting mitochondrial dynamics with life-death pathway forks may arise from the intersection of Bcl-2 family proteins with the proteins and lipids that determine mitochondrial shape and function. Bcl-2 family proteins also have multifaceted influences on cells and mitochondria, including calcium handling, autophagy and energetics, as well as the subcellular localization of mitochondrial organelles to neuronal synapses. The remarkable range of physical or functional interactions by Bcl-2 family proteins is challenging to assimilate into a cohesive understanding. Most of their effects may be distinct from their direct roles in apoptotic cell death and are particularly apparent in the nervous system. Dual roles in mitochondrial dynamics and cell death extend beyond BCL-2 family proteins. In this review, we discuss many processes that govern mitochondrial structure and function in health and disease, and how Bcl-2 family proteins integrate into some of these processes

Crianza artificial de terneros y eficiencia en la utilización de la úrea

Muchos sistemas para la cría de terneros se han ensayado en diferentes países, empleando reemplazo total 0 parcial de La alimentación láctea por sustitutos que puedan supl1r los requerimientos para el desarrollo normal de los animales, la gran escasez de leche en la actualidad tanto para el consumo humano como para la industria procesadora, es una de las condiciones que conduce a buscar Sistemas de cría de terneros con reducidas cantidades de leche por cortos períodos de alimentación láctea, dando como resultado una mayor cantidad de leche disponible, que puede aumentar los niveles de venta en los mercados, ocasionando así la capacidad para un mayor consumo por persona y al mismo tiempo haciendo más rentables las explotaciones ganadera

Tomato CRABS CLAW paralogues interact with chromatin remodelling factors to mediate carpel development and floral determinacy

CRABS CLAW (CRC) orthologues play a crucial role in floral meristem (FM) determinacy and gynoecium formation across angiosperms, the key developmental processes for ensuring successful plant reproduction and crop production. However, the mechanisms behind CRC mediated FM termination are far from fully understood. Here, we addressed the functional characterization of tomato (Solanum lycopersicum) paralogous CRC genes. Using mapping-by-sequencing, RNA interference and CRISPR/Cas9 techniques, expression analyses, protein-protein interaction assays and Arabidopsis complementation experiments, we examined their potential roles in FM determinacy and carpel formation. We revealed that the incomplete penetrance and variable expressivity of the indeterminate carpel-inside-carpel phenotype observed in fruit iterative growth (fig) mutant plants are due to the lack of function of the S. lycopersicum CRC homologue SlCRCa. Furthermore, a detailed functional analysis of tomato CRC paralogues, SlCRCa and SlCRCb, allowed us to propose that they operate as positive regulators of FM determinacy by acting in a compensatory and partially redundant manner to safeguard the proper formation of flowers and fruits. Our results uncover for the first time the physical interaction of putative CRC orthologues with members of the chromatin remodelling complex that epigenetically represses WUSCHEL expression through histone deacetylation to ensure the proper termination of floral stem cell activity.Peer reviewe

Approaching the genetic dissection of indirect adventitious organogenesis process in tomato explants

