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A circular economy process has been developed to convert polyurethane waste into biofertilizing microorganisms through a sequential chemical/biological process. The chemical phase involves the complete depolymerization of polyurethane using ozone attack, generating an aqueous extract (OLE) composed of small, bioavailable molecules such as polyols, isocyanate derivatives, and carboxylic acids. The biological phase utilizes OLE for the generation of biomass with biofertilizing functional activity through Rhodococcus pyridinivorans fermentation. The metabolic-proteomic expression during the biodegradation of OLE involves the synthesis of numerous enzymes such as cutinases, hydrolases, proteases, esterases and oxidoreductases, which participate in the degradation of chemical compounds like benzene derivatives, phenols, or plastic polymers. OLE has been converted into microorganisms with biofertilizing properties, including nitrogen fixation, phytohormone production and siderophores. This process contributes to sustainability by diverting polyurethane waste from landfills, reducing the environmental impact of chemical fertilizers and promoting a more sustainable agricultural system., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: Tropospheric ozone is an air pollutant that causes negative effects on vegetation, leading to significant losses in crop productivity. It is generated by chemical reactions in the presence of sunlight between primary pollutants resulting from human activity, such as nitrogen oxides and volatile organic compounds. Due to the constantly increasing emission of ozone precursors, together with the influence of a warming climate on ozone levels, crop losses may be aggravated in the future. Therefore, the search for solutions to mitigate these losses becomes a priority. Ozone-induced abiotic stress is mainly due to reactive oxygen species generated by the spontaneous decomposition of ozone once it reaches the apoplast. In this regard, compounds with antioxidant activity offer a viable option to alleviate ozone-induced damage. Using enzymatic technology, we have developed a process that enables the production of an extract with biostimulant properties from okara, an industrial soybean byproduct. The biostimulant, named as OEE (Okara Enzymatic Extract), is water-soluble and is enriched in bioactive compounds present in okara, such as isoflavones. Additionally, it contains a significant fraction of protein hydrolysates contributing to its functional effect. Given its antioxidant capacity, we aimed to investigate whether OEE could alleviate ozone-induced damage in plants. For that, pepper plants (Capsicum annuum) exposed to ozone were treated with a foliar application of OEE., Results: OEE mitigated ozone-induced damage, as evidenced by the net photosynthetic rate, electron transport rate, effective quantum yield of PSII, and delayed fluorescence. This protection was confirmed by the level of expression of genes associated with photosystem II. The beneficial effect was primarily due to its antioxidant activity, as evidenced by the lipid peroxidation rate measured through malondialdehyde content. Additionally, OEE triggered a mild oxidative response, indicated by increased activities of antioxidant enzymes in leaves (catalase, superoxide dismutase, and guaiacol peroxidase) and the oxidative stress index, providing further protection against ozone-induced stress., Conclusions: The present results support that OEE protects plants from ozone exposure. Taking into consideration that the promotion of plant resistance against abiotic damage is an important goal of biostimulants, we assume that its use as a new biostimulant could be considered., (© 2024. The Author(s).)

Polyurethane (PU) is a widely used polymer with a highly complex recycling process due to its chemical structure. Eliminating polyurethane is limited to incineration or accumulation in landfills. Biodegradation by enzymes and microorganisms has been studied for decades as an effective method of biological decomposition. In this study, Tenebrio molitor larvae ( T. molitor ) were fed polyurethane foam. They degraded the polymer by 35% in 17 days, resulting in a 14% weight loss in the mealworms. Changes in the T. molitor gut bacterial community and diversity were observed, which may be due to the colonization of the species associated with PU degradation. The physical and structural biodegradation of the PU, as achieved by T. molitor , was observed and compared to the characteristics of the original PU (PU-virgin) using Fourier Transform InfraRed spectroscopy (FTIR), Thermal Gravimetric Analysis (TGA), and Scanning Electron Microphotography (SEM).

Due to the huge potential of CRISPR/Cas9 for synthetic biology and genome engineering, many plant researchers are adopting this technology in their laboratories. CRISPR/Cas9 allows multiplexing of guide RNAs (gRNAs), therefore targeting several loci in the genome simultaneously. However, making DNA constructs for this purpose is not always straightforward for first-time users. Here we show how to make multiplex CRISPR/Cas9 constructs using the GoldenBraid (GB) DNA assembly system. As an example, we create a polycistronic gRNA construct that guides a dead version of Cas9 to three different positions of the nopaline synthase promoter, leading to transcriptional repression. After a description of the reagents, the protocol describes step-by-step the considerations for DNA target selection and the molecular cloning process of the final T-DNA construct as well as its testing by transient expression in Nicotiana benthamiana leaves along with a reporter construct for luciferase expression., (© 2022. Springer Science+Business Media, LLC, part of Springer Nature.)

