Versatile peroxidase (VP) from the white-rot fungus Pleurotus eryngii is a high redox potential peroxidase of biotechnological interest able to oxidize a wide range of recalcitrant substrates ...including lignin, phenolic and non-phenolic aromatic compounds and dyes. However, the relatively low stability towards pH of this and other fungal peroxidases is a drawback for their industrial application. A strategy based on the comparative analysis of the crystal structures of VP and the highly pH-stable manganese peroxidase (MnP4) from Pleurotus ostreatus was followed to improve the VP pH stability. Several interactions, including hydrogen bonds and salt bridges, and charged residues exposed to the solvent were identified as putatively contributing to the pH stability of MnP4. The eight amino acid residues responsible for these interactions and seven surface basic residues were introduced into VP by directed mutagenesis. Furthermore, two cysteines were also included to explore the effect of an extra disulfide bond stabilizing the distal Ca2+ region. Three of the four designed variants were crystallized and new interactions were confirmed, being correlated with the observed improvement in pH stability. The extra hydrogen bonds and salt bridges stabilized the heme pocket at acidic and neutral pH as revealed by UV-visible spectroscopy. They led to a VP variant that retained a significant percentage of the initial activity at both pH 3.5 (61% after 24 h) and pH 7 (55% after 120 h) compared with the native enzyme, which was almost completely inactivated. The introduction of extra solvent-exposed basic residues and an additional disulfide bond into the above variant further improved the stability at acidic pH (85% residual activity at pH 3.5 after 24 h when introduced separately, and 64% at pH 3 when introduced together). The analysis of the results provides a rational explanation to the pH stability improvement achieved.
Hysteresis is a general phenomenon regularly observed in various materials. Usually, hysteretic behavior is an intrinsic property that cannot be circumvented in the nonequilibrium operation of the ...system. Herein, it is shown that, at least with regard to the hysteretic behavior of phase‐separating battery materials, it is possible to enter (deeply) the hysteretic loop at finite battery currents. This newly observed electric response of the electrode, which is inherent to phase‐separating materials, is related to its microscopic origin arising from a (significant) share of the active material residing in an intraparticle phase‐separated state. This intriguing observation is further generalized by revealing that a phase‐separating material can feature (significantly) different chemical potentials at the same bulk lithiation level and temperature when exposed to the same finite current and external voltage hysteresis. Therefore, the intraparticle phase‐separated state significantly affects the DC and AC characteristics of the battery. The experimental evidence for entering the intraparticle phase‐separated state is supported by thermodynamic reasoning and advanced modeling. The current findings will help advance the understanding, control, diagnostics, and monitoring of batteries composed of phase‐separating materials while also providing pertinent motivation for the enhancement of battery design and performance.
A phase‐separating material can feature different potentials at the same bulk lithiation level and temperature when exposed to the same finite current within and outside voltage hysteresis. This fundamental material‐related challenge is interrelated to a newly observed electrochemical signature of the intraparticle phase‐separated state featuring different electrode potential compared to the interparticle phase‐separated state.
Infinite Factorial Unbounded-State Hidden Markov Model Valera, Isabel; Ruiz, Francisco J. R.; Perez-Cruz, Fernando
IEEE transactions on pattern analysis and machine intelligence,
2016-Sept.-1, 2016-09-00, 2016-9-1, 20160901, Letnik:
38, Številka:
9
Journal Article
Recenzirano
There are many scenarios in artificial intelligence, signal processing or medicine, in which a temporal sequence consists of several unknown overlapping independent causes, and we are interested in ...accurately recovering those canonical causes. Factorial hidden Markov models (FHMMs) present the versatility to provide a good fit to these scenarios. However, in some scenarios, the number of causes or the number of states of the FHMM cannot be known or limited a priori. In this paper, we propose an infinite factorial unbounded-state hidden Markov model (IFUHMM), in which the number of parallel hidden Markov models (HMMs) and states in each HMM are potentially unbounded. We rely on a Bayesian nonparametric (BNP) prior over integer-valued matrices, in which the columns represent the Markov chains, the rows the time indexes, and the integers the state for each chain and time instant. First, we extend the existent infinite factorial binary-state HMM to allow for any number of states. Then, we modify this model to allow for an unbounded number of states and derive an MCMC-based inference algorithm that properly deals with the trade-off between the unbounded number of states and chains. We illustrate the performance of our proposed models in the power disaggregation problem.