[EN] The screening of 862 T-DNA lines was carried out to approach the genetic dissection of indirect adventitious organogenesis in tomato. Several mutants defective in different phases of adventitious organogenesis, namely callus growth (tdc-1), bud differentiation (tdb-1,-2,-3) and shoot-bud development (tds-1) were identified and characterized. The alteration of the TDC-1 gene blocked callus proliferation depending on the composition of growth regulators in the culture medium. Calli from tds-1 explants differentiated buds but did not develop normal shoots. Histological analysis showed that their abnormal development is due to failure in the organization of normal adventitious shoot meristems. Interestingly, tdc-1 and tds-1 mutant plants were indistinguishable from WT ones, indicating that the respective altered genes play specific roles in cell proliferation from explant cut zones (TDC-1 gene) or in the organization of adventitious shoot meristems (TDS-1 gene). Unlike the previous, plants of the three mutants defective in the differentiation of adventitious shoot-buds (tdb-1,-2,-3) showed multiple changes in vegetative and reproductive traits. Cosegregation analyses revealed the existence of an association between the phenotype of the tdb-3 mutant and a T-DNA insert, which led to the discovery that the SlMAPKKK17 gene is involved in the shoot-bud differentiation process.Vicente Moreno and Rafael Lozano thank the Ministry of Science and Innovation (State Innovation Agency) for granting the projects PID2019-110833RB-C32 and PID2019-110833RB-C31. Benito Pineda's work in the context of this article has been funded by 'Aid for First Research Projects (PAID-06-18)' by the Vicerrectorado de Investigacion, Innovacion y Transferencia de la Universitat Politecnica de Valencia (UPV), Valencia, Spain'. The PhD fellowship for Jorge Sanchez-Lopez and Marybel Jaquez-Gutierrez were funded by the Universidad de Sinaloa and the CONACYT of Mexico.Sanchez-Lopez, J.; Atarés Huerta, A.; Jaquez-Gutierrez, M.; Ortiz-Atienza, A.; Capel, C.; Pineda Chaza, BJ.; García Sogo, B.... (2021). Approaching the genetic dissection of indirect adventitious organogenesis process in tomato explants. Plant Science. 302:1-14. https://doi.org/10.1016/j.plantsci.2020.110721S11430

Albino T-DNA tomato mutant reveals a key function of 1-deoxy-D-xylulose-5-phosphate synthase (DXS1) in plant development and survival

[EN] Photosynthetic activity is indispensable for plant growth and survival and it depends on the synthesis of plastidial isoprenoids as chlorophylls and carotenoids. In the non-mevalonate pathway (MEP), the 1-deoxy-D-xylulose-5-phosphate synthase 1 (DXS1) enzyme has been postulated to catalyze the ratelimiting step in the formation of plastidial isoprenoids. In tomato, the function of DXS1 has only been studied in fruits, and hence its functional relevance during plant development remains unknown. Here we report the characterization of the wls-2297 tomato mutant, whose severe deficiency in chlorophylls and carotenoids promotes an albino phenotype. Additionally, growth of mutant seedlings was arrested without developing vegetative organs, which resulted in premature lethality. Gene cloning and silencing experiments revealed that the phenotype of wls-2297 mutant was caused by 38.6 kb-deletion promoted by a single T-DNA insertion affecting the DXS1 gene. This was corroborated by in vivo and molecular complementation assays, which allowed the rescue of mutant phenotype. Further characterization of tomato plants overexpressing DXS1 and comparative expression analysis indicate that DXS1 may play other important roles besides to that proposed during fruit carotenoid biosynthesis. Taken together, these results demonstrate that DXS1 is essentially required for the development and survival of tomato plants.This work was supported by research grants from the Spanish Ministry of Economy and Competitiveness and the UE-European Regional Development Fund (AGL2015-64991-C3-1-R, and AGL2015-64991-C3-3-R), and Junta de Andalucia (P12-AGR-1482). PhD fellowship to M.G.-A. was funded by the FPU Programme of the Spanish Ministry of Science and Innovation. The authors thank research facilities provided by the Campus de Excelencia Internacional Agroalimentario (CeiA3).Garcia-Alcazar, M.; Giménez Caminero, ME.; Pineda Chaza, BJ.; Capel, C.; García Sogo, B.; Sánchez Martín-Sauceda, S.; Yuste-Lisbona, FJ.... (2017). Albino T-DNA tomato mutant reveals a key function of 1-deoxy-D-xylulose-5-phosphate synthase (DXS1) in plant development and survival. Scientific Reports. 7:1-12. https://doi.org/10.1038/srep45333112

Mutation at the tomato EXCESSIVE NUMBER OF FLORAL ORGANS (ENO) locus impairs floral meristem development, thus promoting an increased number of floral organs and fruit size