Plant viruses can evolve towards new pathogenic entities that may eventually cause outbreaks and become epidemics or even pandemics. Seven years ago, tomato brown rugose fruit virus (ToBRFV) emerged, overcoming the genetic resistance that had been employed for more than sixty years against tobamoviruses in tomato. Since then, ToBRFV has spread worldwide, producing significant losses in tomato crops. While new resistances are deployed, the only means of control is the implementation of effective prevention and eradication strategies. For this purpose, in this work, we have designed, assessed, and compared an array of tests for the specific and sensitive detection of the ToBRFV in leaf samples. First, two monoclonal antibodies were generated against a singular peptide of the ToBRFV coat protein; antibodies were utilized to devise a double-antibody-sandwich enzyme-linked immunosorbent assay (DAS-ELISA) test that sensitively detects this virus and has no cross-reactivity with other related tobamoviruses. Second, a real-time quantitative PCR (RT-qPCR) test targeting the RNA-dependent replicase open reading frame (ORF) was designed, and its performance and specificity validated in comparison with the CaTa28 and CSP1325 tests recommended by plant protection authorities in Europe. Third, in line with the tendency to use field-deployable diagnostic techniques, we developed and tested two sets of loop-mediated isothermal amplification (LAMP) primers to double-check the detection of the movement protein ORF of ToBRFV, and one set that works as an internal control. Finally, we compared all of these methods by employing a collection of samples with different ToBRFV loads to evaluate the overall performance of each test.

CRISPR/Cas ability to target several loci simultaneously (multiplexing) is a game-changer in plant breeding. Multiplexing not only accelerates trait pyramiding but also can unveil traits hidden by functional redundancy. Furthermore, multiplexing enhances dCas-based programmable gene expression and enables cascade-like gene regulation. However, the design and assembly of multiplex constructs comprising tandemly arrayed guide RNAs (gRNAs) requires scarless cloning and is still troublesome due to the presence of repetitive sequences, thus hampering a more widespread use. Here we present a comprehensive extension of the software-assisted cloning platform GoldenBraid (GB), in which, on top of its multigene cloning software, we integrate new tools for the Type IIS-based easy and rapid assembly of up to six tandemly-arrayed gRNAs with both Cas9 and Cas12a, using the gRNA-tRNA-spaced and the crRNA unspaced approaches, respectively. As stress tests for the new tools, we assembled and used for Agrobacterium-mediated stable transformation a 17 Cas9-gRNAs construct targeting a subset of the Squamosa-Promoter Binding Protein-Like (SPL) gene family in Nicotiana tabacum . The 14 selected genes are targets of miR156, thus potentially playing an important role in juvenile-to-adult and vegetative-to-reproductive phase transitions. With the 17 gRNAs construct we generated a collection of Cas9-free SPL edited T 1 plants harboring up to 9 biallelic mutations and showing leaf juvenility and more branching. The functionality of GB-assembled dCas9 and dCas12a-based CRISPR/Cas activators and repressors using single and multiplexing gRNAs was validated using a Luciferase reporter with the Solanum lycopersicum Mtb promoter or the Agrobacterium tumefaciens nopaline synthase promoter in transient expression in Nicotiana benthamiana . With the incorporation of the new web-based tools and the accompanying collection of DNA parts, the GB4.0 genome edition turns an all-in-one open platform for plant genome engineering., Competing Interests: JQ was employed by the company Idoasis 2002 S.L. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Vazquez-Vilar, Garcia-Carpintero, Selma, Bernabé-Orts, Sanchez-Vicente, Salazar-Sarasua, Ressa, de Paola, Ajenjo, Quintela, Fernández-del-Carmen, Granell and Orzáez.)

Among the different strategies that are being developed to solve the current energy challenge, harvesting energy directly from sunlight through a tandem photoelectrochemical cell (water splitting) is most attractive. Its implementation requires the development of stable and efficient photocathodes, NdFeO 3 being a suitable candidate among ternary oxides. In this study, transparent NdFeO 3 thin-film photocathodes have been successfully prepared by a citric acid-based sol-gel procedure, followed by thermal treatment in air at 640 °C. These electrodes show photocurrents for both the hydrogen evolution and oxygen reduction reactions. Doping with Mg 2+ and Zn 2+ has been observed to significantly enhance the photoelectrocatalytic performance of NdFeO 3 toward oxygen reduction. Magnesium is slightly more efficient as a dopant than Zn, leading to a multiplication of the photocurrent by a factor of 4-5 for a doping level of 5 at % (with respect to iron atoms). This same trend is observed for hydrogen evolution. The beneficial effect of doping is primarily attributed to an increase in the density and a change in the nature of the majority charge carriers. DFT calculations help to rationalize the behavior of NdFeO 3 by pointing to the importance of nanostructuring and doping. All in all, NdFeO 3 has the potential to be used as a photocathode in photoelectrochemical applications, although efforts should be directed to limit surface recombination.