Feeding biomass-fueled gas engines (BFGEs) with olive tree pruning residues offers new opportunities to decrease fossil fuel use in road vehicles and electricity generation. BFGEs, coupled to radial ...distribution systems (RDSs), provide renewable energy and power that can feed electric vehicle (EV) charging stations. However, the combined impact of BFGEs and EVs on RDSs must be assessed to assure the technical constraint fulfilment. Because of the stochastic nature of source/load, it was decided that a probabilistic approach was the most viable option for this assessment. Consequently, this research developed an analytical technique to evaluate the technical constraint fulfilment in RDSs with this combined interaction. The proposed analytical technique (PAT) involved the calculation of cumulants and the linearization of load-flow equations, along with the application of the cumulant method, and Cornish-Fisher expansion. The uncertainties related to biomass stock and its heating value (HV) were important factors that were assessed for the first time. Application of the PAT in a Spanish RDS with BFGEs and EVs confirmed the feasibility of the proposal and its additional benefits. Specifically, BFGEs were found to clearly contribute to the voltage constraint fulfilment. The computational cost of the PAT was lower than that associated with Monte-Carlo simulations (MCSs).
Private contracts in two-sided platforms Llanes, Gastón; Ruiz-Aliseda, Francisco
The Rand journal of economics,
12/2021, Letnik:
52, Številka:
4
Journal Article
Recenzirano
We study a platform that signs private contracts with sellers. Contractual secrecy implies interrelated hold-up problems for buyers and sellers that reduce platform profits and welfare. By increasing ...its control over sellers' prices, the platform is able to increase price transparency and commit to not behaving opportunistically, which increases profits and welfare. Thus, policy prescriptions for dealing with contractual secrecy are reversed in the case of two-sided platforms. We also find a platform may benefit from an erosion of its market power on one side of the market because this erosion may raise the surplus it offers the other side.
Versatile peroxidase (VP) is defined by its capabilities to oxidize the typical substrates of other basidiomycete peroxidases: (i) Mn²⁺, the manganese peroxidase (MnP) substrate (Mn³⁺ being able to ...oxidize phenols and initiate lipid peroxidation reactions); (ii) veratryl alcohol (VA), the typical lignin peroxidase (LiP) substrate; and (iii) simple phenols, which are the substrates of Coprinopsis cinerea peroxidase (CIP). Crystallographic, spectroscopic, directed mutagenesis, and kinetic studies showed that these 'hybrid' properties are due to the coexistence in a single protein of different catalytic sites reminiscent of those present in the other basidiomycete peroxidase families. Crystal structures of wild and recombinant VP, and kinetics of mutated variants, revealed certain differences in its Mn-oxidation site compared with MnP. These result in efficient Mn²⁺ oxidation in the presence of only two of the three acidic residues forming its binding site. On the other hand, a solvent-exposed tryptophan is the catalytically-active residue in VA oxidation, initiating an electron transfer pathway to haem (two other putative pathways were discarded by mutagenesis). Formation of a tryptophanyl radical after VP activation by peroxide was detected using electron paramagnetic resonance. This was the first time that a protein radical was directly demonstrated in a ligninolytic peroxidase. In contrast with LiP, the VP catalytic tryptophan is not β-hydroxylated under hydrogen peroxide excess. It was also shown that the tryptophan environment affected catalysis, its modification introducing some LiP properties in VP. Moreover, some phenols and dyes are oxidized by VP at the edge of the main haem access channel, as found in CIP. Finally, the biotechnological interest of VP is discussed.
Objective
The prevalence of depressive symptoms immediately after the diagnosis of colorectal cancer (CRC) is high and has important implications both psychologically and on the course of the ...disease. The aim of this study is to analyse the association between depressive symptoms and CRC survival at 5 years after diagnosis.
Methods
This multicentre, prospective, observational cohort study was conducted on a sample of 2602 patients with CRC who completed the Hospital Anxiety and Depression Scale (HADS‐D) at 5 years of follow‐up. Survival was analysed using the Kaplan–Meier method and Cox regression models.
Results
According to our analysis, the prevalence of depressive symptoms after a CRC diagnosis was 23.8%. The Cox regression analysis identified depression as an independent risk factor for survival (HR = 1.47; 95% CI: 1.21–1.8), a finding which persisted after adjusting for sex (female: HR = 0.63; 95% CI: 0.51–0.76), age (>70 years: HR = 3.78; 95% CI: 1.94–7.36), need for help (yes: HR = 1.43; 95% CI: 1.17–1.74), provision of social assistance (yes: HR = 1.46; 95% CI: 1.16–1.82), tumour size (T3–T4: HR = 1.56; 95% CI: 1.22–1.99), nodule staging (N1–N2: HR = 2.46; 95% CI: 2.04–2.96), and diagnosis during a screening test (yes: HR = 0.71; 95% CI: 0.55–0.91).
Conclusions
There is a high prevalence of depressive symptoms in patients diagnosed with CRC. These symptoms were negatively associated with the survival rate independently of other clinical variables. Therefore, patients diagnosed with CRC should be screened for depressive symptoms to ensure appropriate treatment can be provided.
