Modeling of a Cable-Based Revolute Joint Using Biphasic Media Variable Stiffness Actuation

In recent times, safe interactions between humans and robots are required for innumerable tasks and environments. This safety can be achieved using compliance design and control of mechanisms. Cable-driven mechanisms are used when applications need to have light structures, meaning that their actuators must be relocated to ground and forces are transferred along tensioned cables. This paper presents a compliant cable-driven revolute joint using biphasic media variable stiffness actuators. Actuator's stiffness is controlled by changing pressure of control fluid into distribution lines. The used control fluid is biphasic, composed of separated gas and liquid fractions with predefined ratio. The mathematical model of the actuator is presented along with its position and stiffness model-based control, then, equations relating to the dynamics of the mechanism are provided with a joint stiffness and orientation controller. Results from simulations are discussed

A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation

Naturally occurring enzyme homologues often display highly divergent activity with non-natural substrates. Exploiting this diversity with enzymes engineered for new or altered function, however, is laborious because the engineering must be replicated for each homologue. A small set of mutations of the tryptophan synthase β-subunit (TrpB) from Pyrococcus furiosus, which mimics the activation afforded by binding of the α-subunit, was demonstrated to have a similar activating effect in different TrpB homologues with as little as 57 % sequence identity. Kinetic and spectroscopic analyses indicate that the mutations function through the same mechanism: mimicry of α-subunit binding. From these enzymes, we identified a new TrpB catalyst that displays a remarkably broad activity profile in the synthesis of 5-substituted tryptophans. This demonstrates that allosteric activation can be recapitulated throughout a protein family to explore natural sequence diversity for desirable biocatalytic transformations

Directed evolution of the tryptophan synthase β-subunit for stand-alone function recapitulates allosteric activation

Enzymes in heteromeric, allosterically regulated complexes catalyze a rich array of chemical reactions. Separating the subunits of such complexes, however, often severely attenuates their catalytic activities, because they can no longer be activated by their protein partners. We used directed evolution to explore allosteric regulation as a source of latent catalytic potential using the β-subunit of tryptophan synthase from Pyrococcus furiosus (PfTrpB). As part of its native αββα complex, TrpB efficiently produces tryptophan and tryptophan analogs; activity drops considerably when it is used as a stand-alone catalyst without the α-subunit. Kinetic, spectroscopic, and X-ray crystallographic data show that this lost activity can be recovered by mutations that reproduce the effects of complexation with the α-subunit. The engineered PfTrpB is a powerful platform for production of Trp analogs and for further directed evolution to expand substrate and reaction scope

Density functional electronic spectrum of the CuO−6−10Cu O_{-6}^{-10} cluster and possible local Jahn-Teller distorsions in the La-Ba-Cu-O superconductor

We present a density functional theory (DFT) calculation in the generalized gradient approximation to study the possibility for the existence of Jahn-Teller (JT) or pseudo Jahn-Teller (PJT) type local distortions in the La-Ba-Cu-O superconducting system. We performed the calculation and correspondingly group theory classification of the electronic ground state of the CuO${_{6}}^{-10}$ elongated octahedra cluster, immersed in a background simulating the superconductor. Part of the motivation to do this study is that the origin of the apical deformation of the CuO${_{6}}^{-10}$ cluster is not due to a pure JT effect, having therefore a non {\it a priori} condition to remove the degeneracy of the electronic ground state of the parent regular octahedron. We present a comparative analysis of the symmetry classified electron spectrum with previously reported results using unrestricted Hartree-Fock calculations (UHF). Both the DFT and UHF calculations produced a non degenerate electronic ground state, not having therefore the necessary condition for a pure JT effect. However, the appearance of a degenerate E$_{g}$ state near to the highest occupied molecular orbital in the DFT calculation, suggests the possibility for a PJT effect responsible for a local distortion of the oxidized CuO$_{6}^{-9}$ cluster.Comment: 12 pages, 3 figures, submitted to International Journal of Modern Physics B (IJMPB

Tryptophan synthase uses an atypical mechanism to achieve substrate specificity

Tryptophan synthase (TrpS) catalyzes the final steps in the biosynthesis of L-tryptophan from L-serine (Ser) and indole-3-glycerol phosphate (IGP). We report that native TrpS can also catalyze a productive reaction with L-threonine (Thr), leading to (2S,3S)-β-methyltryptophan. Surprisingly, β-substitution occurs in vitro with a 3.4-fold higher catalytic efficiency for Ser over Thr using saturating indole, despite >82,000-fold preference for Ser in direct competition using IGP. Structural data identify a novel product binding site and kinetic experiments clarify the atypical mechanism of specificity: Thr binds efficiently but decreases the affinity for indole and disrupts the allosteric signaling that regulates the catalytic cycle

Gobernabilidad en el Estado Patrimonial, referencia al caso venezolano

This essay addresses the determinants of Governance in the so-called Patrimonial State, having as a reference the Fiscal State, with particular reference to the Venezuelan case. Through documentary research, it seeks to show that the emergence and subsequent maturation of a State with its own income was possible thanks to the international oil income, which gives it financial autonomy and a maneuvering capacity to concentrate and centralize power, moving away from democratic guidelines. The entropy resulting from relations without counterweights and the reduction of oil revenues threaten the financial sustainability and viability of the group's political hegemony as government. According to the thesis, the economic-political crisis, that takes place in the second decade of the present century, finds explanation in the contradiction between some norms and institutions designed for a Patrimonial State that struggles to maintain itself and a precarious financial base, characteristic of the Fiscal State.Este ensayo aborda los condicionantes de la Gobernabilidad en el denominado Estado Patrimonial, teniendo como referencia comparativa el Estado Fiscal, con particular referencia caso venezolano. Mediante investigación documental pretende evidenciar que la emergencia y posterior maduración de un Estado con ingresos propios fue posible gracias a la renta petrolera internacional, que lo dota de autonomía financiera y una capacidad de maniobra para concentrar y centralizar el poder, alejándose de pautas democráticas. La entropía resultante de unas relaciones sin contrapesos y la reducción de los ingresos petroleros amenazan la sostenibilidad financiera y la viabilidad de la hegemonía política del grupo en funciones de gobierno. De acuerdo a la tesis manejada, la crisis económico-política que acontece en la segunda década del presente siglo encuentra explicación en la contradicción entre unas normas e instituciones diseñadas para un Estado Patrimonial que pugna por mantenerse y una base financiera precaria, característica del Estado Fiscal