Synthetic biology has advanced from the setup of basic genetic devices to the design of increasingly complex gene circuits to provide organisms with new functions. While many bacterial, fungal and mammalian unicellular chassis have been extensively engineered, this progress has been delayed in plants due to the lack of reliable DNA parts and devices that enable precise control over these new synthetic functions. In particular, memory switches based on DNA site-specific recombination have been the tool of choice to build long-term and stable synthetic memory in other organisms, because they enable a shift between two alternative states registering the information at the DNA level. Here we report a memory switch for whole plants based on the bacteriophage ϕC31 site-specific integrase. The switch was built as a modular device made of standard DNA parts, designed to control the transcriptional state (on or off) of two genes of interest by alternative inversion of a central DNA regulatory element. The state of the switch can be externally operated by action of the ϕC31 integrase (Int), and its recombination directionality factor (RDF). The kinetics, memory, and reversibility of the switch were extensively characterized in Nicotiana benthamiana plants., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The CRISPR/Cas12a editing system opens new possibilities for plant genome engineering. To obtain a comparative assessment of RNA-guided endonuclease (RGEN) types in plants, we adapted the CRISPR/Cas12a system to the GoldenBraid (GB) modular cloning platform and compared the efficiency of Acidaminococcus (As) and Lachnospiraceae (Lb) Cas12a variants with the previously described GB-assembled Streptococcus pyogenes Cas9 (SpCas9) constructs in eight Nicotiana benthamiana loci using transient expression. All three nucleases showed drastic target-dependent differences in efficiency, with LbCas12 producing higher mutagenesis rates in five of the eight loci assayed, as estimated with the T7E1 endonuclease assay. Attempts to engineer crRNA direct repeat (DR) had little effect improving on-target efficiency for AsCas12a and resulted deleterious in the case of LbCas12a. To complete the assessment of Cas12a activity, we carried out genome editing experiments in three different model plants, namely N. benthamiana, Solanum lycopersicum and Arabidopsis thaliana. For the latter, we also resequenced Cas12a-free segregating T2 lines to assess possible off-target effects. Our results showed that the mutagenesis footprint of Cas12a is enriched in deletions of -10 to -2 nucleotides and included in some instances complex rearrangements in the surroundings of the target sites. We found no evidence of off-target mutations neither in related sequences nor somewhere else in the genome. Collectively, this study shows that LbCas12a is a viable alternative to SpCas9 for plant genome engineering., (© 2019 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Improved plants are necessary to meet human needs. Agrobacterium-mediated transformation is the most common method used to rewire plant capabilities. For plant gene delivery, DNA constructs are assembled into binary T-DNA vectors that rely on broad host range origins for bacterial replication. Here we present pLX vectors, a set of mini binary T-DNA plasmids suitable for Type IIS restriction endonuclease- and overlap-based assembly methods. pLX vectors include replicons from compatible broad host range plasmids. Simultaneous usage of pBBR1- and RK2-based pLX vectors in a two-plasmid/one-Agrobacterium strain strategy allowed multigene delivery to plants. Adoption of pLX vectors will facilitate routine plant transformations and targeted mutagenesis, as well as complex part and circuit characterization.

In contrast with the wealth of recent reports about the function of μ-adaptins and clathrin adaptor protein (AP) complexes, there is very little information about the motifs that determine the sorting of membrane proteins within clathrin-coated vesicles in plants. Here, we investigated putative sorting signals in the large cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are involved in the binding of different μ-adaptins in vitro. However, only Phe-165, which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis but also localized to intracellular structures containing several layers of membranes and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin mutant, it accumulated in big intracellular structures containing LysoTracker in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants of other subunits of the AP-3 complex. Our data suggest that Phe-165, through the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis and for PIN1 trafficking along the secretory pathway, respectively., (© 2016 American Society of Plant Biologists. All Rights Reserved.)