[EN] A novel tomato (Solanum lycopersicum L.) mutant affected in reproductive development, excessive number of floral organs (eno), is described in this study. The eno plants yielded flowers with a higher number of floral organs in the three innermost floral whorls and larger fruits than those found in wild-type plants. Scanning-electron microscopy study indicated that the rise in floral organ number and fruit size correlates with an increased size of floral meristem at early developmental stages. It has been reported that mutation at the FASCIATED (FAS) gene causes the development of flowers with supernumerary organs; however, complementation test and genetic mapping analyses proved that ENO is not an allele of the FAS locus. Furthermore, expression of WUSCHEL (SlWUS) and INHIBITOR OF MERISTEM ACTIVITY (IMA), the two main regulators of floral meristem activity in tomato, is altered in eno but not in fas flowers indicating that ENO could exert its function in the floral meristem independently of FAS. Interestingly, the eno mutation delayed the expression of IMA leading to a prolonged expression of SlWUS, which would explain the greater size of floral meristem. Taken together, results showed that ENO plays a significant role in the genetic pathway regulating tomato floral meristem development. (C) 2014 Elsevier Ireland Ltd. All rights reserved.This work was supported by the research grants AGL2012-40150-C02-01 and AGL2012-40150-C02-02 and a fellowship to AF-L from the Spanish Ministry of Economy and Competitiveness. BP was supported by the European Commission through the JAE-Doc Program of the Spanish National Research Council (CSIC). The authors would like to thank the research facilities provided by the Campus de Excelencia Internacional Agroalimentario (CeiA3).Fernández-Lozano, A.; Yuste-Lisbona, FJ.; Pérez-Martín, F.; Pineda Chaza, BJ.; Moreno Ferrero, V.; Lozano, R.; Angosto, T. (2015). Mutation at the tomato EXCESSIVE NUMBER OF FLORAL ORGANS (ENO) locus impairs floral meristem development, thus promoting an increased number of floral organs and fruit size. Plant Science. 232:41-48. doi:10.1016/j.plantsci.2014.12.007S414823

The res (restored cell structure by salinity) tomato mutant reveals the role of the DEAD-box RNA helicase SlDEAD39 in plant development and salt response

[EN] Increasing evidences highlight the importance of DEAD-box RNA helicases in plant development and stress responses. In a previous study, we characterized the tomato res mutant (restored cell structure by salinity), showing chlorosis and development alterations that reverted under salt-stress conditions. Map-based cloning demonstrates that RES gene encodes SlDEAD39, a chloroplast-targeted DEAD-box RNA helicase. Constitutive expression of SlDEAD39 complements the res mutation, while the silencing lines had a similar phenotype than res mutant, which is also reverted under salinity. Functional analysis of res mutant proved SlDEAD39 is involved in the in vivo processing of the chloroplast, 23S rRNA, at the hidden break-B site, a feature also supported by in vitro binding experiments of the protein. In addition, our results show that other genes coding for chloroplast-targeted DEAD-box proteins are induced by salt-stress, which might explain the rescue of the res mutant phenotype. Interestingly, salinity restored the phenotype of res adult plants by increasing their sugar content and fruit yield. Together, these results propose an unprecedented role of a DEAD-box RNA helicase in regulating plant development and stress response through the proper ribosome and chloroplast functioning, which, in turn, represents a potential target to improve salt tolerance in tomato cropsSecretaria de Estado de Investigacion, Desarrollo e Innovacion, Grant/Award Numbers: AGL2015-64991-C3-1-R, AGL2015-64991-C3-2-R, AGL2015-64991-C3-3-R, AGL2017-88702-C2-1-RCapel, C.; Albaladejo, I.; Egea, I.; Massaretto, IL.; Yuste-Lisbona, FJ.; Pineda Chaza, BJ.; García Sogo, B.... (2020). The res (restored cell structure by salinity) tomato mutant reveals the role of the DEAD-box RNA helicase SlDEAD39 in plant development and salt response. Plant Cell & Environment. 43(7):1722-1739. https://doi.org/10.1111/pce.13776S1722173943

Can One Trust Quantum Simulators?