Post-Translational Modifications Modulate Ligand Recognition by the Third PDZ Domain of the MAGUK Protein PSD-95

The relative promiscuity of hub proteins such as postsynaptic density protein-95 (PSD-95) can be achieved by alternative splicing, allosteric regulation, and post-translational modifications, the latter of which is the most efficient method of accelerating cellular responses to environmental changes in vivo. Here, a mutational approach was used to determine the impact of phosphorylation and succinimidation post-translational modifications on the binding affinity of the postsynaptic density protein-95/discs large/zonula occludens-1 (PDZ3) domain of PSD-95. Molecular dynamics simulations revealed that the binding affinity of this domain is influenced by an interplay between salt-bridges linking the α3 helix, the β2–β3 loop and the positively charged Lys residues in its high-affinity hexapeptide ligand KKETAV. The α3 helix is an extra structural element that is not present in other PDZ domains, which links PDZ3 with the following SH3 domain in the PSD-95 protein. This regulatory mechanism was confirmed experimentally via thermodynamic and NMR chemical shift perturbation analyses, discarding intra-domain long-range effects. Taken together, the results presented here reveal the molecular basis of the regulatory role of the α3 extra-element and the effects of post-translational modifications of PDZ3 on its binding affinity, both energetically and dynamically.This research was supported by grants CVI-05915, from the Andalusian Regional Government (http://www.juntadeandalucia.es), BIO2009-13261-C02 and BIO2012-39922-C02, from the Spanish Ministry of Science and Innovation (http://www.idi.mineco.gob.es/portal/site​/MICINN/) and FEDER. JMC received a postdoctoral contract from the Spanish Ministry of Science and Innovation. CCV was a recipient of a Formación de Personal Investigador fellowship from the Spanish Ministry of Science and Innovation

Lattice gas and lattice Boltzman for spatio-temporal simulation of gases in fruit storage chambers

The benefit of controlled and modified atmospheres for extending the storage life of fruits is world wide accepted. However, there are secondary effects such as the incidence of anaerobic respiration or the off-favour occurrence which are not sufficiently known and thus controlled. This study approaches the knowledge of those secondary effects by developing a spatio temporal model gathering fluid flow phenomenon and physic and physiological processes. The lattice Boltzmann model used as framework for mimicking the fluid flow shows to be a very flexible tool which reproduces complex macroscopic behaviours on a down up strategy better than Lattice Gas Cellular Automata (LGCA

The Metabolic Redox Regime of <i>Pseudomonas putida</i> Tunes Its Evolvability toward Novel Xenobiotic Substrates

Some environmental bacteria evolve with new capacities for the aerobic biodegradation of chemical pollutants by adapting preexisting redox reactions to novel compounds. The process typically starts by cooption of enzymes from an available route to act on the chemical structure of the substrate-to-be. The critical bottleneck is generally the first biochemical step, and most of the selective pressure operates on reshaping the initial reaction. The interim uncoupling of the novel substrate to preexisting Rieske nonheme iron oxygenases usually results in formation of highly mutagenic ROS. In this work, we demonstrate that the background metabolic regime of the bacterium that hosts an evolving catabolic pathway (e.g., biodegradation of the xenobiotic 2,4-DNT) determines whether the cells either adopt a genetic diversification regime or a robust ROS-tolerant status. Furthermore, our results offer new perspectives to the rational design of efficient whole-cell biocatalysts, which are pursued in contemporary metabolic engineering.During evolution of biodegradation pathways for xenobiotic compounds involving Rieske nonheme iron oxygenases, the transition toward novel substrates is frequently associated with faulty reactions. Such events release reactive oxygen species (ROS), which are endowed with high mutagenic potential. In this study, we evaluated how the operation of the background metabolic network by an environmental bacterium may either foster or curtail the still-evolving pathway for 2,4-dinitrotoluene (2,4-DNT) catabolism. To this end, the genetically tractable strain Pseudomonas putida EM173 was implanted with the whole genetic complement necessary for the complete biodegradation of 2,4-DNT (recruited from the environmental isolate Burkholderia sp. R34). By using reporter technology and direct measurements of ROS formation, we observed that the engineered P. putida strain experienced oxidative stress when catabolizing the nitroaromatic substrate. However, the formation of ROS was neither translated into significant activation of the SOS response to DNA damage nor did it result in a mutagenic regime (unlike what has been observed in Burkholderia sp. R34, the original host of the pathway). To inspect whether the tolerance of P. putida to oxidative challenges could be traced to its characteristic reductive redox regime, we artificially altered the NAD(P)H pool by means of a water-forming, NADH-specific oxidase. Under the resulting low-NAD(P)H status, catabolism of 2,4-DNT triggered a conspicuous mutagenic and genomic diversification scenario. These results indicate that the background biochemical network of environmental bacteria ultimately determines the evolvability of metabolic pathways. Moreover, the data explain the efficacy of some bacteria (e.g., pseudomonads) to host and evolve with new catabolic routes