Background: The efficiency, versatility and multiplexing capacity of RNA-guided genome engineering using the CRISPR/Cas9 technology enables a variety of applications in plants, ranging from gene editing to the construction of transcriptional gene circuits, many of which depend on the technical ability to compose and transfer complex synthetic instructions into the plant cell. The engineering principles of standardization and modularity applied to DNA cloning are impacting plant genetic engineering, by increasing multigene assembly efficiency and by fostering the exchange of well-defined physical DNA parts with precise functional information., Results: Here we describe the adaptation of the RNA-guided Cas9 system to GoldenBraid (GB), a modular DNA construction framework being increasingly used in Plant Synthetic Biology. In this work, the genetic elements required for CRISPRs-based editing and transcriptional regulation were adapted to GB, and a workflow for gRNAs construction was designed and optimized. New software tools specific for CRISPRs assembly were created and incorporated to the public GB resources site., Conclusions: The functionality and the efficiency of gRNA-Cas9 GB tools were demonstrated in Nicotiana benthamiana using transient expression assays both for gene targeted mutations and for transcriptional regulation. The availability of gRNA-Cas9 GB toolbox will facilitate the application of CRISPR/Cas9 technology to plant genome engineering.

The adsorption and oxidation of oxalic acid at gold electrodes were studied by in-situ infrared spectroscopy. External reflection experiments carried out with gold single-crystal electrodes were combined with internal reflection (ATR-SEIRAS) experiments with gold thin-film electrodes. These gold thin films, with a typical thickness of ca. 35 nm, were deposited on silicon substrates by argon sputtering. As previously reported for evaporated gold films, the voltammetric curves obtained in sulfuric acid solutions after electrochemical annealing show typical features related to the presence of wide bidimensional (111) domains with long-range order. The in-situ infrared data collected for solutions of pH 1 confirmed the potential-dependent adsorption of either oxalate (Au(100)) or a mixture of bioxalate and oxalate (Au(111), Au(110), and gold thin films) anions in a bidentate configuration. The better signal-to-noise ratio associated with the SEIRA effect in the case of the gold thin-film electrodes allows the observation of the carbonyl band for adsorbed bioxalate that was not detected in the external reflection experiments. Besides, additional bands are observed between 2000 and 3000 cm(-)(1) that can be tentatively related to the formation of hydrogen bonds between neighboring bioxalate anions. The intensities of these bands decrease with increasing solution pH values, disappearing for pH 3 solutions in which adsorbed oxalate anions are the predominant species. The analysis of the intensities of the nu(s)(O-C-O) and nu(C-OH) + delta(C-O-H) bands for adsorbed oxalate and bioxalate, respectively, suggests that the pK(a) for the surface equilibrium between these species is significantly lower than that for the solution equilibrium.

The effect of temperature on the voltammetric OH adsorption on Pt(111) and Pt(100) electrodes in perchloric acid media has been studied. From a thermodynamic analysis based on a generalized adsorption isotherm, DeltaG degrees , DeltaH degrees , and DeltaS degrees values for the adsorption of OH have been determined. On Pt(111), the adsorption enthalpy ranges between -265 and -235 kJ mol(-1), becoming less exothermic as the OH coverage increases. These values are in reasonable agreement with experimental data and calculated values for the same reaction in gas phase. The adsorption entropy for OH adsorption on Pt(111) ranges from -200 J mol(-1) K(-1) (low coverage) to -110 J mol(-1) K(-1) (high coverage). On the other hand, the enthalpy and entropy of hydroxyl adsorption on Pt(100) are less sensitive to coverage variations, with values ca. DeltaH degrees = -280 kJ mol(-1) and DeltaS degrees = -180 J mol(-1) K(-1). The different dependence of DeltaS degrees with coverage on both electrode surfaces stresses the important effect of the substrate symmetry on the mobility of adsorbed OH species within the water network directly attached to the metal surface.

The adsorption of acetate anions at silver thin film electrodes has been studied by in-situ infrared spectroscopy experiments with a Kretschmann internal reflection configuration. Stable silver thin films were chemically deposited on germanium substrates. Ex-situ STM images show mean grain sizes ranging from ca. 20 to 90 nm for deposition times between 2 and 20 min, respectively. The thickness of the silver film, measured by AFM, is typically around 10 nm for a deposition time of 10 min and increases up to 50 nm for a deposition time of 20 min. Roughness factors around 2.3 have been obtained for the silver films from the charge involved in lead underpotential deposition (UPD). A noticeable enhancement of the infrared absorption of adsorbed species (SEIRA effect) is observed when the silver films are used as electrodes under internal total reflection conditions. Maximum intensities of the adsorbate bands were observed for a deposition time of 10 min and an angle of incidence around 65 degrees . The potential-dependent infrared spectra of acetate and interfacial water are consistent with previously proposed models involving the existence of weakly hydrogen-bonded water molecules at potentials below the potential of zero charge and the reorientation of water molecules at potentials above the potential of zero charge. Results reported in this work suggest a weak interaction between acetate and water molecules adsorbed at the silver thin film electrodes.