Various fundamental phenomena of strongly-correlated quantum systems such as high-$T_c$ superconductivity, the fractional quantum-Hall effect, and quark confinement are still awaiting a universally accepted explanation. The main obstacle is the computational complexity of solving even the most simplified theoretical models that are designed to capture the relevant quantum correlations of the many-body system of interest. In his seminal 1982 paper [Int. J. Theor. Phys. 21, 467], Richard Feynman suggested that such models might be solved by "simulation" with a new type of computer whose constituent parts are effectively governed by a desired quantum many-body dynamics. Measurements on this engineered machine, now known as a "quantum simulator," would reveal some unknown or difficult to compute properties of a model of interest. We argue that a useful quantum simulator must satisfy four conditions: relevance, controllability, reliability, and efficiency. We review the current state of the art of digital and analog quantum simulators. Whereas so far the majority of the focus, both theoretically and experimentally, has been on controllability of relevant models, we emphasize here the need for a careful analysis of reliability and efficiency in the presence of imperfections. We discuss how disorder and noise can impact these conditions, and illustrate our concerns with novel numerical simulations of a paradigmatic example: a disordered quantum spin chain governed by the Ising model in a transverse magnetic field. We find that disorder can decrease the reliability of an analog quantum simulator of this model, although large errors in local observables are introduced only for strong levels of disorder. We conclude that the answer to the question "Can we trust quantum simulators?" is... to some extent.Comment: 20 pages. Minor changes with respect to version 2 (some additional explanations, added references...

The SlCBL10 calcineurin B-like protein ensures plant growth under salt stress by regulating Na+ and Ca2+ homeostasis

[EN] Characterization of a new tomato (Solanum lycopersicum) T-DNA mutant allowed for the isolation of the CALCINEURIN B-LIKE PROTEIN 10 (SlCBL10) gene whose lack of function was responsible for the severe alterations observed in the shoot apex and reproductive organs under salinity conditions. Physiological studies proved that SlCBL10 gene is required to maintain a proper low Na+/Ca2+ ratio in growing tissues allowing tomato growth under salt stress. Expression analysis of the main responsible genes for Na+ compartmentalization (i.e. Na+/H+ EXCHANGERs, SALT OVERLY SENSITIVE, HIGH-AFFINITY K+ TRANSPORTER 1; 2, H+-pyrophosphatase AVP1 [SlAVP1] and V-ATPase [SlVHA-A1]) supported a reduced capacity to accumulate Na+ in Slcbl10 mutant leaves, which resulted in a lower uploading of Na+ from xylem, allowing the toxic ion to reach apex and flowers. Likewise, the tomato CATION EXCHANGER 1 and TWO-PORE CHANNEL 1 (SlTPC1), key genes for Ca2+ fluxes to the vacuole, showed abnormal expression in Slcbl10 plants indicating an impaired Ca2+ release from vacuole. Additionally, complementation assay revealed that SlCBL10 is a true ortholog of the Arabidopsis (Arabidopsis thaliana) CBL10 gene, supporting that the essential function of CBL10 is conserved in Arabidopsis and tomato. Together, the findings obtained in this study provide new insights into the function of SlCBL10 in salt stress tolerance. Thus, it is proposed that SlCBL10 mediates salt tolerance by regulating Na+ and Ca2+ fluxes in the vacuole, cooperating with the vacuolar cation channel SlTPC1 and the two vacuolar H+-pumps, SlAVP1 and SlVHA-A1, which in turn are revealed as potential targets of SlCBL10.This study was supported by grants from the Plant KBBE Program (EUI2009-04074), the Spanish Ministerio de Economia y Competitividad (AGL2012-40150, AGL2015-64991-C3-1-R/2-R/3-R, and BIO2016-79187-R), as well as the French National Research Agency ENDOREPIGEN project. A.O.-A. was supported by a PhD fellowship from the Ministerio de Economia y Competitividad (BIO2009-11484).Egea, I.; Pineda Chaza, BJ.; Ortiz Atienza, A.; Plasencia, F.; Drevensek, S.; García Sogo, B.; Yuste-Lisbona, FJ.... (2018). The SlCBL10 calcineurin B-like protein ensures plant growth under salt stress by regulating Na+ and Ca2+ homeostasis. PLANT PHYSIOLOGY. 176(2):1676-1693. https://doi.org/10.1104/pp.17.01605S16761693176