Summary
Phosphate (Pi) is a critical macronutrient for the biochemical and molecular functions of cells. Under phosphate limitation, plants manifest adaptative strategies to increase phosphate ...scavenging. However, how low phosphate sensing links to the transcriptional machinery remains unknown.
The role of the MEDIATOR (MED) transcriptional co‐activator, through its MED16 subunit in Arabidopsis root system architecture remodeling in response to phosphate limitation was assessed. Its critical function acting over the SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1)‐ALUMINUM‐ACTIVATED MALATE TRANSPORT1 (ALMT1) signaling module was tested through a combination of genetic, biochemical, and genome‐wide transcriptomic approaches.
Root system configuration in response to phosphate scarcity involved MED16 functioning, which modulates the expression of a large set of low‐phosphate‐induced genes that respond to local and systemic signals in the Arabidopsis root tip, including those directly activated by STOP1. Biomolecular fluorescence complementation analysis suggests that MED16 is required for the transcriptional activation of STOP1 targets, including the membrane permease ALMT1, to increase malate exudation in response to low phosphate.
Our results unveil the function of a critical transcriptional component, MED16, in the root adaptive responses to a scarce plant macronutrient, which helps understanding how plant cells orchestrate root morphogenesis to gene expression with the STOP1‐ALMT1 module.
The dragon fruit is native of Mexico, and Puebla is the third-largest producing state (SIAP 2023). In June 2023, field sampling was conducted in El Paraíso, Atlixco (18° 49' 5.275" N, 98° 26' 52.353" ...W), Puebla, Mexico. The mean temperature and relative humidity were 20 °C and 75% for seven consecutive days. Dragon fruits cv. 'Delight' close to harvest with gray mold symptoms were found in a commercial area of 2 ha, with an incidence of 35 to 40% and an estimated severity of 75% on infected fruit. The symptoms included necrosis at the apex, which later spread throughout the fruit, along with a soft, black rot covered in abundant mycelium and sporulation. The fungus was isolated from 40 symptomatic fruits by disinfesting pieces of necrotic tissue with 3% NaClO for one minute, rinsing with sterile distilled water (SDW), plating on Petri dishes with potato dextrose agar, and incubating at 25 °C in the dark. One isolate was obtained from each diseased fruit by the hyphal-tip method. The colonies were initially white with a growth rate of 1.15-1.32 cm per day and turned gray after 10 days; the mycelium was dense and aerial. Spherical and irregular sclerotia were formed, measuring 0.9-1.4 × 0.6-1.1 mm (n = 100). Each Petri dish produced 56-278 sclerotia (n = 40) after 11 days; these were initially white and gradually turned dark brown. Brown to olive conidiophores were straight, septate, and branched, measuring 1075-1520 × 10-21 μm, with elliptical hyaline to light brown conidia of 6.6-11.5 × 5-8.1 μm (n=100). The isolates were tentatively identified as
based on morphological characteristics (Ellis 1971). Two representative isolates were chosen for molecular identification and genomic DNA was extracted by the CTAB protocol. The ITS region and the heat shock protein (HSP60), RNA polymerase binding II (RPB2) and glyceraldehyde 3-phosphate dehydrogenase (G3PDH) genes were sequenced (White et al. 1990; Staats et al. 2005). The sequences of a representative isolate (BcPh5) were deposited in GenBank (ITS-OR582337; HSP60-OR636622; RPB2-OR636623; and G3PDH-OR636621). BLAST analysis of the partial sequences of ITS (479 bp), HSP60 (1006 bp), RPB2 (1126 bp), and G3PDH (907 bp) showed 100% similarity to
.
isolates (GenBank: KM840848, MH796663, MK919495, MF480679). Phylogenetic analysis confirmed that BcPh5 clustered with
.
strains. Pathogenicity was confirmed by inoculating the non-wounded surface of 20 detached dragon fruits cv. 'Delight' using the BcPh5 isolate by depositing 20 μl of a 10
conidia/ml suspension with a sterile syringe. The fruits were placed on the rim of a plastic container and inserted in a moisture box with 2 cm of water at the bottom. The box was covered with a plastic sheet to maintain humidity. Control fruits were inoculated with SDW. The inoculated fruits became covered with abundant white to gray mycelium, and soft rot developed within eight days, while no symptoms were observed on the controls. The fungus was re-isolated from the inoculated fruits as described above, fulfilling Koch's postulates. The pathogenicity tests were repeated three times. Gray mold caused by
.
was also recently reported in Mexico on pomegranate (Hernández et al. 2023) and rose apple (Isodoro et al. 2023). As far as we know, this is the first report of
.
causing gray mold on dragon fruit in Mexico. This research is essential for designing integrated management strategies against gray mold on dragon fruits.
PDF
